diff --git a/.circleci/run_local_tests.py b/.circleci/run_local_tests.py new file mode 100644 index 000000000..58faa9f61 --- /dev/null +++ b/.circleci/run_local_tests.py @@ -0,0 +1,92 @@ +#!/usr/bin/env python3 +"""Run tests locally.""" +import argparse +import os +import subprocess + + +def _get_parser(): + """Parse command line inputs for tests. + + Returns + ------- + parser.parse_args() : argparse dict + """ + parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter) + parser.add_argument( + "-k", + dest="test_regex", + metavar="PATTERN", + type=str, + help="Test pattern.", + required=False, + default=None, + ) + parser.add_argument( + "-m", + dest="test_mark", + metavar="LABEL", + type=str, + help="Test mark label.", + required=False, + default=None, + ) + return parser + + +def run_command(command, env=None): + """Run a given shell command with certain environment variables set.""" + merged_env = os.environ + if env: + merged_env.update(env) + process = subprocess.Popen( + command, + stdout=subprocess.PIPE, + stderr=subprocess.STDOUT, + shell=True, + env=merged_env, + ) + while True: + line = process.stdout.readline() + line = str(line, "utf-8")[:-1] + print(line) + if line == "" and process.poll() is not None: + break + + if process.returncode != 0: + raise RuntimeError( + f"Non zero return code: {process.returncode}\n" f"{command}\n\n{process.stdout.read()}" + ) + + +def run_tests(test_regex, test_mark): + """Run the tests.""" + local_patch = os.path.dirname(os.path.dirname(os.path.abspath(__file__))) + mounted_code = "/usr/local/miniconda/lib/python3.8/site-packages/aslprep" + run_str = "docker run --rm -ti " + run_str += f"-v {local_patch}:/usr/local/miniconda/lib/python3.8/site-packages/aslprep " + run_str += "--entrypoint pytest " + run_str += "pennlinc/aslprep:unstable " + run_str += ( + f"{mounted_code}/aslprep " + f"--data_dir={mounted_code}/aslprep/tests/data/test_data " + f"--output_dir={mounted_code}/aslprep/tests/data/test_data/run_pytests/out " + f"--working_dir={mounted_code}/aslprep/tests/data/test_data/run_pytests/work " + ) + if test_regex: + run_str += f"-k {test_regex} " + elif test_mark: + run_str += f"-rP -o log_cli=true -m {test_mark} " + + run_command(run_str) + + +def _main(argv=None): + """Run the tests.""" + options = _get_parser().parse_args(argv) + kwargs = vars(options) + run_tests(**kwargs) + + +if __name__ == "__main__": + _main() diff --git a/.gitignore b/.gitignore index fd7acdd46..a97882433 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,4 @@ +aslprep/tests/data/test_data .circleci/local_aslprep_path.txt .DS_Store diff --git a/aslprep/data/aslprep_bids_config.json b/aslprep/data/aslprep_bids_config.json index bd76d4738..a38d19e3d 100755 --- a/aslprep/data/aslprep_bids_config.json +++ b/aslprep/data/aslprep_bids_config.json @@ -13,11 +13,19 @@ { "name": "measure", "pattern": "(?:^|_)measure-([a-zA-Z0-9]+)" + }, + { + "name": "resolution", + "pattern": "res-([a-zA-Z0-9]+)" + }, + { + "name": "density", + "pattern": "den-([a-zA-Z0-9]+)" } ], "default_path_patterns": [ - "[space-{space}_]atlas-{atlas}[_cohort-{cohort}][_res-{res}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.tsv|.json>|.nii.gz}", - "[space-{space}_]atlas-{atlas}[_cohort-{cohort}][_den-{den}][_desc-{desc}]_{suffix}{extension<.dlabel.nii|.tsv|.json>|.dlabel.nii}", + "[space-{space}_]atlas-{atlas}[_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix}{extension<.nii|.nii.gz|.tsv|.json>|.nii.gz}", + "[space-{space}_]atlas-{atlas}[_cohort-{cohort}][_den-{density}][_desc-{desc}]_{suffix}{extension<.dlabel.nii|.tsv|.json>|.dlabel.nii}", "sub-{subject}[/ses-{session}]/{datatype|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", "sub-{subject}[/ses-{session}]/{datatype|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_mod-{modality}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", "sub-{subject}[/ses-{session}]/{datatype|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}]_{suffix}{extension<.nii|.nii.gz|.json>|.nii.gz}", diff --git a/aslprep/data/atlas/HarvardOxford/HarvardOxford.bib b/aslprep/data/atlas/HarvardOxford/HarvardOxford.bib deleted file mode 100644 index 0ed9c5f1c..000000000 --- a/aslprep/data/atlas/HarvardOxford/HarvardOxford.bib +++ /dev/null @@ -1 +0,0 @@ -https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlases \ No newline at end of file diff --git a/aslprep/data/atlas/HarvardOxford/HarvardOxfordMNI.nii.gz b/aslprep/data/atlas/HarvardOxford/HarvardOxfordMNI.nii.gz deleted file mode 100644 index fc7d04418..000000000 Binary files a/aslprep/data/atlas/HarvardOxford/HarvardOxfordMNI.nii.gz and /dev/null differ diff --git a/aslprep/data/atlas/HarvardOxford/HarvardOxfordNodeIndex.1D b/aslprep/data/atlas/HarvardOxford/HarvardOxfordNodeIndex.1D deleted file mode 100644 index cb1575586..000000000 --- a/aslprep/data/atlas/HarvardOxford/HarvardOxfordNodeIndex.1D +++ /dev/null @@ -1,112 +0,0 @@ -10 -11 -20 -21 -30 -31 -40 -41 -50 -51 -60 -61 -70 -71 -80 -81 -90 -91 -100 -101 -110 -111 -120 -121 -130 -131 -140 -141 -150 -151 -160 -161 -170 -171 -180 -181 -190 -191 -200 -201 -210 -211 -220 -221 -230 -231 -240 -241 -250 -251 -260 -261 -270 -271 -280 -281 -290 -291 -300 -301 -310 -311 -320 -321 -330 -331 -340 -341 -350 -351 -360 -361 -370 -371 -380 -381 -390 -391 -400 -401 -410 -411 -420 -421 -430 -431 -440 -441 -450 -451 -460 -461 -470 -471 -480 -481 -1016 -1116 -2010 -2049 -3011 -3050 -4012 -4051 -5013 -5052 -6017 -6053 -7018 -7054 -8026 -8058 \ No newline at end of file diff --git a/aslprep/data/atlas/HarvardOxford/HarvardOxfordNodeNames.txt b/aslprep/data/atlas/HarvardOxford/HarvardOxfordNodeNames.txt deleted file mode 100644 index 0456f4912..000000000 --- a/aslprep/data/atlas/HarvardOxford/HarvardOxfordNodeNames.txt +++ /dev/null @@ -1,112 +0,0 @@ -FrontalPole_R -FrontalPole_L -InsularCortex_R -InsularCortex_L -SuperiorFrontalGyrus_R -SuperiorFrontalGyrus_L -MiddleFrontalGyrus_R -MiddleFrontalGyrus_L -InferiorFrontalGyrusparstriangularis_R -InferiorFrontalGyrusparstriangularis_L -InferiorFrontalGyrusparsopercularis_R -InferiorFrontalGyrusparsopercularis_L -PrecentralGyrus_R -PrecentralGyrus_L -TemporalPole_R -TemporalPole_L -SuperiorTemporalGyrusanteriordivision_R -SuperiorTemporalGyrusanteriordivision_L -SuperiorTemporalGyrusposteriordivision_R -SuperiorTemporalGyrusposteriordivision_L -MiddleTemporalGyrusanteriordivision_R -MiddleTemporalGyrusanteriordivision_L -MiddleTemporalGyrusposteriordivision_R -MiddleTemporalGyrusposteriordivision_L -MiddleTemporalGyrustemporooccipitalpart_R -MiddleTemporalGyrustemporooccipitalpart_L -InferiorTemporalGyrusanteriordivision_R -InferiorTemporalGyrusanteriordivision_L -InferiorTemporalGyrusposteriordivision_R -InferiorTemporalGyrusposteriordivision_L -InferiorTemporalGyrustemporooccipitalpart_R -InferiorTemporalGyrustemporooccipitalpart_L -PostcentralGyrus_R -PostcentralGyrus_L -SuperiorParietalLobule_R -SuperiorParietalLobule_L -SupramarginalGyrusanteriordivision_R -SupramarginalGyrusanteriordivision_L -SupramarginalGyrusposteriordivision_R -SupramarginalGyrusposteriordivision_L -AngularGyrus_R -AngularGyrus_L -LateralOccipitalCortexsuperiordivision_R -LateralOccipitalCortexsuperiordivision_L -LateralOccipitalCortexinferiordivision_R -LateralOccipitalCortexinferiordivision_L -IntracalcarineCortex_R -IntracalcarineCortex_L -FrontalMedialCortex_R -FrontalMedialCortex_L -JuxtapositionalLobuleCortex_R -JuxtapositionalLobuleCortex_L -SubcallosalCortex_R -SubcallosalCortex_L -ParacingulateGyrus_R -ParacingulateGyrus_L -CingulateGyrusanteriordivision_R -CingulateGyrusanteriordivision_L -CingulateGyrusposteriordivision_R -CingulateGyrusposteriordivision_L -PrecuneousCortex_R -PrecuneousCortex_L -CunealCortex_R -CunealCortex_L -FrontalOrbitalCortex_R -FrontalOrbitalCortex_L -ParahippocampalGyrusanteriordivision_R -ParahippocampalGyrusanteriordivision_L -ParahippocampalGyrusposteriordivision_R -ParahippocampalGyrusposteriordivision_L -LingualGyrus_R -LingualGyrus_L -TemporalFusiformCortexanteriordivision_R -TemporalFusiformCortexanteriordivision_L -TemporalFusiformCortexposteriordivision_R -TemporalFusiformCortexposteriordivision_L -TemporalOccipitalFusiformCortex_R -TemporalOccipitalFusiformCortex_L -OccipitalFusiformGyrus_R -OccipitalFusiformGyrus_L -FrontalOperculumCortex_R -FrontalOperculumCortex_L -CentralOpercularCortex_R -CentralOpercularCortex_L -ParietalOperculumCortex_R -ParietalOperculumCortex_L -PlanumPolare_R -PlanumPolare_L -HeschlsGyrus_R -HeschlsGyrus_L -PlanumTemporale_R -PlanumTemporale_L -SupracalcarineCortex_R -SupracalcarineCortex_L -OccipitalPole_R -OccipitalPole_L -Brain-Stem_R -Brain-Stem_L -Thalamus_R -Thalamus_L -Caudate_R -Caudate_L -Putamen_R -Putamen_L -Pallidum_R -Pallidum_L -Hippocampus_R -Hippocampus_L -Amygdala_R -Amygdala_L -Accumbens_R -Accumbens_L \ No newline at end of file diff --git a/aslprep/data/atlas/schaefer200x17/schaefer200x17MNI.nii.gz b/aslprep/data/atlas/schaefer200x17/schaefer200x17MNI.nii.gz deleted file mode 100644 index fe2cd39d1..000000000 Binary files a/aslprep/data/atlas/schaefer200x17/schaefer200x17MNI.nii.gz and /dev/null differ diff --git a/aslprep/data/atlas/schaefer200x7/schaefer200x7MNI.nii.gz b/aslprep/data/atlas/schaefer200x7/schaefer200x7MNI.nii.gz deleted file mode 100644 index 7bc815b99..000000000 Binary files a/aslprep/data/atlas/schaefer200x7/schaefer200x7MNI.nii.gz and /dev/null differ diff --git a/aslprep/data/atlas/schaefer400x17/schaefer400x17MNI.nii.gz b/aslprep/data/atlas/schaefer400x17/schaefer400x17MNI.nii.gz deleted file mode 100644 index 08f6a7f67..000000000 Binary files a/aslprep/data/atlas/schaefer400x17/schaefer400x17MNI.nii.gz and /dev/null differ diff --git a/aslprep/data/atlas/schaefer400x7/schaefer400x7MNI.nii.gz b/aslprep/data/atlas/schaefer400x7/schaefer400x7MNI.nii.gz deleted file mode 100644 index f2d023111..000000000 Binary files a/aslprep/data/atlas/schaefer400x7/schaefer400x7MNI.nii.gz and /dev/null differ diff --git a/aslprep/data/niftiatlas/Glasser_360Parcels_info.tsv b/aslprep/data/niftiatlas/Glasser_360Parcels_info.tsv new file mode 100644 index 000000000..2acef97bc --- /dev/null +++ b/aslprep/data/niftiatlas/Glasser_360Parcels_info.tsv @@ -0,0 +1,361 @@ +index name +1 Right_V1 +2 Right_MST +3 Right_V6 +4 Right_V2 +5 Right_V3 +6 Right_V4 +7 Right_V8 +8 Right_4 +9 Right_3b +10 Right_FEF +11 Right_PEF +12 Right_55b +13 Right_V3A +14 Right_RSC +15 Right_POS2 +16 Right_V7 +17 Right_IPS1 +18 Right_FFC +19 Right_V3B +20 Right_LO1 +21 Right_LO2 +22 Right_PIT +23 Right_MT +24 Right_A1 +25 Right_PSL +26 Right_SFL +27 Right_PCV +28 Right_STV +29 Right_7Pm +30 Right_7m +31 Right_POS1 +32 Right_23d +33 Right_v23ab +34 Right_d23ab +35 Right_31pv +36 Right_5m +37 Right_5mv +38 Right_23c +39 Right_5L +40 Right_24dd +41 Right_24dv +42 Right_7AL +43 Right_SCEF +44 Right_6ma +45 Right_7Am +46 Right_7PL +47 Right_7PC +48 Right_LIPv +49 Right_VIP +50 Right_MIP +51 Right_1 +52 Right_2 +53 Right_3a +54 Right_6d +55 Right_6mp +56 Right_6v +57 Right_p24pr +58 Right_33pr +59 Right_a24pr +60 Right_p32pr +61 Right_a24 +62 Right_d32 +63 Right_8BM +64 Right_p32 +65 Right_10r +66 Right_47m +67 Right_8Av +68 Right_8Ad +69 Right_9m +70 Right_8BL +71 Right_9p +72 Right_10d +73 Right_8C +74 Right_44 +75 Right_45 +76 Right_47l +77 Right_a47r +78 Right_6r +79 Right_IFJa +80 Right_IFJp +81 Right_IFSp +82 Right_IFSa +83 Right_p9-46v +84 Right_46 +85 Right_a9-46v +86 Right_9-46d +87 Right_9a +88 Right_10v +89 Right_a10p +90 Right_10pp +91 Right_11l +92 Right_13l +93 Right_OFC +94 Right_47s +95 Right_LIPd +96 Right_6a +97 Right_i6-8 +98 Right_s6-8 +99 Right_43 +100 Right_OP4 +101 Right_OP1 +102 Right_OP2-3 +103 Right_52 +104 Right_RI +105 Right_PFcm +106 Right_PoI2 +107 Right_TA2 +108 Right_FOP4 +109 Right_MI +110 Right_Pir +111 Right_AVI +112 Right_AAIC +113 Right_FOP1 +114 Right_FOP3 +115 Right_FOP2 +116 Right_PFt +117 Right_AIP +118 Right_EC +119 Right_PreS +120 Right_H +121 Right_ProS +122 Right_PeEc +123 Right_STGa +124 Right_PBelt +125 Right_A5 +126 Right_PHA1 +127 Right_PHA3 +128 Right_STSda +129 Right_STSdp +130 Right_STSvp +131 Right_TGd +132 Right_TE1a +133 Right_TE1p +134 Right_TE2a +135 Right_TF +136 Right_TE2p +137 Right_PHT +138 Right_PH +139 Right_TPOJ1 +140 Right_TPOJ2 +141 Right_TPOJ3 +142 Right_DVT +143 Right_PGp +144 Right_IP2 +145 Right_IP1 +146 Right_IP0 +147 Right_PFop +148 Right_PF +149 Right_PFm +150 Right_PGi +151 Right_PGs +152 Right_V6A +153 Right_VMV1 +154 Right_VMV3 +155 Right_PHA2 +156 Right_V4t +157 Right_FST +158 Right_V3CD +159 Right_LO3 +160 Right_VMV2 +161 Right_31pd +162 Right_31a +163 Right_VVC +164 Right_25 +165 Right_s32 +166 Right_pOFC +167 Right_PoI1 +168 Right_Ig +169 Right_FOP5 +170 Right_p10p +171 Right_p47r +172 Right_TGv +173 Right_MBelt +174 Right_LBelt +175 Right_A4 +176 Right_STSva +177 Right_TE1m +178 Right_PI +179 Right_a32pr +180 Right_p24 +181 Left_V1 +182 Left_MST +183 Left_V6 +184 Left_V2 +185 Left_V3 +186 Left_V4 +187 Left_V8 +188 Left_4 +189 Left_3b +190 Left_FEF +191 Left_PEF +192 Left_55b +193 Left_V3A +194 Left_RSC +195 Left_POS2 +196 Left_V7 +197 Left_IPS1 +198 Left_FFC +199 Left_V3B +200 Left_LO1 +201 Left_LO2 +202 Left_PIT +203 Left_MT +204 Left_A1 +205 Left_PSL +206 Left_SFL +207 Left_PCV +208 Left_STV +209 Left_7Pm +210 Left_7m +211 Left_POS1 +212 Left_23d +213 Left_v23ab +214 Left_d23ab +215 Left_31pv +216 Left_5m +217 Left_5mv +218 Left_23c +219 Left_5L +220 Left_24dd +221 Left_24dv +222 Left_7AL +223 Left_SCEF +224 Left_6ma +225 Left_7Am +226 Left_7PL +227 Left_7PC +228 Left_LIPv +229 Left_VIP +230 Left_MIP +231 Left_1 +232 Left_2 +233 Left_3a +234 Left_6d +235 Left_6mp +236 Left_6v +237 Left_p24pr +238 Left_33pr +239 Left_a24pr +240 Left_p32pr +241 Left_a24 +242 Left_d32 +243 Left_8BM +244 Left_p32 +245 Left_10r +246 Left_47m +247 Left_8Av +248 Left_8Ad +249 Left_9m +250 Left_8BL +251 Left_9p +252 Left_10d +253 Left_8C +254 Left_44 +255 Left_45 +256 Left_47l +257 Left_a47r +258 Left_6r +259 Left_IFJa +260 Left_IFJp +261 Left_IFSp +262 Left_IFSa +263 Left_p9-46v +264 Left_46 +265 Left_a9-46v +266 Left_9-46d +267 Left_9a +268 Left_10v +269 Left_a10p +270 Left_10pp +271 Left_11l +272 Left_13l +273 Left_OFC +274 Left_47s +275 Left_LIPd +276 Left_6a +277 Left_i6-8 +278 Left_s6-8 +279 Left_43 +280 Left_OP4 +281 Left_OP1 +282 Left_OP2-3 +283 Left_52 +284 Left_RI +285 Left_PFcm +286 Left_PoI2 +287 Left_TA2 +288 Left_FOP4 +289 Left_MI +290 Left_Pir +291 Left_AVI +292 Left_AAIC +293 Left_FOP1 +294 Left_FOP3 +295 Left_FOP2 +296 Left_PFt +297 Left_AIP +298 Left_EC +299 Left_PreS +300 Left_H +301 Left_ProS +302 Left_PeEc +303 Left_STGa +304 Left_PBelt +305 Left_A5 +306 Left_PHA1 +307 Left_PHA3 +308 Left_STSda +309 Left_STSdp +310 Left_STSvp +311 Left_TGd +312 Left_TE1a +313 Left_TE1p +314 Left_TE2a +315 Left_TF +316 Left_TE2p +317 Left_PHT +318 Left_PH +319 Left_TPOJ1 +320 Left_TPOJ2 +321 Left_TPOJ3 +322 Left_DVT +323 Left_PGp +324 Left_IP2 +325 Left_IP1 +326 Left_IP0 +327 Left_PFop +328 Left_PF +329 Left_PFm +330 Left_PGi +331 Left_PGs +332 Left_V6A +333 Left_VMV1 +334 Left_VMV3 +335 Left_PHA2 +336 Left_V4t +337 Left_FST +338 Left_V3CD +339 Left_LO3 +340 Left_VMV2 +341 Left_31pd +342 Left_31a +343 Left_VVC +344 Left_25 +345 Left_s32 +346 Left_pOFC +347 Left_PoI1 +348 Left_Ig +349 Left_FOP5 +350 Left_p10p +351 Left_p47r +352 Left_TGv +353 Left_MBelt +354 Left_LBelt +355 Left_A4 +356 Left_STSva +357 Left_TE1m +358 Left_PI +359 Left_a32pr +360 Left_p24 diff --git a/aslprep/data/niftiatlas/Gordon_333Parcels_info.tsv b/aslprep/data/niftiatlas/Gordon_333Parcels_info.tsv new file mode 100644 index 000000000..5c255c249 --- /dev/null +++ b/aslprep/data/niftiatlas/Gordon_333Parcels_info.tsv @@ -0,0 +1,334 @@ +index name +1 L_Default_1 +2 L_SMhand_2 +3 L_SMmouth_3 +4 L_Default_4 +5 L_Visual_5 +6 L_Default_6 +7 L_FrontoParietal_7 +8 L__8 +9 L__9 +10 L_Auditory_10 +11 L_None_11 +12 L_CinguloParietal_12 +13 L_RetrosplenialTemporal_13 +14 L_RetrosplenialTemporal_14 +15 L_Visual_15 +16 L_Visual_16 +17 L_Visual_17 +18 L__18 +19 L__19 +20 L__20 +21 L_CinguloOperc_21 +22 L_CinguloOperc_22 +23 L_VentralAttn_23 +24 L_FrontoParietal_24 +25 L_Default_25 +26 L_Default_26 +27 L_CinguloOperc_27 +28 L_CinguloOperc_28 +29 L_Salience_29 +30 L_SMhand_30 +31 L_SMhand_31 +32 L_SMhand_32 +33 L_SMhand_33 +34 L_CinguloOperc_34 +35 L_SMhand_35 +36 L_SMhand_36 +37 L_SMhand_37 +38 L_SMhand_38 +39 L_SMmouth_39 +40 L_CinguloOperc_40 +41 L_DorsalAttn_41 +42 L_DorsalAttn_42 +43 L_DorsalAttn_43 +44 L_Default_44 +45 L_SMhand_45 +46 L_SMhand_46 +47 L_SMhand_47 +48 L_SMhand_48 +49 L_DorsalAttn_49 +50 L_SMhand_50 +51 L_DorsalAttn_51 +52 L_DorsalAttn_52 +53 L_SMmouth_53 +54 L_SMhand_54 +55 L_DorsalAttn_55 +56 L_SMhand_56 +57 L_SMhand_57 +58 L_SMhand_58 +59 L_SMmouth_59 +60 L_VentralAttn_60 +61 L_VentralAttn_61 +62 L_VentralAttn_62 +63 L_CinguloOperc_63 +64 L_Auditory_64 +65 L_Auditory_65 +66 L_Auditory_66 +67 L_Auditory_67 +68 L_Auditory_68 +69 L_Auditory_69 +70 L_Auditory_70 +71 L__71 +72 L__72 +73 L_None_73 +74 L_DorsalAttn_74 +75 L_VentralAttn_75 +76 L_CinguloOperc_76 +77 L_Auditory_77 +78 L_FrontoParietal_78 +79 L_VentralAttn_79 +80 L_VentralAttn_80 +81 L_CinguloOperc_81 +82 L_CinguloOperc_82 +83 L_Salience_83 +84 L_CinguloOperc_84 +85 L_VentralAttn_85 +86 L_VentralAttn_86 +87 L_DorsalAttn_87 +88 L_DorsalAttn_88 +89 L_CinguloParietal_89 +90 L_Visual_90 +91 L_DorsalAttn_91 +92 L_DorsalAttn_92 +93 L_CinguloParietal_93 +94 L_Default_94 +95 L_DorsalAttn_95 +96 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17Networks_RH_DefaultB_Temp_1 +949 17Networks_RH_DefaultB_Temp_2 +950 17Networks_RH_DefaultB_Temp_3 +951 17Networks_RH_DefaultB_AntTemp_1 +952 17Networks_RH_DefaultB_AntTemp_2 +953 17Networks_RH_DefaultB_AntTemp_3 +954 17Networks_RH_DefaultB_AntTemp_4 +955 17Networks_RH_DefaultB_PFCd_1 +956 17Networks_RH_DefaultB_PFCd_2 +957 17Networks_RH_DefaultB_PFCd_3 +958 17Networks_RH_DefaultB_PFCd_4 +959 17Networks_RH_DefaultB_PFCd_5 +960 17Networks_RH_DefaultB_PFCd_6 +961 17Networks_RH_DefaultB_PFCd_7 +962 17Networks_RH_DefaultB_PFCd_8 +963 17Networks_RH_DefaultB_PFCv_1 +964 17Networks_RH_DefaultB_PFCv_2 +965 17Networks_RH_DefaultB_PFCv_3 +966 17Networks_RH_DefaultB_PFCv_4 +967 17Networks_RH_DefaultB_PFCv_5 +968 17Networks_RH_DefaultB_PFCv_6 +969 17Networks_RH_DefaultC_IPL_1 +970 17Networks_RH_DefaultC_IPL_2 +971 17Networks_RH_DefaultC_Rsp_1 +972 17Networks_RH_DefaultC_Rsp_2 +973 17Networks_RH_DefaultC_Rsp_3 +974 17Networks_RH_DefaultC_Rsp_4 +975 17Networks_RH_DefaultC_PHC_1 +976 17Networks_RH_DefaultC_PHC_2 +977 17Networks_RH_DefaultC_PHC_3 +978 17Networks_RH_DefaultC_PHC_4 +979 17Networks_RH_TempPar_1 +980 17Networks_RH_TempPar_2 +981 17Networks_RH_TempPar_3 +982 17Networks_RH_TempPar_4 +983 17Networks_RH_TempPar_5 +984 17Networks_RH_TempPar_6 +985 17Networks_RH_TempPar_7 +986 17Networks_RH_TempPar_8 +987 17Networks_RH_TempPar_9 +988 17Networks_RH_TempPar_10 +989 17Networks_RH_TempPar_11 +990 17Networks_RH_TempPar_12 +991 17Networks_RH_TempPar_13 +992 17Networks_RH_TempPar_14 +993 17Networks_RH_TempPar_15 +994 17Networks_RH_TempPar_16 +995 17Networks_RH_TempPar_17 +996 17Networks_RH_TempPar_18 +997 17Networks_RH_TempPar_19 +998 17Networks_RH_TempPar_20 +999 17Networks_RH_TempPar_21 +1000 17Networks_RH_TempPar_22 diff --git a/aslprep/data/niftiatlas/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii b/aslprep/data/niftiatlas/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii new file mode 100644 index 000000000..0cc73d4f6 Binary files /dev/null and b/aslprep/data/niftiatlas/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii differ diff --git a/aslprep/data/niftiatlas/Schaefer2018_100Parcels_17Networks_order_info.tsv b/aslprep/data/niftiatlas/Schaefer2018_100Parcels_17Networks_order_info.tsv new file mode 100644 index 000000000..280e7dcf8 --- /dev/null +++ b/aslprep/data/niftiatlas/Schaefer2018_100Parcels_17Networks_order_info.tsv @@ -0,0 +1,101 @@ +index name +1 17Networks_LH_VisCent_ExStr_1 +2 17Networks_LH_VisCent_ExStr_2 +3 17Networks_LH_VisCent_Striate_1 +4 17Networks_LH_VisCent_ExStr_3 +5 17Networks_LH_VisPeri_ExStrInf_1 +6 17Networks_LH_VisPeri_StriCal_1 +7 17Networks_LH_VisPeri_ExStrSup_1 +8 17Networks_LH_SomMotA_1 +9 17Networks_LH_SomMotA_2 +10 17Networks_LH_SomMotB_Aud_1 +11 17Networks_LH_SomMotB_S2_1 +12 17Networks_LH_SomMotB_S2_2 +13 17Networks_LH_SomMotB_Cent_1 +14 17Networks_LH_DorsAttnA_TempOcc_1 +15 17Networks_LH_DorsAttnA_ParOcc_1 +16 17Networks_LH_DorsAttnA_SPL_1 +17 17Networks_LH_DorsAttnB_PostC_1 +18 17Networks_LH_DorsAttnB_PostC_2 +19 17Networks_LH_DorsAttnB_PostC_3 +20 17Networks_LH_DorsAttnB_FEF_1 +21 17Networks_LH_SalVentAttnA_ParOper_1 +22 17Networks_LH_SalVentAttnA_Ins_1 +23 17Networks_LH_SalVentAttnA_Ins_2 +24 17Networks_LH_SalVentAttnA_ParMed_1 +25 17Networks_LH_SalVentAttnA_FrMed_1 +26 17Networks_LH_SalVentAttnB_PFCl_1 +27 17Networks_LH_SalVentAttnB_PFCmp_1 +28 17Networks_LH_LimbicB_OFC_1 +29 17Networks_LH_LimbicA_TempPole_1 +30 17Networks_LH_LimbicA_TempPole_2 +31 17Networks_LH_ContA_IPS_1 +32 17Networks_LH_ContA_PFCl_1 +33 17Networks_LH_ContA_PFCl_2 +34 17Networks_LH_ContB_PFClv_1 +35 17Networks_LH_ContC_pCun_1 +36 17Networks_LH_ContC_pCun_2 +37 17Networks_LH_ContC_Cingp_1 +38 17Networks_LH_DefaultA_PFCd_1 +39 17Networks_LH_DefaultA_pCunPCC_1 +40 17Networks_LH_DefaultA_PFCm_1 +41 17Networks_LH_DefaultB_Temp_1 +42 17Networks_LH_DefaultB_Temp_2 +43 17Networks_LH_DefaultB_IPL_1 +44 17Networks_LH_DefaultB_PFCd_1 +45 17Networks_LH_DefaultB_PFCl_1 +46 17Networks_LH_DefaultB_PFCv_1 +47 17Networks_LH_DefaultB_PFCv_2 +48 17Networks_LH_DefaultC_Rsp_1 +49 17Networks_LH_DefaultC_PHC_1 +50 17Networks_LH_TempPar_1 +51 17Networks_RH_VisCent_ExStr_1 +52 17Networks_RH_VisCent_ExStr_2 +53 17Networks_RH_VisCent_ExStr_3 +54 17Networks_RH_VisPeri_StriCal_1 +55 17Networks_RH_VisPeri_ExStrInf_1 +56 17Networks_RH_VisPeri_ExStrSup_1 +57 17Networks_RH_SomMotA_1 +58 17Networks_RH_SomMotA_2 +59 17Networks_RH_SomMotA_3 +60 17Networks_RH_SomMotA_4 +61 17Networks_RH_SomMotB_Aud_1 +62 17Networks_RH_SomMotB_S2_1 +63 17Networks_RH_SomMotB_S2_2 +64 17Networks_RH_SomMotB_Cent_1 +65 17Networks_RH_DorsAttnA_TempOcc_1 +66 17Networks_RH_DorsAttnA_ParOcc_1 +67 17Networks_RH_DorsAttnA_SPL_1 +68 17Networks_RH_DorsAttnB_PostC_1 +69 17Networks_RH_DorsAttnB_PostC_2 +70 17Networks_RH_DorsAttnB_FEF_1 +71 17Networks_RH_SalVentAttnA_ParOper_1 +72 17Networks_RH_SalVentAttnA_Ins_1 +73 17Networks_RH_SalVentAttnA_ParMed_1 +74 17Networks_RH_SalVentAttnA_FrMed_1 +75 17Networks_RH_SalVentAttnB_IPL_1 +76 17Networks_RH_SalVentAttnB_PFCl_1 +77 17Networks_RH_SalVentAttnB_PFCmp_1 +78 17Networks_RH_LimbicB_OFC_1 +79 17Networks_RH_LimbicA_TempPole_1 +80 17Networks_RH_ContA_IPS_1 +81 17Networks_RH_ContA_PFCl_1 +82 17Networks_RH_ContA_PFCl_2 +83 17Networks_RH_ContB_Temp_1 +84 17Networks_RH_ContB_IPL_1 +85 17Networks_RH_ContB_PFCld_1 +86 17Networks_RH_ContB_PFClv_1 +87 17Networks_RH_ContC_Cingp_1 +88 17Networks_RH_ContC_pCun_1 +89 17Networks_RH_DefaultA_IPL_1 +90 17Networks_RH_DefaultA_PFCd_1 +91 17Networks_RH_DefaultA_pCunPCC_1 +92 17Networks_RH_DefaultA_PFCm_1 +93 17Networks_RH_DefaultB_PFCd_1 +94 17Networks_RH_DefaultB_PFCv_1 +95 17Networks_RH_DefaultB_PFCv_2 +96 17Networks_RH_DefaultC_Rsp_1 +97 17Networks_RH_DefaultC_PHC_1 +98 17Networks_RH_TempPar_1 +99 17Networks_RH_TempPar_2 +100 17Networks_RH_TempPar_3 diff --git a/aslprep/data/niftiatlas/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii b/aslprep/data/niftiatlas/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii new file mode 100644 index 000000000..86e4a8ef7 Binary files /dev/null and b/aslprep/data/niftiatlas/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii differ diff --git a/aslprep/data/niftiatlas/Schaefer2018_200Parcels_17Networks_order_info.tsv b/aslprep/data/niftiatlas/Schaefer2018_200Parcels_17Networks_order_info.tsv new file mode 100644 index 000000000..7133d4f66 --- /dev/null +++ b/aslprep/data/niftiatlas/Schaefer2018_200Parcels_17Networks_order_info.tsv @@ -0,0 +1,201 @@ +index name +1 17Networks_LH_VisCent_ExStr_1 +2 17Networks_LH_VisCent_ExStr_2 +3 17Networks_LH_VisCent_Striate_1 +4 17Networks_LH_VisCent_ExStr_3 +5 17Networks_LH_VisCent_ExStr_4 +6 17Networks_LH_VisCent_ExStr_5 +7 17Networks_LH_VisPeri_ExStrInf_1 +8 17Networks_LH_VisPeri_ExStrInf_2 +9 17Networks_LH_VisPeri_ExStrInf_3 +10 17Networks_LH_VisPeri_StriCal_1 +11 17Networks_LH_VisPeri_ExStrSup_1 +12 17Networks_LH_VisPeri_ExStrSup_2 +13 17Networks_LH_SomMotA_1 +14 17Networks_LH_SomMotA_2 +15 17Networks_LH_SomMotA_3 +16 17Networks_LH_SomMotA_4 +17 17Networks_LH_SomMotA_5 +18 17Networks_LH_SomMotA_6 +19 17Networks_LH_SomMotA_7 +20 17Networks_LH_SomMotA_8 +21 17Networks_LH_SomMotB_Aud_1 +22 17Networks_LH_SomMotB_Aud_2 +23 17Networks_LH_SomMotB_S2_1 +24 17Networks_LH_SomMotB_S2_2 +25 17Networks_LH_SomMotB_Aud_3 +26 17Networks_LH_SomMotB_S2_3 +27 17Networks_LH_SomMotB_Cent_1 +28 17Networks_LH_SomMotB_Cent_2 +29 17Networks_LH_DorsAttnA_TempOcc_1 +30 17Networks_LH_DorsAttnA_TempOcc_2 +31 17Networks_LH_DorsAttnA_ParOcc_1 +32 17Networks_LH_DorsAttnA_SPL_1 +33 17Networks_LH_DorsAttnA_SPL_2 +34 17Networks_LH_DorsAttnA_SPL_3 +35 17Networks_LH_DorsAttnB_PostC_1 +36 17Networks_LH_DorsAttnB_PostC_2 +37 17Networks_LH_DorsAttnB_PostC_3 +38 17Networks_LH_DorsAttnB_PostC_4 +39 17Networks_LH_DorsAttnB_FEF_1 +40 17Networks_LH_SalVentAttnA_ParOper_1 +41 17Networks_LH_SalVentAttnA_Ins_1 +42 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index 000000000..95c992de0 --- /dev/null +++ b/aslprep/data/niftiatlas/Schaefer2018_300Parcels_17Networks_order_info.tsv @@ -0,0 +1,301 @@ +index name +1 17Networks_LH_VisCent_ExStr_1 +2 17Networks_LH_VisCent_ExStr_2 +3 17Networks_LH_VisCent_ExStr_3 +4 17Networks_LH_VisCent_ExStr_4 +5 17Networks_LH_VisCent_ExStr_5 +6 17Networks_LH_VisCent_ExStr_6 +7 17Networks_LH_VisCent_Striate_1 +8 17Networks_LH_VisCent_ExStr_7 +9 17Networks_LH_VisCent_ExStr_8 +10 17Networks_LH_VisCent_ExStr_9 +11 17Networks_LH_VisCent_ExStr_10 +12 17Networks_LH_VisPeri_ExStrInf_1 +13 17Networks_LH_VisPeri_ExStrInf_2 +14 17Networks_LH_VisPeri_ExStrInf_3 +15 17Networks_LH_VisPeri_ExStrInf_4 +16 17Networks_LH_VisPeri_StriCal_1 +17 17Networks_LH_VisPeri_ExStrSup_1 +18 17Networks_LH_VisPeri_ExStrSup_2 +19 17Networks_LH_VisPeri_ExStrSup_3 +20 17Networks_LH_VisPeri_ExStrSup_4 +21 17Networks_LH_SomMotA_1 +22 17Networks_LH_SomMotA_2 +23 17Networks_LH_SomMotA_3 +24 17Networks_LH_SomMotA_4 +25 17Networks_LH_SomMotA_5 +26 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17Networks_RH_LimbicA_TempPole_2 +727 17Networks_RH_LimbicA_TempPole_3 +728 17Networks_RH_LimbicA_TempPole_4 +729 17Networks_RH_LimbicA_TempPole_5 +730 17Networks_RH_LimbicA_TempPole_6 +731 17Networks_RH_LimbicA_TempPole_7 +732 17Networks_RH_LimbicA_TempPole_8 +733 17Networks_RH_LimbicA_TempPole_9 +734 17Networks_RH_LimbicA_TempPole_10 +735 17Networks_RH_LimbicA_TempPole_11 +736 17Networks_RH_LimbicA_TempPole_12 +737 17Networks_RH_LimbicA_TempPole_13 +738 17Networks_RH_LimbicA_TempPole_14 +739 17Networks_RH_LimbicA_TempPole_15 +740 17Networks_RH_LimbicA_TempPole_16 +741 17Networks_RH_LimbicA_TempPole_17 +742 17Networks_RH_ContA_Temp_1 +743 17Networks_RH_ContA_Temp_2 +744 17Networks_RH_ContA_IPS_1 +745 17Networks_RH_ContA_IPS_2 +746 17Networks_RH_ContA_IPS_3 +747 17Networks_RH_ContA_IPS_4 +748 17Networks_RH_ContA_IPS_5 +749 17Networks_RH_ContA_IPS_6 +750 17Networks_RH_ContA_IPS_7 +751 17Networks_RH_ContA_IPS_8 +752 17Networks_RH_ContA_PFCd_1 +753 17Networks_RH_ContA_PFCd_2 +754 17Networks_RH_ContA_PFCl_1 +755 17Networks_RH_ContA_PFCl_2 +756 17Networks_RH_ContA_PFCl_3 +757 17Networks_RH_ContA_PFCl_4 +758 17Networks_RH_ContA_PFCl_5 +759 17Networks_RH_ContA_PFCl_6 +760 17Networks_RH_ContA_PFCl_7 +761 17Networks_RH_ContA_PFCl_8 +762 17Networks_RH_ContA_PFCl_9 +763 17Networks_RH_ContA_Cingm_1 +764 17Networks_RH_ContA_Cingm_2 +765 17Networks_RH_ContB_Temp_1 +766 17Networks_RH_ContB_Temp_2 +767 17Networks_RH_ContB_Temp_3 +768 17Networks_RH_ContB_Temp_4 +769 17Networks_RH_ContB_Temp_5 +770 17Networks_RH_ContB_IPL_1 +771 17Networks_RH_ContB_IPL_2 +772 17Networks_RH_ContB_IPL_3 +773 17Networks_RH_ContB_IPL_4 +774 17Networks_RH_ContB_IPL_5 +775 17Networks_RH_ContB_IPL_6 +776 17Networks_RH_ContB_IPL_7 +777 17Networks_RH_ContB_IPL_8 +778 17Networks_RH_ContB_IPL_9 +779 17Networks_RH_ContB_PFCld_1 +780 17Networks_RH_ContB_PFCld_2 +781 17Networks_RH_ContB_PFCld_3 +782 17Networks_RH_ContB_PFCld_4 +783 17Networks_RH_ContB_PFCld_5 +784 17Networks_RH_ContB_PFCld_6 +785 17Networks_RH_ContB_PFCld_7 +786 17Networks_RH_ContB_PFCld_8 +787 17Networks_RH_ContB_PFCld_9 +788 17Networks_RH_ContB_PFClv_1 +789 17Networks_RH_ContB_PFClv_2 +790 17Networks_RH_ContB_PFClv_3 +791 17Networks_RH_ContB_PFClv_4 +792 17Networks_RH_ContB_PFClv_5 +793 17Networks_RH_ContB_PFClv_6 +794 17Networks_RH_ContB_PFClv_7 +795 17Networks_RH_ContB_PFClv_8 +796 17Networks_RH_ContB_PFClv_9 +797 17Networks_RH_ContB_PFCmp_1 +798 17Networks_RH_ContB_PFCmp_2 +799 17Networks_RH_ContC_pCun_1 +800 17Networks_RH_ContC_pCun_2 +801 17Networks_RH_ContC_pCun_3 +802 17Networks_RH_ContC_pCun_4 +803 17Networks_RH_ContC_pCun_5 +804 17Networks_RH_ContC_pCun_6 +805 17Networks_RH_ContC_pCun_7 +806 17Networks_RH_ContC_pCun_8 +807 17Networks_RH_ContC_Cingp_1 +808 17Networks_RH_ContC_Cingp_2 +809 17Networks_RH_ContC_Cingp_3 +810 17Networks_RH_ContC_Cingp_4 +811 17Networks_RH_DefaultA_Temp_1 +812 17Networks_RH_DefaultA_Temp_2 +813 17Networks_RH_DefaultA_IPL_1 +814 17Networks_RH_DefaultA_IPL_2 +815 17Networks_RH_DefaultA_IPL_3 +816 17Networks_RH_DefaultA_IPL_4 +817 17Networks_RH_DefaultA_IPL_5 +818 17Networks_RH_DefaultA_IPL_6 +819 17Networks_RH_DefaultA_IPL_7 +820 17Networks_RH_DefaultA_PFCd_1 +821 17Networks_RH_DefaultA_PFCd_2 +822 17Networks_RH_DefaultA_PFCd_3 +823 17Networks_RH_DefaultA_PFCd_4 +824 17Networks_RH_DefaultA_PFCd_5 +825 17Networks_RH_DefaultA_pCunPCC_1 +826 17Networks_RH_DefaultA_pCunPCC_2 +827 17Networks_RH_DefaultA_pCunPCC_3 +828 17Networks_RH_DefaultA_pCunPCC_4 +829 17Networks_RH_DefaultA_pCunPCC_5 +830 17Networks_RH_DefaultA_pCunPCC_6 +831 17Networks_RH_DefaultA_pCunPCC_7 +832 17Networks_RH_DefaultA_pCunPCC_8 +833 17Networks_RH_DefaultA_pCunPCC_9 +834 17Networks_RH_DefaultA_pCunPCC_10 +835 17Networks_RH_DefaultA_pCunPCC_11 +836 17Networks_RH_DefaultA_PFCm_1 +837 17Networks_RH_DefaultA_PFCm_2 +838 17Networks_RH_DefaultA_PFCm_3 +839 17Networks_RH_DefaultA_PFCm_4 +840 17Networks_RH_DefaultA_PFCm_5 +841 17Networks_RH_DefaultA_PFCm_6 +842 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17Networks_RH_DefaultC_IPL_1 +871 17Networks_RH_DefaultC_IPL_2 +872 17Networks_RH_DefaultC_IPL_3 +873 17Networks_RH_DefaultC_Rsp_1 +874 17Networks_RH_DefaultC_Rsp_2 +875 17Networks_RH_DefaultC_Rsp_3 +876 17Networks_RH_DefaultC_Rsp_4 +877 17Networks_RH_DefaultC_PHC_1 +878 17Networks_RH_DefaultC_PHC_2 +879 17Networks_RH_DefaultC_PHC_3 +880 17Networks_RH_DefaultC_PHC_4 +881 17Networks_RH_TempPar_1 +882 17Networks_RH_TempPar_2 +883 17Networks_RH_TempPar_3 +884 17Networks_RH_TempPar_4 +885 17Networks_RH_TempPar_5 +886 17Networks_RH_TempPar_6 +887 17Networks_RH_TempPar_7 +888 17Networks_RH_TempPar_8 +889 17Networks_RH_TempPar_9 +890 17Networks_RH_TempPar_10 +891 17Networks_RH_TempPar_11 +892 17Networks_RH_TempPar_12 +893 17Networks_RH_TempPar_13 +894 17Networks_RH_TempPar_14 +895 17Networks_RH_TempPar_15 +896 17Networks_RH_TempPar_16 +897 17Networks_RH_TempPar_17 +898 17Networks_RH_TempPar_18 +899 17Networks_RH_TempPar_19 +900 17Networks_RH_TempPar_20 diff --git a/aslprep/data/niftiatlas/TianSubcortical/Tian_Subcortex_S3_3T.nii.gz b/aslprep/data/niftiatlas/TianSubcortical/Tian_Subcortex_S3_3T.nii.gz new file mode 100755 index 000000000..2946c9768 Binary files /dev/null and b/aslprep/data/niftiatlas/TianSubcortical/Tian_Subcortex_S3_3T.nii.gz differ diff --git a/aslprep/data/niftiatlas/TianSubcortical/Tian_Subcortex_S3_3T_label.txt b/aslprep/data/niftiatlas/TianSubcortical/Tian_Subcortex_S3_3T_label.txt new file mode 100755 index 000000000..d8a348a9e --- /dev/null +++ b/aslprep/data/niftiatlas/TianSubcortical/Tian_Subcortex_S3_3T_label.txt @@ -0,0 +1,100 @@ +HIP-head-m-rh +1 0 0 255 255 +HIP-head-l-rh +2 0 0 255 255 +HIP-body-rh +3 0 0 255 255 +HIP-tail-rh +4 0 0 255 255 +THA-VPm-rh +5 0 0 255 255 +THA-VPl-rh +6 0 0 255 255 +THA-VAi-rh +7 0 0 255 255 +THA-VAs-rh +8 0 0 255 255 +THA-DAm-rh +9 0 0 255 255 +THA-DAl-rh +10 0 0 255 255 +PUT-VA-rh +11 0 0 255 255 +PUT-DA-rh +12 0 0 255 255 +PUT-VP-rh +13 0 0 255 255 +PUT-DP-rh +14 0 0 255 255 +CAU-VA-rh +15 0 0 255 255 +CAU-DA-rh +16 0 0 255 255 +CAU-body-rh +17 0 0 255 255 +CAU-tail-rh +18 0 0 255 255 +lAMY-rh +19 0 0 255 255 +mAMY-rh +20 0 0 255 255 +THA-DP-rh +21 0 0 255 255 +NAc-shell-rh +22 0 0 255 255 +NAc-core-rh +23 0 0 255 255 +pGP-rh +24 0 0 255 255 +aGP-rh +25 0 0 255 255 +HIP-head-m-lh +26 0 0 255 255 +HIP-head-l-l +27 0 0 255 255 +HIP-body-l +28 0 0 255 255 +HIP-tail-lh +29 0 0 255 255 +THA-VPm-lh +30 0 0 255 255 +THA-VPl-lh +31 0 0 255 255 +THA-VAi-lh +32 0 0 255 255 +THA-VAs-lh +33 0 0 255 255 +THA-DAm-lh +34 0 0 255 255 +THA-DAl-lh +35 0 0 255 255 +PUT-VA-lh +36 0 0 255 255 +PUT-DA-l +37 0 0 255 255 +PUT-VP-lh +38 0 0 255 255 +PUT-DP-lh +39 0 0 255 255 +CAU-VA-lh +40 0 0 255 255 +CAU-DA-lh +41 0 0 255 255 +CAU-body-lh +42 0 0 255 255 +CAU-tail-lh +43 0 0 255 255 +lAMY-lh +44 0 0 255 255 +mAMY-lh +45 0 0 255 255 +THA-DP-lh +46 0 0 255 255 +NAc-shell-lh +47 0 0 255 255 +NAc-core-lh +48 0 0 255 255 +pGP-lh +49 0 0 255 255 +aGP-lh +50 0 0 255 255 \ No newline at end of file diff --git a/aslprep/data/niftiatlas/TianSubcortical/references.txt b/aslprep/data/niftiatlas/TianSubcortical/references.txt new file mode 100755 index 000000000..80ff7910c --- /dev/null +++ b/aslprep/data/niftiatlas/TianSubcortical/references.txt @@ -0,0 +1,2 @@ +https://www.nature.com/articles/s41593-020-00711-6 +https://github.com/yetianmed/subcortex/tree/master/Group-Parcellation/3T/Cortex-Subcortex \ No newline at end of file diff --git a/aslprep/data/niftiatlas/Tian_info.tsv b/aslprep/data/niftiatlas/Tian_info.tsv new file mode 100644 index 000000000..1a95e6324 --- /dev/null +++ b/aslprep/data/niftiatlas/Tian_info.tsv @@ -0,0 +1,51 @@ +index name +1 HIP-head-m-rh +2 HIP-head-l-rh +3 HIP-body-rh +4 HIP-tail-rh +5 THA-VPm-rh +6 THA-VPl-rh +7 THA-VAi-rh +8 THA-VAs-rh +9 THA-DAm-rh +10 THA-DAl-rh +11 PUT-VA-rh +12 PUT-DA-rh +13 PUT-VP-rh +14 PUT-DP-rh +15 CAU-VA-rh +16 CAU-DA-rh +17 CAU-body-rh +18 CAU-tail-rh +19 lAMY-rh +20 mAMY-rh +21 THA-DP-rh +22 NAc-shell-rh +23 NAc-core-rh +24 pGP-rh +25 aGP-rh +26 HIP-head-m-lh +27 HIP-head-l-l +28 HIP-body-l +29 HIP-tail-lh +30 THA-VPm-lh +31 THA-VPl-lh +32 THA-VAi-lh +33 THA-VAs-lh +34 THA-DAm-lh +35 THA-DAl-lh +36 PUT-VA-lh +37 PUT-DA-l +38 PUT-VP-lh +39 PUT-DP-lh +40 CAU-VA-lh +41 CAU-DA-lh +42 CAU-body-lh +43 CAU-tail-lh +44 lAMY-lh +45 mAMY-lh +46 THA-DP-lh +47 NAc-shell-lh +48 NAc-core-lh +49 pGP-lh +50 aGP-lh diff --git a/aslprep/data/niftiatlas/glasser360/README.md b/aslprep/data/niftiatlas/glasser360/README.md new file mode 100755 index 000000000..532c77422 --- /dev/null +++ b/aslprep/data/niftiatlas/glasser360/README.md @@ -0,0 +1,2 @@ +# glasser360 +360-node volumetric atlas derived from the multimodal parcellation from Glasser and colleagues diff --git a/aslprep/data/niftiatlas/glasser360/glasser360MNI.nii.gz b/aslprep/data/niftiatlas/glasser360/glasser360MNI.nii.gz new file mode 100644 index 000000000..742182a70 Binary files /dev/null and b/aslprep/data/niftiatlas/glasser360/glasser360MNI.nii.gz differ diff --git a/aslprep/data/niftiatlas/glasser360/glasser360NodeIndex.1D b/aslprep/data/niftiatlas/glasser360/glasser360NodeIndex.1D new file mode 100755 index 000000000..f06607ffe --- /dev/null +++ b/aslprep/data/niftiatlas/glasser360/glasser360NodeIndex.1D @@ -0,0 +1,360 @@ +1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +13 +14 +15 +16 +17 +18 +19 +20 +21 +22 +23 +24 +25 +26 +27 +28 +29 +30 +31 +32 +33 +34 +35 +36 +37 +38 +39 +40 +41 +42 +43 +44 +45 +46 +47 +48 +49 +50 +51 +52 +53 +54 +55 +56 +57 +58 +59 +60 +61 +62 +63 +64 +65 +66 +67 +68 +69 +70 +71 +72 +73 +74 +75 +76 +77 +78 +79 +80 +81 +82 +83 +84 +85 +86 +87 +88 +89 +90 +91 +92 +93 +94 +95 +96 +97 +98 +99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +137 +138 +139 +140 +141 +142 +143 +144 +145 +146 +147 +148 +149 +150 +151 +152 +153 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+354 +355 +356 +357 +358 +359 +360 diff --git a/aslprep/data/niftiatlas/glasser360/glasser360NodeNames.txt b/aslprep/data/niftiatlas/glasser360/glasser360NodeNames.txt new file mode 100755 index 000000000..df843b9e7 --- /dev/null +++ b/aslprep/data/niftiatlas/glasser360/glasser360NodeNames.txt @@ -0,0 +1,360 @@ +Right_V1 +Right_MST +Right_V6 +Right_V2 +Right_V3 +Right_V4 +Right_V8 +Right_4 +Right_3b +Right_FEF +Right_PEF +Right_55b +Right_V3A +Right_RSC +Right_POS2 +Right_V7 +Right_IPS1 +Right_FFC +Right_V3B +Right_LO1 +Right_LO2 +Right_PIT +Right_MT +Right_A1 +Right_PSL +Right_SFL +Right_PCV +Right_STV +Right_7Pm +Right_7m +Right_POS1 +Right_23d +Right_v23ab +Right_d23ab +Right_31pv +Right_5m +Right_5mv +Right_23c +Right_5L +Right_24dd +Right_24dv +Right_7AL +Right_SCEF +Right_6ma +Right_7Am +Right_7PL +Right_7PC +Right_LIPv +Right_VIP +Right_MIP +Right_1 +Right_2 +Right_3a +Right_6d +Right_6mp +Right_6v +Right_p24pr +Right_33pr +Right_a24pr +Right_p32pr +Right_a24 +Right_d32 +Right_8BM +Right_p32 +Right_10r +Right_47m +Right_8Av +Right_8Ad +Right_9m +Right_8BL +Right_9p +Right_10d +Right_8C +Right_44 +Right_45 +Right_47l +Right_a47r +Right_6r +Right_IFJa +Right_IFJp +Right_IFSp +Right_IFSa +Right_p9-46v +Right_46 +Right_a9-46v +Right_9-46d +Right_9a +Right_10v +Right_a10p +Right_10pp +Right_11l +Right_13l +Right_OFC +Right_47s +Right_LIPd +Right_6a +Right_i6-8 +Right_s6-8 +Right_43 +Right_OP4 +Right_OP1 +Right_OP2-3 +Right_52 +Right_RI +Right_PFcm +Right_PoI2 +Right_TA2 +Right_FOP4 +Right_MI +Right_Pir +Right_AVI +Right_AAIC +Right_FOP1 +Right_FOP3 +Right_FOP2 +Right_PFt +Right_AIP +Right_EC +Right_PreS +Right_H +Right_ProS +Right_PeEc +Right_STGa +Right_PBelt +Right_A5 +Right_PHA1 +Right_PHA3 +Right_STSda +Right_STSdp +Right_STSvp +Right_TGd +Right_TE1a +Right_TE1p +Right_TE2a +Right_TF +Right_TE2p +Right_PHT +Right_PH +Right_TPOJ1 +Right_TPOJ2 +Right_TPOJ3 +Right_DVT +Right_PGp +Right_IP2 +Right_IP1 +Right_IP0 +Right_PFop +Right_PF +Right_PFm +Right_PGi +Right_PGs +Right_V6A +Right_VMV1 +Right_VMV3 +Right_PHA2 +Right_V4t +Right_FST +Right_V3CD +Right_LO3 +Right_VMV2 +Right_31pd +Right_31a +Right_VVC +Right_25 +Right_s32 +Right_pOFC +Right_PoI1 +Right_Ig +Right_FOP5 +Right_p10p +Right_p47r +Right_TGv +Right_MBelt +Right_LBelt +Right_A4 +Right_STSva +Right_TE1m +Right_PI +Right_a32pr +Right_p24 +Left_V1 +Left_MST +Left_V6 +Left_V2 +Left_V3 +Left_V4 +Left_V8 +Left_4 +Left_3b +Left_FEF +Left_PEF +Left_55b +Left_V3A +Left_RSC +Left_POS2 +Left_V7 +Left_IPS1 +Left_FFC +Left_V3B +Left_LO1 +Left_LO2 +Left_PIT +Left_MT +Left_A1 +Left_PSL +Left_SFL +Left_PCV +Left_STV +Left_7Pm +Left_7m +Left_POS1 +Left_23d +Left_v23ab +Left_d23ab +Left_31pv +Left_5m +Left_5mv +Left_23c +Left_5L +Left_24dd +Left_24dv +Left_7AL +Left_SCEF +Left_6ma +Left_7Am +Left_7PL +Left_7PC +Left_LIPv +Left_VIP +Left_MIP +Left_1 +Left_2 +Left_3a +Left_6d +Left_6mp +Left_6v +Left_p24pr +Left_33pr +Left_a24pr +Left_p32pr +Left_a24 +Left_d32 +Left_8BM +Left_p32 +Left_10r +Left_47m +Left_8Av +Left_8Ad +Left_9m +Left_8BL +Left_9p +Left_10d +Left_8C +Left_44 +Left_45 +Left_47l +Left_a47r +Left_6r +Left_IFJa +Left_IFJp +Left_IFSp +Left_IFSa +Left_p9-46v +Left_46 +Left_a9-46v +Left_9-46d +Left_9a +Left_10v +Left_a10p +Left_10pp +Left_11l +Left_13l +Left_OFC +Left_47s +Left_LIPd +Left_6a +Left_i6-8 +Left_s6-8 +Left_43 +Left_OP4 +Left_OP1 +Left_OP2-3 +Left_52 +Left_RI +Left_PFcm +Left_PoI2 +Left_TA2 +Left_FOP4 +Left_MI +Left_Pir +Left_AVI +Left_AAIC +Left_FOP1 +Left_FOP3 +Left_FOP2 +Left_PFt +Left_AIP +Left_EC +Left_PreS +Left_H +Left_ProS +Left_PeEc +Left_STGa +Left_PBelt +Left_A5 +Left_PHA1 +Left_PHA3 +Left_STSda +Left_STSdp +Left_STSvp +Left_TGd +Left_TE1a +Left_TE1p +Left_TE2a +Left_TF +Left_TE2p +Left_PHT +Left_PH +Left_TPOJ1 +Left_TPOJ2 +Left_TPOJ3 +Left_DVT +Left_PGp +Left_IP2 +Left_IP1 +Left_IP0 +Left_PFop +Left_PF +Left_PFm +Left_PGi +Left_PGs +Left_V6A +Left_VMV1 +Left_VMV3 +Left_PHA2 +Left_V4t +Left_FST +Left_V3CD +Left_LO3 +Left_VMV2 +Left_31pd +Left_31a +Left_VVC +Left_25 +Left_s32 +Left_pOFC +Left_PoI1 +Left_Ig +Left_FOP5 +Left_p10p +Left_p47r +Left_TGv +Left_MBelt +Left_LBelt +Left_A4 +Left_STSva +Left_TE1m +Left_PI +Left_a32pr +Left_p24 diff --git a/aslprep/data/niftiatlas/glasser360/glasser360Reference.bib b/aslprep/data/niftiatlas/glasser360/glasser360Reference.bib new file mode 100755 index 000000000..74d3c13f9 --- /dev/null +++ b/aslprep/data/niftiatlas/glasser360/glasser360Reference.bib @@ -0,0 +1,13 @@ +@article{Glasser_2016, + doi = {10.1038/nature18933}, + url = {https://doi.org/10.1038%2Fnature18933}, + year = 2016, + month = {jul}, + publisher = {Springer Nature}, + volume = {536}, + number = {7615}, + pages = {171--178}, + author = {Matthew F. Glasser and Timothy S. Coalson and Emma C. Robinson and Carl D. Hacker and John Harwell and Essa Yacoub and Kamil Ugurbil and Jesper Andersson and Christian F. Beckmann and Mark Jenkinson and Stephen M. Smith and David C. Van Essen}, + title = {A multi-modal parcellation of human cerebral cortex}, + journal = {Nature} +} diff --git a/aslprep/data/niftiatlas/gordon333/README.md b/aslprep/data/niftiatlas/gordon333/README.md new file mode 100755 index 000000000..e7831eca1 --- /dev/null +++ b/aslprep/data/niftiatlas/gordon333/README.md @@ -0,0 +1,2 @@ +# gordon333 +RSFC homogeneity-based cortical area parcellation from Gordon and colleagues diff --git a/aslprep/data/niftiatlas/gordon333/gordon333CommunityAffiliation.1D b/aslprep/data/niftiatlas/gordon333/gordon333CommunityAffiliation.1D new file mode 100755 index 000000000..62de59af6 --- /dev/null +++ b/aslprep/data/niftiatlas/gordon333/gordon333CommunityAffiliation.1D @@ -0,0 +1,333 @@ +1 +2 +3 +1 +4 +1 +5 +4 +5 +6 +13 +7 +8 +8 +4 +4 +4 +13 +13 +4 +9 +9 +10 +5 +1 +1 +9 +9 +11 +2 +2 +2 +2 +9 +2 +2 +2 +2 +3 +9 +12 +12 +12 +1 +2 +2 +2 +2 +12 +2 +12 +12 +3 +2 +12 +2 +2 +2 +3 +10 +10 +10 +9 +6 +6 +6 +6 +6 +6 +6 +9 +9 +13 +12 +10 +9 +6 +5 +10 +10 +9 +9 +11 +9 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000000000..de4b088a3 --- /dev/null +++ b/aslprep/data/niftiatlas/gordon333/gordon333CommunityNames.txt @@ -0,0 +1,13 @@ +default +somatomotorHand +somatomotorMouth +visual +frontoparietal +auditory +cinguloparietal +retrosplenialTemporal +cinguloopercular +ventralAttention +salience +dorsalAttention +none diff --git a/aslprep/data/niftiatlas/gordon333/gordon333MNI.nii.gz b/aslprep/data/niftiatlas/gordon333/gordon333MNI.nii.gz new file mode 100644 index 000000000..85467dd2a Binary files /dev/null and b/aslprep/data/niftiatlas/gordon333/gordon333MNI.nii.gz differ diff --git a/aslprep/data/niftiatlas/gordon333/gordon333NodeIndex.1D b/aslprep/data/niftiatlas/gordon333/gordon333NodeIndex.1D new file mode 100755 index 000000000..a9d429973 --- /dev/null +++ b/aslprep/data/niftiatlas/gordon333/gordon333NodeIndex.1D @@ -0,0 +1,333 @@ +1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +13 +14 +15 +16 +17 +18 +19 +20 +21 +22 +23 +24 +25 +26 +27 +28 +29 +30 +31 +32 +33 +34 +35 +36 +37 +38 +39 +40 +41 +42 +43 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+L_FrontoParietal_24 +L_Default_25 +L_Default_26 +L_CinguloOperc_27 +L_CinguloOperc_28 +L_Salience_29 +L_SMhand_30 +L_SMhand_31 +L_SMhand_32 +L_SMhand_33 +L_CinguloOperc_34 +L_SMhand_35 +L_SMhand_36 +L_SMhand_37 +L_SMhand_38 +L_SMmouth_39 +L_CinguloOperc_40 +L_DorsalAttn_41 +L_DorsalAttn_42 +L_DorsalAttn_43 +L_Default_44 +L_SMhand_45 +L_SMhand_46 +L_SMhand_47 +L_SMhand_48 +L_DorsalAttn_49 +L_SMhand_50 +L_DorsalAttn_51 +L_DorsalAttn_52 +L_SMmouth_53 +L_SMhand_54 +L_DorsalAttn_55 +L_SMhand_56 +L_SMhand_57 +L_SMhand_58 +L_SMmouth_59 +L_VentralAttn_60 +L_VentralAttn_61 +L_VentralAttn_62 +L_CinguloOperc_63 +L_Auditory_64 +L_Auditory_65 +L_Auditory_66 +L_Auditory_67 +L_Auditory_68 +L_Auditory_69 +L_Auditory_70 +L__71 +L__72 +L_None_73 +L_DorsalAttn_74 +L_VentralAttn_75 +L_CinguloOperc_76 +L_Auditory_77 +L_FrontoParietal_78 +L_VentralAttn_79 +L_VentralAttn_80 +L_CinguloOperc_81 +L_CinguloOperc_82 +L_Salience_83 +L_CinguloOperc_84 +L_VentralAttn_85 +L_VentralAttn_86 +L_DorsalAttn_87 +L_DorsalAttn_88 +L_CinguloParietal_89 +L_Visual_90 +L_DorsalAttn_91 +L_DorsalAttn_92 +L_CinguloParietal_93 +L_Default_94 +L_DorsalAttn_95 +L_FrontoParietal_96 +L_Visual_97 +L__98 +L_Visual_99 +L__100 +L_CinguloOperc_101 +L_Auditory_102 +L_CinguloOperc_103 +L_Auditory_104 +L_CinguloOperc_105 +L_DorsalAttn_106 +L_DorsalAttn_107 +L_FrontoParietal_108 +L_FrontoParietal_109 +L_DorsalAttn_110 +L_CinguloOperc_111 +L_CinguloOperc_112 +L_DorsalAttn_113 +L_Default_114 +L_None_115 +L_Default_116 +L_Default_117 +L_None_118 +L_None_119 +L_None_120 +L_None_121 +L_None_122 +L_None_123 +L_None_124 +L_None_125 +L__126 +L__127 +L__128 +L_None_129 +L__130 +L__131 +L__132 +L__133 +L__134 +L__135 +L__136 +L_Visual_137 +L__138 +L__139 +L__140 +L__141 +L__142 +L__143 +L__144 +L_Default_145 +L_Default_146 +L_CinguloOperc_147 +L_FrontoParietal_148 +L_FrontoParietal_149 +L_Default_150 +L_Default_151 +L_Default_152 +L_CinguloOperc_153 +L_Default_154 +L_DorsalAttn_155 +L_Default_156 +L_Default_157 +L_VentralAttn_158 +L_None_159 +L__160 +L__161 +R_Default_162 +R_SMhand_163 +R_SMmouth_164 +R_Default_165 +R_Visual_166 +R_FrontoParietal_167 +R_FrontoParietal_168 +R_Visual_169 +R_FrontoParietal_170 +R_Auditory_171 +R_None_172 +R_CinguloParietal_173 +R_RetrosplenialTemporal_174 +R_Visual_175 +R_Visual_176 +R_Visual_177 +R_None_178 +R_None_179 +R_CinguloOperc_180 +R_CinguloOperc_181 +R_FrontoParietal_182 +R_Salience_183 +R_Default_184 +R_CinguloOperc_185 +R_Default_186 +R_CinguloOperc_187 +R_CinguloOperc_188 +R_DorsalAttn_189 +R_SMhand_190 +R_SMhand_191 +R_CinguloOperc_192 +R_SMhand_193 +R_SMhand_194 +R_SMhand_195 +R_CinguloOperc_196 +R_SMmouth_197 +R_CinguloOperc_198 +R_DorsalAttn_199 +R_Default_200 +R_SMhand_201 +R_SMhand_202 +R_DorsalAttn_203 +R_SMhand_204 +R_SMhand_205 +R_SMhand_206 +R_SMhand_207 +R_DorsalAttn_208 +R_SMhand_209 +R_SMhand_210 +R_DorsalAttn_211 +R_SMmouth_212 +R_SMhand_213 +R_SMhand_214 +R_SMhand_215 +R_SMhand_216 +R_SMhand_217 +R_SMmouth_218 +R_CinguloOperc_219 +R_Default_220 +R_VentralAttn_221 +R_VentralAttn_222 +R_CinguloOperc_223 +R_Auditory_224 +R_Default_225 +R_VentralAttn_226 +R_Auditory_227 +R_VentralAttn_228 +R_VentralAttn_229 +R_Auditory_230 +R_VentralAttn_231 +R_Auditory_232 +R_Auditory_233 +R_CinguloOperc_234 +R_CinguloOperc_235 +R_DorsalAttn_236 +R_VentralAttn_237 +R_CinguloOperc_238 +R_Auditory_239 +R_FrontoParietal_240 +R_VentralAttn_241 +R_VentralAttn_242 +R_VentralAttn_243 +R_Auditory_244 +R_CinguloOperc_245 +R_CinguloOperc_246 +R_Salience_247 +R_CinguloOperc_248 +R_CinguloOperc_249 +R_DorsalAttn_250 +R_Visual_251 +R_DorsalAttn_252 +R_DorsalAttn_253 +R_CinguloParietal_254 +R_Visual_255 +R_Visual_256 +R_Default_257 +R_Visual_258 +R_Default_259 +R_FrontoParietal_260 +R_FrontoParietal_261 +R_DorsalAttn_262 +R_Visual_263 +R_Visual_264 +R_Visual_265 +R_DorsalAttn_266 +R_Visual_267 +R_Auditory_268 +R_Auditory_269 +R_SMhand_270 +R_DorsalAttn_271 +R_FrontoParietal_272 +R_FrontoParietal_273 +R_CinguloOperc_274 +R_DorsalAttn_275 +R_FrontoParietal_276 +R_FrontoParietal_277 +R_Default_278 +R_Default_279 +R_None_280 +R_None_281 +R_None_282 +R_None_283 +R_None_284 +R_None_285 +R_None_286 +R_None_287 +R_None_288 +R_None_289 +R_Default_290 +R_None_291 +R_None_292 +R_Visual_293 +R_RetrosplenialTemporal_294 +R_RetrosplenialTemporal_295 +R_None_296 +R_None_297 +R_Visual_298 +R_Visual_299 +R_None_300 +R_None_301 +R_None_302 +R_None_303 +R_None_304 +R_None_305 +R_None_306 +R_Visual_307 +R_Visual_308 +R_Visual_309 +R_Visual_310 +R_Visual_311 +R_None_312 +R_RetrosplenialTemporal_313 +R_None_314 +R_Default_315 +R_Default_316 +R_CinguloOperc_317 +R_CinguloOperc_318 +R_FrontoParietal_319 +R_FrontoParietal_320 +R_Default_321 +R_Default_322 +R_Default_323 +R_Default_324 +R_Default_325 +R_Default_326 +R_FrontoParietal_327 +R_FrontoParietal_328 +R_Auditory_329 +R_Auditory_330 +R_Default_331 +R_VentralAttn_332 +R_VentralAttn_333 diff --git a/aslprep/data/niftiatlas/gordon333/gordon333Reference.bib b/aslprep/data/niftiatlas/gordon333/gordon333Reference.bib new file mode 100755 index 000000000..37fc04eaf --- /dev/null +++ b/aslprep/data/niftiatlas/gordon333/gordon333Reference.bib @@ -0,0 +1,13 @@ +@article{Gordon_2014, + doi = {10.1093/cercor/bhu239}, + url = {https://doi.org/10.1093%2Fcercor%2Fbhu239}, + year = 2014, + month = {oct}, + publisher = {Oxford University Press ({OUP})}, + volume = {26}, + number = {1}, + pages = {288--303}, + author = {Evan M. Gordon and Timothy O. Laumann and Babatunde Adeyemo and Jeremy F. Huckins and William M. Kelley and Steven E. Petersen}, + title = {Generation and Evaluation of a Cortical Area Parcellation from Resting-State Correlations}, + journal = {Cerebral Cortex} +} diff --git a/aslprep/data/niftiatlas/niftiatlas/Schaefer_Community/Schaefer2018_1000Parcels_17Networks_order_info.txt b/aslprep/data/niftiatlas/niftiatlas/Schaefer_Community/Schaefer2018_1000Parcels_17Networks_order_info.txt new file mode 100644 index 000000000..1a5378205 --- /dev/null +++ b/aslprep/data/niftiatlas/niftiatlas/Schaefer_Community/Schaefer2018_1000Parcels_17Networks_order_info.txt @@ -0,0 +1,2000 @@ +17Networks_LH_VisCent_Striate_1 +1 120 18 135 255 +17Networks_LH_VisCent_Striate_2 +2 120 18 136 255 +17Networks_LH_VisCent_Striate_3 +3 120 18 137 255 +17Networks_LH_VisCent_Striate_4 +4 120 18 138 255 +17Networks_LH_VisCent_ExStr_1 +5 120 17 130 255 +17Networks_LH_VisCent_ExStr_2 +6 120 17 131 255 +17Networks_LH_VisCent_ExStr_3 +7 120 17 132 255 +17Networks_LH_VisCent_ExStr_4 +8 120 17 133 255 +17Networks_LH_VisCent_ExStr_5 +9 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255 +7Networks_RH_Default_pCunPCC_14 +895 204 65 79 255 +7Networks_RH_Default_pCunPCC_15 +896 204 65 80 255 +7Networks_RH_Default_pCunPCC_16 +897 204 65 81 255 +7Networks_RH_Default_pCunPCC_17 +898 204 65 82 255 +7Networks_RH_Default_pCunPCC_18 +899 204 65 83 255 +7Networks_RH_Default_pCunPCC_19 +900 204 65 84 255 diff --git a/aslprep/data/niftiatlas/niftiatlas/TianSubcortical/Tian_Subcortex_S2_3T_1mm.nii.gz b/aslprep/data/niftiatlas/niftiatlas/TianSubcortical/Tian_Subcortex_S2_3T_1mm.nii.gz new file mode 100644 index 000000000..c01c3b478 Binary files /dev/null and b/aslprep/data/niftiatlas/niftiatlas/TianSubcortical/Tian_Subcortex_S2_3T_1mm.nii.gz differ diff --git a/aslprep/data/niftiatlas/niftiatlas/TianSubcortical/Tian_Subcortex_S3_3T.nii.gz b/aslprep/data/niftiatlas/niftiatlas/TianSubcortical/Tian_Subcortex_S3_3T.nii.gz new file mode 100755 index 000000000..54bd7f85a Binary files /dev/null and b/aslprep/data/niftiatlas/niftiatlas/TianSubcortical/Tian_Subcortex_S3_3T.nii.gz differ diff --git a/aslprep/data/niftiatlas/niftiatlas/TianSubcortical/Tian_Subcortex_S3_3T_label.txt b/aslprep/data/niftiatlas/niftiatlas/TianSubcortical/Tian_Subcortex_S3_3T_label.txt new file mode 100755 index 000000000..d8a348a9e --- /dev/null +++ b/aslprep/data/niftiatlas/niftiatlas/TianSubcortical/Tian_Subcortex_S3_3T_label.txt @@ -0,0 +1,100 @@ +HIP-head-m-rh +1 0 0 255 255 +HIP-head-l-rh +2 0 0 255 255 +HIP-body-rh +3 0 0 255 255 +HIP-tail-rh +4 0 0 255 255 +THA-VPm-rh +5 0 0 255 255 +THA-VPl-rh +6 0 0 255 255 +THA-VAi-rh +7 0 0 255 255 +THA-VAs-rh +8 0 0 255 255 +THA-DAm-rh +9 0 0 255 255 +THA-DAl-rh +10 0 0 255 255 +PUT-VA-rh +11 0 0 255 255 +PUT-DA-rh +12 0 0 255 255 +PUT-VP-rh +13 0 0 255 255 +PUT-DP-rh +14 0 0 255 255 +CAU-VA-rh +15 0 0 255 255 +CAU-DA-rh +16 0 0 255 255 +CAU-body-rh +17 0 0 255 255 +CAU-tail-rh +18 0 0 255 255 +lAMY-rh +19 0 0 255 255 +mAMY-rh +20 0 0 255 255 +THA-DP-rh +21 0 0 255 255 +NAc-shell-rh +22 0 0 255 255 +NAc-core-rh +23 0 0 255 255 +pGP-rh +24 0 0 255 255 +aGP-rh +25 0 0 255 255 +HIP-head-m-lh +26 0 0 255 255 +HIP-head-l-l +27 0 0 255 255 +HIP-body-l +28 0 0 255 255 +HIP-tail-lh +29 0 0 255 255 +THA-VPm-lh +30 0 0 255 255 +THA-VPl-lh +31 0 0 255 255 +THA-VAi-lh +32 0 0 255 255 +THA-VAs-lh +33 0 0 255 255 +THA-DAm-lh +34 0 0 255 255 +THA-DAl-lh +35 0 0 255 255 +PUT-VA-lh +36 0 0 255 255 +PUT-DA-l +37 0 0 255 255 +PUT-VP-lh +38 0 0 255 255 +PUT-DP-lh +39 0 0 255 255 +CAU-VA-lh +40 0 0 255 255 +CAU-DA-lh +41 0 0 255 255 +CAU-body-lh +42 0 0 255 255 +CAU-tail-lh +43 0 0 255 255 +lAMY-lh +44 0 0 255 255 +mAMY-lh +45 0 0 255 255 +THA-DP-lh +46 0 0 255 255 +NAc-shell-lh +47 0 0 255 255 +NAc-core-lh +48 0 0 255 255 +pGP-lh +49 0 0 255 255 +aGP-lh +50 0 0 255 255 \ No newline at end of file diff --git a/aslprep/data/niftiatlas/niftiatlas/TianSubcortical/references.txt b/aslprep/data/niftiatlas/niftiatlas/TianSubcortical/references.txt new file mode 100755 index 000000000..80ff7910c --- /dev/null +++ b/aslprep/data/niftiatlas/niftiatlas/TianSubcortical/references.txt @@ -0,0 +1,2 @@ +https://www.nature.com/articles/s41593-020-00711-6 +https://github.com/yetianmed/subcortex/tree/master/Group-Parcellation/3T/Cortex-Subcortex \ No newline at end of file diff --git a/aslprep/data/niftiatlas/niftiatlas/glasser360/README.md b/aslprep/data/niftiatlas/niftiatlas/glasser360/README.md new file mode 100755 index 000000000..532c77422 --- /dev/null +++ b/aslprep/data/niftiatlas/niftiatlas/glasser360/README.md @@ -0,0 +1,2 @@ +# glasser360 +360-node volumetric atlas derived from the multimodal parcellation from Glasser and colleagues diff --git a/aslprep/data/niftiatlas/niftiatlas/glasser360/glasser360MNI.nii.gz b/aslprep/data/niftiatlas/niftiatlas/glasser360/glasser360MNI.nii.gz new file mode 100644 index 000000000..e6aeec037 Binary files /dev/null and b/aslprep/data/niftiatlas/niftiatlas/glasser360/glasser360MNI.nii.gz differ diff --git a/aslprep/data/niftiatlas/niftiatlas/glasser360/glasser360NodeIndex.1D b/aslprep/data/niftiatlas/niftiatlas/glasser360/glasser360NodeIndex.1D new file mode 100755 index 000000000..f06607ffe --- /dev/null +++ b/aslprep/data/niftiatlas/niftiatlas/glasser360/glasser360NodeIndex.1D @@ -0,0 +1,360 @@ +1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +13 +14 +15 +16 +17 +18 +19 +20 +21 +22 +23 +24 +25 +26 +27 +28 +29 +30 +31 +32 +33 +34 +35 +36 +37 +38 +39 +40 +41 +42 +43 +44 +45 +46 +47 +48 +49 +50 +51 +52 +53 +54 +55 +56 +57 +58 +59 +60 +61 +62 +63 +64 +65 +66 +67 +68 +69 +70 +71 +72 +73 +74 +75 +76 +77 +78 +79 +80 +81 +82 +83 +84 +85 +86 +87 +88 +89 +90 +91 +92 +93 +94 +95 +96 +97 +98 +99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +137 +138 +139 +140 +141 +142 +143 +144 +145 +146 +147 +148 +149 +150 +151 +152 +153 +154 +155 +156 +157 +158 +159 +160 +161 +162 +163 +164 +165 +166 +167 +168 +169 +170 +171 +172 +173 +174 +175 +176 +177 +178 +179 +180 +181 +182 +183 +184 +185 +186 +187 +188 +189 +190 +191 +192 +193 +194 +195 +196 +197 +198 +199 +200 +201 +202 +203 +204 +205 +206 +207 +208 +209 +210 +211 +212 +213 +214 +215 +216 +217 +218 +219 +220 +221 +222 +223 +224 +225 +226 +227 +228 +229 +230 +231 +232 +233 +234 +235 +236 +237 +238 +239 +240 +241 +242 +243 +244 +245 +246 +247 +248 +249 +250 +251 +252 +253 +254 +255 +256 +257 +258 +259 +260 +261 +262 +263 +264 +265 +266 +267 +268 +269 +270 +271 +272 +273 +274 +275 +276 +277 +278 +279 +280 +281 +282 +283 +284 +285 +286 +287 +288 +289 +290 +291 +292 +293 +294 +295 +296 +297 +298 +299 +300 +301 +302 +303 +304 +305 +306 +307 +308 +309 +310 +311 +312 +313 +314 +315 +316 +317 +318 +319 +320 +321 +322 +323 +324 +325 +326 +327 +328 +329 +330 +331 +332 +333 +334 +335 +336 +337 +338 +339 +340 +341 +342 +343 +344 +345 +346 +347 +348 +349 +350 +351 +352 +353 +354 +355 +356 +357 +358 +359 +360 diff --git a/aslprep/data/niftiatlas/niftiatlas/glasser360/glasser360NodeNames.txt b/aslprep/data/niftiatlas/niftiatlas/glasser360/glasser360NodeNames.txt new file mode 100755 index 000000000..df843b9e7 --- /dev/null +++ b/aslprep/data/niftiatlas/niftiatlas/glasser360/glasser360NodeNames.txt @@ -0,0 +1,360 @@ +Right_V1 +Right_MST +Right_V6 +Right_V2 +Right_V3 +Right_V4 +Right_V8 +Right_4 +Right_3b +Right_FEF +Right_PEF +Right_55b +Right_V3A +Right_RSC +Right_POS2 +Right_V7 +Right_IPS1 +Right_FFC +Right_V3B +Right_LO1 +Right_LO2 +Right_PIT +Right_MT +Right_A1 +Right_PSL +Right_SFL +Right_PCV +Right_STV +Right_7Pm +Right_7m +Right_POS1 +Right_23d +Right_v23ab +Right_d23ab +Right_31pv +Right_5m +Right_5mv +Right_23c +Right_5L +Right_24dd +Right_24dv +Right_7AL +Right_SCEF +Right_6ma +Right_7Am +Right_7PL +Right_7PC +Right_LIPv +Right_VIP +Right_MIP +Right_1 +Right_2 +Right_3a +Right_6d +Right_6mp +Right_6v +Right_p24pr +Right_33pr +Right_a24pr +Right_p32pr +Right_a24 +Right_d32 +Right_8BM +Right_p32 +Right_10r +Right_47m +Right_8Av +Right_8Ad +Right_9m +Right_8BL +Right_9p +Right_10d +Right_8C +Right_44 +Right_45 +Right_47l +Right_a47r +Right_6r +Right_IFJa +Right_IFJp +Right_IFSp +Right_IFSa +Right_p9-46v +Right_46 +Right_a9-46v +Right_9-46d +Right_9a +Right_10v +Right_a10p +Right_10pp +Right_11l +Right_13l +Right_OFC +Right_47s +Right_LIPd +Right_6a +Right_i6-8 +Right_s6-8 +Right_43 +Right_OP4 +Right_OP1 +Right_OP2-3 +Right_52 +Right_RI +Right_PFcm +Right_PoI2 +Right_TA2 +Right_FOP4 +Right_MI +Right_Pir +Right_AVI +Right_AAIC +Right_FOP1 +Right_FOP3 +Right_FOP2 +Right_PFt +Right_AIP +Right_EC +Right_PreS +Right_H +Right_ProS +Right_PeEc +Right_STGa +Right_PBelt +Right_A5 +Right_PHA1 +Right_PHA3 +Right_STSda +Right_STSdp +Right_STSvp +Right_TGd +Right_TE1a +Right_TE1p +Right_TE2a +Right_TF +Right_TE2p +Right_PHT +Right_PH +Right_TPOJ1 +Right_TPOJ2 +Right_TPOJ3 +Right_DVT +Right_PGp +Right_IP2 +Right_IP1 +Right_IP0 +Right_PFop +Right_PF +Right_PFm +Right_PGi +Right_PGs +Right_V6A +Right_VMV1 +Right_VMV3 +Right_PHA2 +Right_V4t +Right_FST +Right_V3CD +Right_LO3 +Right_VMV2 +Right_31pd +Right_31a +Right_VVC +Right_25 +Right_s32 +Right_pOFC +Right_PoI1 +Right_Ig +Right_FOP5 +Right_p10p +Right_p47r +Right_TGv +Right_MBelt +Right_LBelt +Right_A4 +Right_STSva +Right_TE1m +Right_PI +Right_a32pr +Right_p24 +Left_V1 +Left_MST +Left_V6 +Left_V2 +Left_V3 +Left_V4 +Left_V8 +Left_4 +Left_3b +Left_FEF +Left_PEF +Left_55b +Left_V3A +Left_RSC +Left_POS2 +Left_V7 +Left_IPS1 +Left_FFC +Left_V3B +Left_LO1 +Left_LO2 +Left_PIT +Left_MT +Left_A1 +Left_PSL +Left_SFL +Left_PCV +Left_STV +Left_7Pm +Left_7m +Left_POS1 +Left_23d +Left_v23ab +Left_d23ab +Left_31pv +Left_5m +Left_5mv +Left_23c +Left_5L +Left_24dd +Left_24dv +Left_7AL +Left_SCEF +Left_6ma +Left_7Am +Left_7PL +Left_7PC +Left_LIPv +Left_VIP +Left_MIP +Left_1 +Left_2 +Left_3a +Left_6d +Left_6mp +Left_6v +Left_p24pr +Left_33pr +Left_a24pr +Left_p32pr +Left_a24 +Left_d32 +Left_8BM +Left_p32 +Left_10r +Left_47m +Left_8Av +Left_8Ad +Left_9m +Left_8BL +Left_9p +Left_10d +Left_8C +Left_44 +Left_45 +Left_47l +Left_a47r +Left_6r +Left_IFJa +Left_IFJp +Left_IFSp +Left_IFSa +Left_p9-46v +Left_46 +Left_a9-46v +Left_9-46d +Left_9a +Left_10v +Left_a10p +Left_10pp +Left_11l +Left_13l +Left_OFC +Left_47s +Left_LIPd +Left_6a +Left_i6-8 +Left_s6-8 +Left_43 +Left_OP4 +Left_OP1 +Left_OP2-3 +Left_52 +Left_RI +Left_PFcm +Left_PoI2 +Left_TA2 +Left_FOP4 +Left_MI +Left_Pir +Left_AVI +Left_AAIC +Left_FOP1 +Left_FOP3 +Left_FOP2 +Left_PFt +Left_AIP +Left_EC +Left_PreS +Left_H +Left_ProS +Left_PeEc +Left_STGa +Left_PBelt +Left_A5 +Left_PHA1 +Left_PHA3 +Left_STSda +Left_STSdp +Left_STSvp +Left_TGd +Left_TE1a +Left_TE1p +Left_TE2a +Left_TF +Left_TE2p +Left_PHT +Left_PH +Left_TPOJ1 +Left_TPOJ2 +Left_TPOJ3 +Left_DVT +Left_PGp +Left_IP2 +Left_IP1 +Left_IP0 +Left_PFop +Left_PF +Left_PFm +Left_PGi +Left_PGs +Left_V6A +Left_VMV1 +Left_VMV3 +Left_PHA2 +Left_V4t +Left_FST +Left_V3CD +Left_LO3 +Left_VMV2 +Left_31pd +Left_31a +Left_VVC +Left_25 +Left_s32 +Left_pOFC +Left_PoI1 +Left_Ig +Left_FOP5 +Left_p10p +Left_p47r +Left_TGv +Left_MBelt +Left_LBelt +Left_A4 +Left_STSva +Left_TE1m +Left_PI +Left_a32pr +Left_p24 diff --git a/aslprep/data/niftiatlas/niftiatlas/glasser360/glasser360Reference.bib b/aslprep/data/niftiatlas/niftiatlas/glasser360/glasser360Reference.bib new file mode 100755 index 000000000..74d3c13f9 --- /dev/null +++ b/aslprep/data/niftiatlas/niftiatlas/glasser360/glasser360Reference.bib @@ -0,0 +1,13 @@ +@article{Glasser_2016, + doi = {10.1038/nature18933}, + url = {https://doi.org/10.1038%2Fnature18933}, + year = 2016, + month = {jul}, + publisher = {Springer Nature}, + volume = {536}, + number = {7615}, + pages = {171--178}, + author = {Matthew F. Glasser and Timothy S. Coalson and Emma C. Robinson and Carl D. Hacker and John Harwell and Essa Yacoub and Kamil Ugurbil and Jesper Andersson and Christian F. Beckmann and Mark Jenkinson and Stephen M. Smith and David C. Van Essen}, + title = {A multi-modal parcellation of human cerebral cortex}, + journal = {Nature} +} diff --git a/aslprep/data/niftiatlas/niftiatlas/gordon333/README.md b/aslprep/data/niftiatlas/niftiatlas/gordon333/README.md new file mode 100755 index 000000000..e7831eca1 --- /dev/null +++ b/aslprep/data/niftiatlas/niftiatlas/gordon333/README.md @@ -0,0 +1,2 @@ +# gordon333 +RSFC homogeneity-based cortical area parcellation from Gordon and colleagues diff --git a/aslprep/data/niftiatlas/niftiatlas/gordon333/gordon333CommunityAffiliation.1D b/aslprep/data/niftiatlas/niftiatlas/gordon333/gordon333CommunityAffiliation.1D new file mode 100755 index 000000000..62de59af6 --- /dev/null +++ b/aslprep/data/niftiatlas/niftiatlas/gordon333/gordon333CommunityAffiliation.1D @@ -0,0 +1,333 @@ +1 +2 +3 +1 +4 +1 +5 +4 +5 +6 +13 +7 +8 +8 +4 +4 +4 +13 +13 +4 +9 +9 +10 +5 +1 +1 +9 +9 +11 +2 +2 +2 +2 +9 +2 +2 +2 +2 +3 +9 +12 +12 +12 +1 +2 +2 +2 +2 +12 +2 +12 +12 +3 +2 +12 +2 +2 +2 +3 +10 +10 +10 +9 +6 +6 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+R_FrontoParietal_328 +R_Auditory_329 +R_Auditory_330 +R_Default_331 +R_VentralAttn_332 +R_VentralAttn_333 diff --git a/aslprep/data/niftiatlas/niftiatlas/gordon333/gordon333Reference.bib b/aslprep/data/niftiatlas/niftiatlas/gordon333/gordon333Reference.bib new file mode 100755 index 000000000..37fc04eaf --- /dev/null +++ b/aslprep/data/niftiatlas/niftiatlas/gordon333/gordon333Reference.bib @@ -0,0 +1,13 @@ +@article{Gordon_2014, + doi = {10.1093/cercor/bhu239}, + url = {https://doi.org/10.1093%2Fcercor%2Fbhu239}, + year = 2014, + month = {oct}, + publisher = {Oxford University Press ({OUP})}, + volume = {26}, + number = {1}, + pages = {288--303}, + author = {Evan M. Gordon and Timothy O. Laumann and Babatunde Adeyemo and Jeremy F. Huckins and William M. Kelley and Steven E. Petersen}, + title = {Generation and Evaluation of a Cortical Area Parcellation from Resting-State Correlations}, + journal = {Cerebral Cortex} +} diff --git a/aslprep/data/atlas/schaefer200x17/README.md b/aslprep/data/niftiatlas/niftiatlas/schaefer200x17/README.md old mode 100644 new mode 100755 similarity index 100% rename from aslprep/data/atlas/schaefer200x17/README.md rename to aslprep/data/niftiatlas/niftiatlas/schaefer200x17/README.md diff --git a/aslprep/data/atlas/schaefer200x17/schaefer200x17CommunityAffiliation.1D b/aslprep/data/niftiatlas/niftiatlas/schaefer200x17/schaefer200x17CommunityAffiliation.1D old mode 100644 new mode 100755 similarity index 100% rename from aslprep/data/atlas/schaefer200x17/schaefer200x17CommunityAffiliation.1D rename to aslprep/data/niftiatlas/niftiatlas/schaefer200x17/schaefer200x17CommunityAffiliation.1D diff --git a/aslprep/data/atlas/schaefer200x17/schaefer200x17CommunityNames.txt 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aslprep/data/niftiatlas/niftiatlas/schaefer400x7/schaefer400x7CommunityAffiliation.1D diff --git a/aslprep/data/atlas/schaefer400x7/schaefer400x7CommunityNames.txt b/aslprep/data/niftiatlas/niftiatlas/schaefer400x7/schaefer400x7CommunityNames.txt old mode 100644 new mode 100755 similarity index 100% rename from aslprep/data/atlas/schaefer400x7/schaefer400x7CommunityNames.txt rename to aslprep/data/niftiatlas/niftiatlas/schaefer400x7/schaefer400x7CommunityNames.txt diff --git a/aslprep/data/niftiatlas/niftiatlas/schaefer400x7/schaefer400x7MNI.nii.gz b/aslprep/data/niftiatlas/niftiatlas/schaefer400x7/schaefer400x7MNI.nii.gz new file mode 100755 index 000000000..858cccc4d Binary files /dev/null and b/aslprep/data/niftiatlas/niftiatlas/schaefer400x7/schaefer400x7MNI.nii.gz differ diff --git a/aslprep/data/atlas/schaefer400x7/schaefer400x7NodeIndex.1D b/aslprep/data/niftiatlas/niftiatlas/schaefer400x7/schaefer400x7NodeIndex.1D old mode 100644 new mode 100755 similarity index 100% rename from aslprep/data/atlas/schaefer400x7/schaefer400x7NodeIndex.1D rename to aslprep/data/niftiatlas/niftiatlas/schaefer400x7/schaefer400x7NodeIndex.1D diff --git a/aslprep/data/atlas/schaefer400x7/schaefer400x7NodeNames.txt b/aslprep/data/niftiatlas/niftiatlas/schaefer400x7/schaefer400x7NodeNames.txt old mode 100644 new mode 100755 similarity index 100% rename from aslprep/data/atlas/schaefer400x7/schaefer400x7NodeNames.txt rename to aslprep/data/niftiatlas/niftiatlas/schaefer400x7/schaefer400x7NodeNames.txt diff --git a/aslprep/data/atlas/schaefer400x7/schaefer400x7Reference.bib b/aslprep/data/niftiatlas/niftiatlas/schaefer400x7/schaefer400x7Reference.bib old mode 100644 new mode 100755 similarity index 100% rename from aslprep/data/atlas/schaefer400x7/schaefer400x7Reference.bib rename to aslprep/data/niftiatlas/niftiatlas/schaefer400x7/schaefer400x7Reference.bib diff --git a/aslprep/data/niftiatlas/schaefer200x17/README.md b/aslprep/data/niftiatlas/schaefer200x17/README.md new file mode 100755 index 000000000..63a485ab6 --- /dev/null +++ b/aslprep/data/niftiatlas/schaefer200x17/README.md @@ -0,0 +1,2 @@ +# schaefer200 +Multiscale local-global functional atlas from Schaefer and colleagues: 200-node resolution diff --git a/aslprep/data/niftiatlas/schaefer200x17/schaefer200x17CommunityAffiliation.1D b/aslprep/data/niftiatlas/schaefer200x17/schaefer200x17CommunityAffiliation.1D new file mode 100755 index 000000000..e20f78eb8 --- /dev/null +++ b/aslprep/data/niftiatlas/schaefer200x17/schaefer200x17CommunityAffiliation.1D @@ -0,0 +1,200 @@ +1 +1 +1 +1 +1 +1 +2 +2 +2 +2 +2 +2 +3 +3 +3 +3 +3 +3 +3 +3 +4 +4 +4 +4 +4 +4 +4 +4 +5 +5 +5 +5 +5 +5 +6 +6 +6 +6 +6 +7 +7 +7 +7 +7 +7 +7 +8 +8 +8 +8 +9 +9 +10 +10 +10 +10 +11 +11 +11 +11 +11 +11 +11 +11 +11 +11 +12 +12 +12 +12 +12 +13 +13 +13 +14 +14 +14 +14 +14 +15 +15 +15 +16 +16 +16 +16 +16 +16 +16 +16 +16 +16 +16 +16 +16 +16 +16 +16 +17 +17 +1 +1 +1 +1 +1 +1 +2 +2 +2 +2 +2 +2 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +4 +4 +4 +4 +4 +4 +4 +5 +5 +5 +5 +5 +5 +6 +6 +6 +6 +6 +7 +7 +7 +7 +7 +7 +7 +7 +7 +8 +8 +8 +8 +8 +8 +9 +9 +9 +9 +10 +10 +10 +10 +11 +11 +11 +11 +11 +11 +12 +12 +12 +12 +12 +12 +12 +12 +12 +12 +13 +13 +13 +14 +14 +14 +14 +14 +14 +15 +15 +15 +15 +16 +16 +16 +17 +17 +17 +17 diff --git a/aslprep/data/niftiatlas/schaefer200x17/schaefer200x17CommunityNames.txt b/aslprep/data/niftiatlas/schaefer200x17/schaefer200x17CommunityNames.txt new file mode 100755 index 000000000..e1adf74b3 --- /dev/null +++ b/aslprep/data/niftiatlas/schaefer200x17/schaefer200x17CommunityNames.txt @@ -0,0 +1,17 @@ +visualCentral +visualPeripheral +somatomotorA +somatomotorBAuditory +dorsalAttentionA +dorsalAttentionB +salienceVentralAttentionA +salienceVentralAttentionB +limbicOrbitofrontal +limbicTemporopolar +frontoparietalControlA +frontoparietalControlB +frontoparietalControlC +defaultA +defaultB +defaultC +temporoparietal diff --git a/aslprep/data/niftiatlas/schaefer200x17/schaefer200x17MNI.nii.gz b/aslprep/data/niftiatlas/schaefer200x17/schaefer200x17MNI.nii.gz new file mode 100755 index 000000000..27608ed2b Binary files /dev/null and b/aslprep/data/niftiatlas/schaefer200x17/schaefer200x17MNI.nii.gz differ diff --git a/aslprep/data/niftiatlas/schaefer200x17/schaefer200x17NodeIndex.1D b/aslprep/data/niftiatlas/schaefer200x17/schaefer200x17NodeIndex.1D new file mode 100755 index 000000000..aa5e3f802 --- /dev/null +++ b/aslprep/data/niftiatlas/schaefer200x17/schaefer200x17NodeIndex.1D @@ -0,0 +1,200 @@ +1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +13 +14 +15 +16 +17 +18 +19 +20 +21 +22 +23 +24 +25 +26 +27 +28 +29 +30 +31 +32 +33 +34 +35 +36 +37 +38 +39 +40 +41 +42 +43 +44 +45 +46 +47 +48 +49 +50 +51 +52 +53 +54 +55 +56 +57 +58 +59 +60 +61 +62 +63 +64 +65 +66 +67 +68 +69 +70 +71 +72 +73 +74 +75 +76 +77 +78 +79 +80 +81 +82 +83 +84 +85 +86 +87 +88 +89 +90 +91 +92 +93 +94 +95 +96 +97 +98 +99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +137 +138 +139 +140 +141 +142 +143 +144 +145 +146 +147 +148 +149 +150 +151 +152 +153 +154 +155 +156 +157 +158 +159 +160 +161 +162 +163 +164 +165 +166 +167 +168 +169 +170 +171 +172 +173 +174 +175 +176 +177 +178 +179 +180 +181 +182 +183 +184 +185 +186 +187 +188 +189 +190 +191 +192 +193 +194 +195 +196 +197 +198 +199 +200 diff --git a/aslprep/data/niftiatlas/schaefer200x17/schaefer200x17NodeNames.txt b/aslprep/data/niftiatlas/schaefer200x17/schaefer200x17NodeNames.txt new file mode 100755 index 000000000..8bae15a5b --- /dev/null +++ b/aslprep/data/niftiatlas/schaefer200x17/schaefer200x17NodeNames.txt @@ -0,0 +1,210 @@ +LH_VisCent_ExStr_1 +LH_VisCent_ExStr_2 +LH_VisCent_ExStr_3 +LH_VisCent_ExStr_4 +LH_VisCent_ExStr_5 +LH_VisCent_ExStr_6 +LH_VisPeri_ExStrSup_1 +LH_VisPeri_ExStrSup_2 +LH_VisPeri_ExStrSup_3 +LH_VisPeri_ExStrSup_4 +LH_VisPeri_ExStrSup_5 +LH_VisPeri_ExStrSup_6 +LH_SomMotA_1 +LH_SomMotA_2 +LH_SomMotA_3 +LH_SomMotA_4 +LH_SomMotA_5 +LH_SomMotA_6 +LH_SomMotA_7 +LH_SomMotA_8 +LH_SomMotB_Aud_1 +LH_SomMotB_Aud_2 +LH_SomMotB_Aud_3 +LH_SomMotB_Aud_4 +LH_SomMotB_Aud_5 +LH_SomMotB_Aud_6 +LH_SomMotB_Aud_7 +LH_SomMotB_Aud_8 +LH_DorsAttnA_TempOcc_1 +LH_DorsAttnA_TempOcc_2 +LH_DorsAttnA_TempOcc_3 +LH_DorsAttnA_SPL_1 +LH_DorsAttnA_SPL_2 +LH_DorsAttnA_SPL_3 +LH_DorsAttnB_PostC_1 +LH_DorsAttnB_PostC_2 +LH_DorsAttnB_PostC_3 +LH_DorsAttnB_PostC_4 +LH_DorsAttnB_FEF_1 +LH_SalVentAttnA_ParOper_1 +LH_SalVentAttnA_Ins_1 +LH_SalVentAttnA_Ins_2 +LH_SalVentAttnA_Ins_3 +LH_SalVentAttnA_ParMed_1 +LH_SalVentAttnA_FrMed_1 +LH_SalVentAttnA_FrMed_2 +LH_SalVentAttnB_IPL_1 +LH_SalVentAttnB_PFCl_1 +LH_SalVentAttnB_PFCv_1 +LH_SalVentAttnB_PFCmp_1 +LH_Limbic_OFC_1 +LH_Limbic_OFC_2 +LH_Limbic_TempPole_1 +LH_Limbic_TempPole_2 +LH_Limbic_TempPole_3 +LH_Limbic_TempPole_4 +LH_ContA_Temp_1 +LH_ContA_IPS_1 +LH_ContA_IPS_2 +LH_ContA_IPS_3 +LH_ContA_PFCd_1 +LH_ContA_PFCl_1 +LH_ContA_PFCl_2 +LH_ContA_PFCl_3 +LH_ContA_PFCl_4 +LH_ContA_Cinga_1 +LH_ContB_Temp_1 +LH_ContB_IPL_1 +LH_ContB_PFCl_1 +LH_ContB_PFClv_1 +LH_ContB_PFClv_2 +LH_ContC_pCun_1 +LH_ContC_pCun_2 +LH_ContC_Cingp_1 +LH_DefaultA_IPL_1 +LH_DefaultA_PFCd_1 +LH_DefaultA_PCC_1 +LH_DefaultA_PCC_2 +LH_DefaultA_PCC_3 +LH_DefaultA_PFCm_1 +LH_DefaultA_PFCm_2 +LH_DefaultA_PFCm_3 +LH_DefaultB_Temp_1 +LH_DefaultB_Temp_2 +LH_DefaultB_Temp_3 +LH_DefaultB_Temp_4 +LH_DefaultB_IPL_1 +LH_DefaultB_PFCd_1 +LH_DefaultB_PFCd_2 +LH_DefaultB_PFCd_3 +LH_DefaultB_PFCd_4 +LH_DefaultB_PFCv_1 +LH_DefaultB_PFCv_2 +LH_DefaultB_PFCv_3 +LH_DefaultB_PFCv_4 +LH_DefaultC_IPL_1 +LH_DefaultC_Rsp_1 +LH_DefaultC_PHC_1 +LH_TempPar_1 +LH_TempPar_2 +RH_VisCent_ExStr_1 +RH_VisCent_ExStr_2 +RH_VisCent_ExStr_3 +RH_VisCent_ExStr_4 +RH_VisCent_ExStr_5 +RH_VisCent_ExStr_6 +RH_VisPeri_ExStrSup_1 +RH_VisPeri_ExStrSup_2 +RH_VisPeri_ExStrSup_3 +RH_VisPeri_ExStrSup_4 +RH_VisPeri_ExStrSup_5 +RH_VisPeri_ExStrSup_6 +RH_SomMotA_1 +RH_SomMotA_2 +RH_SomMotA_3 +RH_SomMotA_4 +RH_SomMotA_5 +RH_SomMotA_6 +RH_SomMotA_7 +RH_SomMotA_8 +RH_SomMotA_9 +RH_SomMotA_10 +RH_SomMotA_11 +RH_SomMotB_S2_1 +RH_SomMotB_S2_2 +RH_SomMotB_S2_3 +RH_SomMotB_S2_4 +RH_SomMotB_S2_5 +RH_SomMotB_S2_6 +RH_SomMotB_S2_7 +RH_DorsAttnA_TempOcc_1 +RH_DorsAttnA_TempOcc_2 +RH_DorsAttnA_SPL_1 +RH_DorsAttnA_SPL_2 +RH_DorsAttnA_SPL_3 +RH_DorsAttnA_SPL_4 +RH_DorsAttnB_PostC_1 +RH_DorsAttnB_PostC_2 +RH_DorsAttnB_PostC_3 +RH_DorsAttnB_PostC_4 +RH_DorsAttnB_FEF_1 +RH_SalVentAttnA_ParOper_1 +RH_SalVentAttnA_PrC_1 +RH_SalVentAttnA_Ins_1 +RH_SalVentAttnA_Ins_2 +RH_SalVentAttnA_Ins_3 +RH_SalVentAttnA_FrMed_1 +RH_SalVentAttnA_FrMed_2 +RH_SalVentAttnA_FrMed_3 +RH_SalVentAttnA_FrMed_4 +RH_SalVentAttnB_IPL_1 +RH_SalVentAttnB_PFCl_1 +RH_SalVentAttnB_PFCl_2 +RH_SalVentAttnB_PFCv_1 +RH_SalVentAttnB_PFCv_2 +RH_SalVentAttnB_PFCmp_1 +RH_Limbic_OFC_1 +RH_Limbic_OFC_2 +RH_Limbic_OFC_3 +RH_Limbic_OFC_4 +RH_Limbic_TempPole_1 +RH_Limbic_TempPole_2 +RH_Limbic_TempPole_3 +RH_Limbic_TempPole_4 +RH_ContA_IPS_1 +RH_ContA_IPS_2 +RH_ContA_PFCd_1 +RH_ContA_PFCl_1 +RH_ContA_PFCl_2 +RH_ContA_Cinga_1 +RH_ContB_Temp_1 +RH_ContB_Temp_2 +RH_ContB_IPL_1 +RH_ContB_IPL_2 +RH_ContB_PFCld_1 +RH_ContB_PFCld_2 +RH_ContB_PFClv_1 +RH_ContB_PFClv_2 +RH_ContB_PFCmp_1 +RH_ContB_PFCmp_2 +RH_ContC_pCun_1 +RH_ContC_pCun_2 +RH_ContC_Cingp_1 +RH_DefaultA_IPL_1 +RH_DefaultA_PFCd_1 +RH_DefaultA_PCC_1 +RH_DefaultA_PFCm_1 +RH_DefaultA_PFCm_2 +RH_DefaultA_PFCm_3 +RH_DefaultB_Temp_1 +RH_DefaultB_AntTemp_1 +RH_DefaultB_PFCd_1 +RH_DefaultB_PFCv_1 +RH_DefaultC_IPL_1 +RH_DefaultC_Rsp_1 +RH_DefaultC_PHC_1 +RH_TempPar_1 +RH_TempPar_2 +RH_TempPar_3 +RH_TempPar_4 + + + + + + + + + + diff --git a/aslprep/data/niftiatlas/schaefer200x17/schaefer200x17Reference.bib b/aslprep/data/niftiatlas/schaefer200x17/schaefer200x17Reference.bib new file mode 100755 index 000000000..5da2c8744 --- /dev/null +++ b/aslprep/data/niftiatlas/schaefer200x17/schaefer200x17Reference.bib @@ -0,0 +1,24 @@ +@article{Schaefer_2017, + doi = {10.1093/cercor/bhx179}, + url = {https://doi.org/10.1093%2Fcercor%2Fbhx179}, + year = 2017, + month = {jul}, + publisher = {Oxford University Press ({OUP})}, + pages = {1--20}, + author = {Alexander Schaefer and Ru Kong and Evan M. Gordon and Timothy O. Laumann and Xi-Nian Zuo and Avram J. Holmes and Simon B. Eickhoff and B.T. Thomas Yeo}, + title = {Local-Global Parcellation of the Human Cerebral Cortex from Intrinsic Functional Connectivity {MRI}}, + journal = {Cerebral Cortex} +} +@article{Thomas_Yeo_2011, + doi = {10.1152/jn.00338.2011}, + url = {https://doi.org/10.1152%2Fjn.00338.2011}, + year = 2011, + month = {jun}, + publisher = {American Physiological Society}, + volume = {106}, + number = {3}, + pages = {1125--1165}, + author = {B. T. Thomas Yeo and F. M. Krienen and J. Sepulcre and M. R. Sabuncu and D. Lashkari and M. Hollinshead and J. L. Roffman and J. W. Smoller and L. Zollei and J. R. Polimeni and B. Fischl and H. Liu and R. L. Buckner}, + title = {The organization of the human cerebral cortex estimated by intrinsic functional connectivity}, + journal = {Journal of Neurophysiology} +} diff --git a/aslprep/data/niftiatlas/schaefer200x7/schaefer200x7CommunityAffiliation.1D b/aslprep/data/niftiatlas/schaefer200x7/schaefer200x7CommunityAffiliation.1D new file mode 100755 index 000000000..9436a8379 --- /dev/null +++ b/aslprep/data/niftiatlas/schaefer200x7/schaefer200x7CommunityAffiliation.1D @@ -0,0 +1,200 @@ +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +4 +4 +4 +4 +4 +4 +4 +4 +4 +4 +4 +5 +5 +5 +5 +5 +5 +6 +6 +6 +6 +6 +6 +6 +6 +6 +6 +6 +6 +6 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +4 +4 +4 +4 +4 +4 +4 +4 +4 +4 +4 +5 +5 +5 +5 +5 +5 +6 +6 +6 +6 +6 +6 +6 +6 +6 +6 +6 +6 +6 +6 +6 +6 +6 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 diff --git a/aslprep/data/niftiatlas/schaefer200x7/schaefer200x7CommunityNames.txt b/aslprep/data/niftiatlas/schaefer200x7/schaefer200x7CommunityNames.txt new file mode 100755 index 000000000..566409f3b --- /dev/null +++ b/aslprep/data/niftiatlas/schaefer200x7/schaefer200x7CommunityNames.txt @@ -0,0 +1,7 @@ +visual +somatomotor +dorsalAttention +salienceVentralAttention +limbic +frontoparietalControl +default diff --git a/aslprep/data/niftiatlas/schaefer200x7/schaefer200x7MNI.nii.gz b/aslprep/data/niftiatlas/schaefer200x7/schaefer200x7MNI.nii.gz new file mode 100755 index 000000000..40f43c2a4 Binary files /dev/null and b/aslprep/data/niftiatlas/schaefer200x7/schaefer200x7MNI.nii.gz differ diff --git a/aslprep/data/niftiatlas/schaefer200x7/schaefer200x7NodeIndex.1D b/aslprep/data/niftiatlas/schaefer200x7/schaefer200x7NodeIndex.1D new file mode 100755 index 000000000..aa5e3f802 --- /dev/null +++ b/aslprep/data/niftiatlas/schaefer200x7/schaefer200x7NodeIndex.1D @@ -0,0 +1,200 @@ +1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +13 +14 +15 +16 +17 +18 +19 +20 +21 +22 +23 +24 +25 +26 +27 +28 +29 +30 +31 +32 +33 +34 +35 +36 +37 +38 +39 +40 +41 +42 +43 +44 +45 +46 +47 +48 +49 +50 +51 +52 +53 +54 +55 +56 +57 +58 +59 +60 +61 +62 +63 +64 +65 +66 +67 +68 +69 +70 +71 +72 +73 +74 +75 +76 +77 +78 +79 +80 +81 +82 +83 +84 +85 +86 +87 +88 +89 +90 +91 +92 +93 +94 +95 +96 +97 +98 +99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +137 +138 +139 +140 +141 +142 +143 +144 +145 +146 +147 +148 +149 +150 +151 +152 +153 +154 +155 +156 +157 +158 +159 +160 +161 +162 +163 +164 +165 +166 +167 +168 +169 +170 +171 +172 +173 +174 +175 +176 +177 +178 +179 +180 +181 +182 +183 +184 +185 +186 +187 +188 +189 +190 +191 +192 +193 +194 +195 +196 +197 +198 +199 +200 diff --git a/aslprep/data/niftiatlas/schaefer200x7/schaefer200x7NodeNames.txt b/aslprep/data/niftiatlas/schaefer200x7/schaefer200x7NodeNames.txt new file mode 100755 index 000000000..9047a2a51 --- /dev/null +++ b/aslprep/data/niftiatlas/schaefer200x7/schaefer200x7NodeNames.txt @@ -0,0 +1,200 @@ +LH_Vis_1 +LH_Vis_2 +LH_Vis_3 +LH_Vis_4 +LH_Vis_5 +LH_Vis_6 +LH_Vis_7 +LH_Vis_8 +LH_Vis_9 +LH_Vis_10 +LH_Vis_11 +LH_Vis_12 +LH_Vis_13 +LH_Vis_14 +LH_SomMot_1 +LH_SomMot_2 +LH_SomMot_3 +LH_SomMot_4 +LH_SomMot_5 +LH_SomMot_6 +LH_SomMot_7 +LH_SomMot_8 +LH_SomMot_9 +LH_SomMot_10 +LH_SomMot_11 +LH_SomMot_12 +LH_SomMot_13 +LH_SomMot_14 +LH_SomMot_15 +LH_SomMot_16 +LH_DorsAttn_Post_1 +LH_DorsAttn_Post_2 +LH_DorsAttn_Post_3 +LH_DorsAttn_Post_4 +LH_DorsAttn_Post_5 +LH_DorsAttn_Post_6 +LH_DorsAttn_Post_7 +LH_DorsAttn_Post_8 +LH_DorsAttn_Post_9 +LH_DorsAttn_Post_10 +LH_DorsAttn_FEF_1 +LH_DorsAttn_FEF_2 +LH_DorsAttn_PrCv_1 +LH_SalVentAttn_ParOper_1 +LH_SalVentAttn_ParOper_2 +LH_SalVentAttn_ParOper_3 +LH_SalVentAttn_FrOper_1 +LH_SalVentAttn_FrOper_2 +LH_SalVentAttn_FrOper_3 +LH_SalVentAttn_FrOper_4 +LH_SalVentAttn_PFCl_1 +LH_SalVentAttn_Med_1 +LH_SalVentAttn_Med_2 +LH_SalVentAttn_Med_3 +LH_Limbic_OFC_1 +LH_Limbic_OFC_2 +LH_Limbic_TempPole_1 +LH_Limbic_TempPole_2 +LH_Limbic_TempPole_3 +LH_Limbic_TempPole_4 +LH_Cont_Par_1 +LH_Cont_Par_2 +LH_Cont_Par_3 +LH_Cont_Temp_1 +LH_Cont_PFCl_1 +LH_Cont_PFCl_2 +LH_Cont_PFCl_3 +LH_Cont_PFCl_4 +LH_Cont_PFCl_5 +LH_Cont_PFCl_6 +LH_Cont_pCun_1 +LH_Cont_Cing_1 +LH_Cont_Cing_2 +LH_Default_Temp_1 +LH_Default_Temp_2 +LH_Default_Temp_3 +LH_Default_Temp_4 +LH_Default_Temp_5 +LH_Default_Temp_6 +LH_Default_Temp_7 +LH_Default_Temp_8 +LH_Default_Temp_9 +LH_Default_PFC_1 +LH_Default_PFC_2 +LH_Default_PFC_3 +LH_Default_PFC_4 +LH_Default_PFC_5 +LH_Default_PFC_6 +LH_Default_PFC_7 +LH_Default_PFC_8 +LH_Default_PFC_9 +LH_Default_PFC_10 +LH_Default_PFC_11 +LH_Default_PFC_12 +LH_Default_PFC_13 +LH_Default_PCC_1 +LH_Default_PCC_2 +LH_Default_PCC_3 +LH_Default_PCC_4 +LH_Default_PHC_1 +RH_Vis_1 +RH_Vis_2 +RH_Vis_3 +RH_Vis_4 +RH_Vis_5 +RH_Vis_6 +RH_Vis_7 +RH_Vis_8 +RH_Vis_9 +RH_Vis_10 +RH_Vis_11 +RH_Vis_12 +RH_Vis_13 +RH_Vis_14 +RH_Vis_15 +RH_SomMot_1 +RH_SomMot_2 +RH_SomMot_3 +RH_SomMot_4 +RH_SomMot_5 +RH_SomMot_6 +RH_SomMot_7 +RH_SomMot_8 +RH_SomMot_9 +RH_SomMot_10 +RH_SomMot_11 +RH_SomMot_12 +RH_SomMot_13 +RH_SomMot_14 +RH_SomMot_15 +RH_SomMot_16 +RH_SomMot_17 +RH_SomMot_18 +RH_SomMot_19 +RH_DorsAttn_Post_1 +RH_DorsAttn_Post_2 +RH_DorsAttn_Post_3 +RH_DorsAttn_Post_4 +RH_DorsAttn_Post_5 +RH_DorsAttn_Post_6 +RH_DorsAttn_Post_7 +RH_DorsAttn_Post_8 +RH_DorsAttn_Post_9 +RH_DorsAttn_Post_10 +RH_DorsAttn_FEF_1 +RH_DorsAttn_FEF_2 +RH_DorsAttn_PrCv_1 +RH_SalVentAttn_TempOccPar_1 +RH_SalVentAttn_TempOccPar_2 +RH_SalVentAttn_TempOccPar_3 +RH_SalVentAttn_PrC_1 +RH_SalVentAttn_FrOper_1 +RH_SalVentAttn_FrOper_2 +RH_SalVentAttn_FrOper_3 +RH_SalVentAttn_FrOper_4 +RH_SalVentAttn_Med_1 +RH_SalVentAttn_Med_2 +RH_SalVentAttn_Med_3 +RH_Limbic_OFC_1 +RH_Limbic_OFC_2 +RH_Limbic_OFC_3 +RH_Limbic_TempPole_1 +RH_Limbic_TempPole_2 +RH_Limbic_TempPole_3 +RH_Cont_Par_1 +RH_Cont_Par_2 +RH_Cont_Par_3 +RH_Cont_Temp_1 +RH_Cont_PFCv_1 +RH_Cont_PFCl_1 +RH_Cont_PFCl_2 +RH_Cont_PFCl_3 +RH_Cont_PFCl_4 +RH_Cont_PFCl_5 +RH_Cont_PFCl_6 +RH_Cont_PFCl_7 +RH_Cont_pCun_1 +RH_Cont_PFCmp_1 +RH_Cont_PFCmp_2 +RH_Cont_PFCmp_3 +RH_Cont_PFCmp_4 +RH_Default_Par_1 +RH_Default_Par_2 +RH_Default_Par_3 +RH_Default_Temp_1 +RH_Default_Temp_2 +RH_Default_Temp_3 +RH_Default_Temp_4 +RH_Default_Temp_5 +RH_Default_PFCv_1 +RH_Default_PFCm_1 +RH_Default_PFCm_2 +RH_Default_PFCm_3 +RH_Default_PFCm_4 +RH_Default_PFCm_5 +RH_Default_PFCm_6 +RH_Default_PFCm_7 +RH_Default_PCC_1 +RH_Default_PCC_2 +RH_Default_PCC_3 diff --git a/aslprep/data/niftiatlas/schaefer200x7/schaefer200x7Reference.bib b/aslprep/data/niftiatlas/schaefer200x7/schaefer200x7Reference.bib new file mode 100755 index 000000000..5da2c8744 --- /dev/null +++ b/aslprep/data/niftiatlas/schaefer200x7/schaefer200x7Reference.bib @@ -0,0 +1,24 @@ +@article{Schaefer_2017, + doi = {10.1093/cercor/bhx179}, + url = {https://doi.org/10.1093%2Fcercor%2Fbhx179}, + year = 2017, + month = {jul}, + publisher = {Oxford University Press ({OUP})}, + pages = {1--20}, + author = {Alexander Schaefer and Ru Kong and Evan M. Gordon and Timothy O. Laumann and Xi-Nian Zuo and Avram J. Holmes and Simon B. Eickhoff and B.T. Thomas Yeo}, + title = {Local-Global Parcellation of the Human Cerebral Cortex from Intrinsic Functional Connectivity {MRI}}, + journal = {Cerebral Cortex} +} +@article{Thomas_Yeo_2011, + doi = {10.1152/jn.00338.2011}, + url = {https://doi.org/10.1152%2Fjn.00338.2011}, + year = 2011, + month = {jun}, + publisher = {American Physiological Society}, + volume = {106}, + number = {3}, + pages = {1125--1165}, + author = {B. T. Thomas Yeo and F. M. Krienen and J. Sepulcre and M. R. Sabuncu and D. Lashkari and M. Hollinshead and J. L. Roffman and J. W. Smoller and L. Zollei and J. R. Polimeni and B. Fischl and H. Liu and R. L. Buckner}, + title = {The organization of the human cerebral cortex estimated by intrinsic functional connectivity}, + journal = {Journal of Neurophysiology} +} diff --git a/aslprep/data/niftiatlas/schaefer400x17/README.md b/aslprep/data/niftiatlas/schaefer400x17/README.md new file mode 100755 index 000000000..892462ff6 --- /dev/null +++ b/aslprep/data/niftiatlas/schaefer400x17/README.md @@ -0,0 +1,2 @@ +# schaefer400 +Multiscale local-global functional atlas from Schaefer and colleagues: 400-node resolution diff --git a/aslprep/data/niftiatlas/schaefer400x17/schaefer400x17CommunityAffiliation.1D b/aslprep/data/niftiatlas/schaefer400x17/schaefer400x17CommunityAffiliation.1D new file mode 100755 index 000000000..83209ea8a --- /dev/null +++ b/aslprep/data/niftiatlas/schaefer400x17/schaefer400x17CommunityAffiliation.1D @@ -0,0 +1,400 @@ +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +4 +4 +4 +4 +4 +4 +4 +4 +4 +4 +4 +4 +4 +4 +4 +4 +5 +5 +5 +5 +5 +5 +5 +5 +5 +5 +5 +5 +5 +6 +6 +6 +6 +6 +6 +6 +6 +6 +6 +6 +6 +6 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +8 +8 +8 +8 +8 +8 +8 +8 +9 +9 +9 +9 +9 +10 +10 +10 +10 +10 +10 +10 +11 +11 +11 +11 +11 +11 +11 +11 +11 +11 +11 +11 +11 +12 +12 +12 +12 +12 +12 +12 +12 +12 +12 +13 +13 +13 +13 +13 +15 +15 +15 +15 +15 +15 +15 +15 +15 +15 +15 +15 +15 +15 +15 +15 +15 +15 +16 +16 +16 +16 +16 +16 +16 +16 +16 +16 +16 +16 +16 +16 +16 +16 +16 +16 +16 +16 +16 +16 +16 +16 +16 +16 +16 +16 +17 +17 +17 +17 +17 +17 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +4 +4 +4 +4 +4 +4 +4 +4 +4 +4 +4 +4 +4 +4 +4 +5 +5 +5 +5 +5 +5 +5 +5 +5 +5 +5 +5 +5 +5 +6 +6 +6 +6 +6 +6 +6 +6 +6 +6 +6 +6 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +8 +8 +8 +8 +8 +8 +8 +8 +8 +9 +9 +9 +9 +9 +9 +10 +10 +10 +10 +10 +10 +11 +11 +11 +11 +11 +11 +11 +11 +11 +11 +11 +11 +11 +12 +12 +12 +12 +12 +12 +12 +12 +12 +12 +12 +12 +12 +13 +13 +13 +13 +13 +13 +13 +14 +14 +14 +14 +14 +14 +14 +14 +14 +14 +15 +15 +15 +15 +15 +15 +15 +15 +15 +15 +15 +15 +15 +15 +15 +15 +15 +16 +16 +16 +16 +16 +16 +17 +17 +17 +17 +17 +17 +17 +17 +17 +17 diff --git a/aslprep/data/niftiatlas/schaefer400x17/schaefer400x17CommunityNames.txt b/aslprep/data/niftiatlas/schaefer400x17/schaefer400x17CommunityNames.txt new file mode 100755 index 000000000..e1adf74b3 --- /dev/null +++ b/aslprep/data/niftiatlas/schaefer400x17/schaefer400x17CommunityNames.txt @@ -0,0 +1,17 @@ +visualCentral +visualPeripheral +somatomotorA +somatomotorBAuditory +dorsalAttentionA +dorsalAttentionB +salienceVentralAttentionA +salienceVentralAttentionB +limbicOrbitofrontal +limbicTemporopolar +frontoparietalControlA +frontoparietalControlB +frontoparietalControlC +defaultA +defaultB +defaultC +temporoparietal diff --git a/aslprep/data/niftiatlas/schaefer400x17/schaefer400x17MNI.nii.gz b/aslprep/data/niftiatlas/schaefer400x17/schaefer400x17MNI.nii.gz new file mode 100755 index 000000000..95901b3ba Binary files /dev/null and b/aslprep/data/niftiatlas/schaefer400x17/schaefer400x17MNI.nii.gz differ diff --git a/aslprep/data/niftiatlas/schaefer400x17/schaefer400x17NodeIndex.1D b/aslprep/data/niftiatlas/schaefer400x17/schaefer400x17NodeIndex.1D new file mode 100755 index 000000000..7b5d34d5c --- /dev/null +++ b/aslprep/data/niftiatlas/schaefer400x17/schaefer400x17NodeIndex.1D @@ -0,0 +1,400 @@ +1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +13 +14 +15 +16 +17 +18 +19 +20 +21 +22 +23 +24 +25 +26 +27 +28 +29 +30 +31 +32 +33 +34 +35 +36 +37 +38 +39 +40 +41 +42 +43 +44 +45 +46 +47 +48 +49 +50 +51 +52 +53 +54 +55 +56 +57 +58 +59 +60 +61 +62 +63 +64 +65 +66 +67 +68 +69 +70 +71 +72 +73 +74 +75 +76 +77 +78 +79 +80 +81 +82 +83 +84 +85 +86 +87 +88 +89 +90 +91 +92 +93 +94 +95 +96 +97 +98 +99 +100 +101 +102 +103 +104 +105 +106 +107 +108 +109 +110 +111 +112 +113 +114 +115 +116 +117 +118 +119 +120 +121 +122 +123 +124 +125 +126 +127 +128 +129 +130 +131 +132 +133 +134 +135 +136 +137 +138 +139 +140 +141 +142 +143 +144 +145 +146 +147 +148 +149 +150 +151 +152 +153 +154 +155 +156 +157 +158 +159 +160 +161 +162 +163 +164 +165 +166 +167 +168 +169 +170 +171 +172 +173 +174 +175 +176 +177 +178 +179 +180 +181 +182 +183 +184 +185 +186 +187 +188 +189 +190 +191 +192 +193 +194 +195 +196 +197 +198 +199 +200 +201 +202 +203 +204 +205 +206 +207 +208 +209 +210 +211 +212 +213 +214 +215 +216 +217 +218 +219 +220 +221 +222 +223 +224 +225 +226 +227 +228 +229 +230 +231 +232 +233 +234 +235 +236 +237 +238 +239 +240 +241 +242 +243 +244 +245 +246 +247 +248 +249 +250 +251 +252 +253 +254 +255 +256 +257 +258 +259 +260 +261 +262 +263 +264 +265 +266 +267 +268 +269 +270 +271 +272 +273 +274 +275 +276 +277 +278 +279 +280 +281 +282 +283 +284 +285 +286 +287 +288 +289 +290 +291 +292 +293 +294 +295 +296 +297 +298 +299 +300 +301 +302 +303 +304 +305 +306 +307 +308 +309 +310 +311 +312 +313 +314 +315 +316 +317 +318 +319 +320 +321 +322 +323 +324 +325 +326 +327 +328 +329 +330 +331 +332 +333 +334 +335 +336 +337 +338 +339 +340 +341 +342 +343 +344 +345 +346 +347 +348 +349 +350 +351 +352 +353 +354 +355 +356 +357 +358 +359 +360 +361 +362 +363 +364 +365 +366 +367 +368 +369 +370 +371 +372 +373 +374 +375 +376 +377 +378 +379 +380 +381 +382 +383 +384 +385 +386 +387 +388 +389 +390 +391 +392 +393 +394 +395 +396 +397 +398 +399 +400 diff --git a/aslprep/data/niftiatlas/schaefer400x17/schaefer400x17NodeNames.txt b/aslprep/data/niftiatlas/schaefer400x17/schaefer400x17NodeNames.txt new file mode 100755 index 000000000..73b71332c --- /dev/null +++ b/aslprep/data/niftiatlas/schaefer400x17/schaefer400x17NodeNames.txt @@ -0,0 +1,400 @@ +LH_VisCent_ExStr_1 +LH_VisCent_ExStr_2 +LH_VisCent_ExStr_3 +LH_VisCent_ExStr_4 +LH_VisCent_ExStr_5 +LH_VisCent_ExStr_6 +LH_VisCent_ExStr_7 +LH_VisCent_ExStr_8 +LH_VisCent_ExStr_9 +LH_VisCent_ExStr_10 +LH_VisCent_ExStr_11 +LH_VisCent_ExStr_12 +LH_VisPeri_ExStrSup_1 +LH_VisPeri_ExStrSup_2 +LH_VisPeri_ExStrSup_3 +LH_VisPeri_ExStrSup_4 +LH_VisPeri_ExStrSup_5 +LH_VisPeri_ExStrSup_6 +LH_VisPeri_ExStrSup_7 +LH_VisPeri_ExStrSup_8 +LH_VisPeri_ExStrSup_9 +LH_VisPeri_ExStrSup_10 +LH_VisPeri_ExStrSup_11 +LH_VisPeri_ExStrSup_12 +LH_SomMotA_1 +LH_SomMotA_2 +LH_SomMotA_3 +LH_SomMotA_4 +LH_SomMotA_5 +LH_SomMotA_6 +LH_SomMotA_7 +LH_SomMotA_8 +LH_SomMotA_9 +LH_SomMotA_10 +LH_SomMotA_11 +LH_SomMotA_12 +LH_SomMotA_13 +LH_SomMotA_14 +LH_SomMotA_15 +LH_SomMotA_16 +LH_SomMotA_17 +LH_SomMotA_18 +LH_SomMotA_19 +LH_SomMotB_Aud_1 +LH_SomMotB_Aud_2 +LH_SomMotB_Aud_3 +LH_SomMotB_Aud_4 +LH_SomMotB_Aud_5 +LH_SomMotB_Aud_6 +LH_SomMotB_Aud_7 +LH_SomMotB_Aud_8 +LH_SomMotB_Aud_9 +LH_SomMotB_Aud_10 +LH_SomMotB_Aud_11 +LH_SomMotB_Aud_12 +LH_SomMotB_Aud_13 +LH_SomMotB_Aud_14 +LH_SomMotB_Aud_15 +LH_SomMotB_Aud_16 +LH_DorsAttnA_TempOcc_1 +LH_DorsAttnA_TempOcc_2 +LH_DorsAttnA_TempOcc_3 +LH_DorsAttnA_TempOcc_4 +LH_DorsAttnA_ParOcc_1 +LH_DorsAttnA_SPL_1 +LH_DorsAttnA_SPL_2 +LH_DorsAttnA_SPL_3 +LH_DorsAttnA_SPL_4 +LH_DorsAttnA_SPL_5 +LH_DorsAttnA_SPL_6 +LH_DorsAttnA_SPL_7 +LH_DorsAttnA_SPL_8 +LH_DorsAttnB_PostC_1 +LH_DorsAttnB_PostC_2 +LH_DorsAttnB_PostC_3 +LH_DorsAttnB_PostC_4 +LH_DorsAttnB_PostC_5 +LH_DorsAttnB_PostC_6 +LH_DorsAttnB_PostC_7 +LH_DorsAttnB_PostC_8 +LH_DorsAttnB_PostC_9 +LH_DorsAttnB_FEF_1 +LH_DorsAttnB_FEF_2 +LH_DorsAttnB_FEF_3 +LH_DorsAttnB_PrCv_1 +LH_SalVentAttnA_ParOper_1 +LH_SalVentAttnA_ParOper_2 +LH_SalVentAttnA_ParOper_3 +LH_SalVentAttnA_Ins_1 +LH_SalVentAttnA_Ins_2 +LH_SalVentAttnA_Ins_3 +LH_SalVentAttnA_Ins_4 +LH_SalVentAttnA_Ins_5 +LH_SalVentAttnA_Ins_6 +LH_SalVentAttnA_ParMed_1 +LH_SalVentAttnA_ParMed_2 +LH_SalVentAttnA_ParMed_3 +LH_SalVentAttnA_FrMed_1 +LH_SalVentAttnA_FrMed_2 +LH_SalVentAttnA_FrMed_3 +LH_SalVentAttnB_PFCl_1 +LH_SalVentAttnB_PFCl_2 +LH_SalVentAttnB_PFCl_3 +LH_SalVentAttnB_PFCv_1 +LH_SalVentAttnB_PFCv_2 +LH_SalVentAttnB_PFCv_3 +LH_SalVentAttnB_OFC_1 +LH_SalVentAttnB_PFCmp_1 +LH_Limbic_OFC_1 +LH_Limbic_OFC_2 +LH_Limbic_OFC_3 +LH_Limbic_OFC_4 +LH_Limbic_OFC_5 +LH_Limbic_TempPole_1 +LH_Limbic_TempPole_2 +LH_Limbic_TempPole_3 +LH_Limbic_TempPole_4 +LH_Limbic_TempPole_5 +LH_Limbic_TempPole_6 +LH_Limbic_TempPole_7 +LH_ContA_Temp_1 +LH_ContA_IPS_1 +LH_ContA_IPS_2 +LH_ContA_IPS_3 +LH_ContA_IPS_4 +LH_ContA_IPS_5 +LH_ContA_PFCd_1 +LH_ContA_PFCl_1 +LH_ContA_PFCl_2 +LH_ContA_PFCl_3 +LH_ContA_PFCl_4 +LH_ContA_PFCl_5 +LH_ContA_Cinga_1 +LH_ContB_Temp_1 +LH_ContB_Temp_2 +LH_ContB_IPL_1 +LH_ContB_IPL_2 +LH_ContB_IPL_3 +LH_ContB_PFCd_1 +LH_ContB_PFClv_1 +LH_ContB_PFClv_2 +LH_ContB_PFClv_3 +LH_ContB_PFCmp_1 +LH_ContC_pCun_1 +LH_ContC_pCun_2 +LH_ContC_pCun_3 +LH_ContC_Cingp_1 +LH_ContC_Cingp_2 +LH_DefaultA_IPL_1 +LH_DefaultA_IPL_2 +LH_DefaultA_PFCd_1 +LH_DefaultA_PFCd_2 +LH_DefaultA_PFCd_3 +LH_DefaultA_PCC_1 +LH_DefaultA_PCC_2 +LH_DefaultA_PCC_3 +LH_DefaultA_PCC_4 +LH_DefaultA_PCC_5 +LH_DefaultA_PCC_6 +LH_DefaultA_PCC_7 +LH_DefaultA_PFCm_1 +LH_DefaultA_PFCm_2 +LH_DefaultA_PFCm_3 +LH_DefaultA_PFCm_4 +LH_DefaultA_PFCm_5 +LH_DefaultA_PFCm_6 +LH_DefaultB_Temp_1 +LH_DefaultB_Temp_2 +LH_DefaultB_Temp_3 +LH_DefaultB_Temp_4 +LH_DefaultB_Temp_5 +LH_DefaultB_Temp_6 +LH_DefaultB_IPL_1 +LH_DefaultB_IPL_2 +LH_DefaultB_PFCd_1 +LH_DefaultB_PFCd_2 +LH_DefaultB_PFCd_3 +LH_DefaultB_PFCd_4 +LH_DefaultB_PFCd_5 +LH_DefaultB_PFCd_6 +LH_DefaultB_PFCl_1 +LH_DefaultB_PFCl_2 +LH_DefaultB_PFCv_1 +LH_DefaultB_PFCv_2 +LH_DefaultB_PFCv_3 +LH_DefaultB_PFCv_4 +LH_DefaultB_PFCv_5 +LH_DefaultC_IPL_1 +LH_DefaultC_Rsp_1 +LH_DefaultC_Rsp_2 +LH_DefaultC_Rsp_3 +LH_DefaultC_PHC_1 +LH_DefaultC_PHC_2 +LH_DefaultC_PHC_3 +LH_TempPar_1 +LH_TempPar_2 +LH_TempPar_3 +LH_TempPar_4 +LH_TempPar_5 +LH_TempPar_6 +RH_VisCent_ExStr_1 +RH_VisCent_ExStr_2 +RH_VisCent_ExStr_3 +RH_VisCent_ExStr_4 +RH_VisCent_ExStr_5 +RH_VisCent_ExStr_6 +RH_VisCent_ExStr_7 +RH_VisCent_ExStr_8 +RH_VisCent_ExStr_9 +RH_VisCent_ExStr_10 +RH_VisCent_ExStr_11 +RH_VisCent_ExStr_12 +RH_VisPeri_ExStrSup_1 +RH_VisPeri_ExStrSup_2 +RH_VisPeri_ExStrSup_3 +RH_VisPeri_ExStrSup_4 +RH_VisPeri_ExStrSup_5 +RH_VisPeri_ExStrSup_6 +RH_VisPeri_ExStrSup_7 +RH_VisPeri_ExStrSup_8 +RH_VisPeri_ExStrSup_9 +RH_VisPeri_ExStrSup_10 +RH_VisPeri_ExStrSup_11 +RH_SomMotA_1 +RH_SomMotA_2 +RH_SomMotA_3 +RH_SomMotA_4 +RH_SomMotA_5 +RH_SomMotA_6 +RH_SomMotA_7 +RH_SomMotA_8 +RH_SomMotA_9 +RH_SomMotA_10 +RH_SomMotA_11 +RH_SomMotA_12 +RH_SomMotA_13 +RH_SomMotA_14 +RH_SomMotA_15 +RH_SomMotA_16 +RH_SomMotA_17 +RH_SomMotA_18 +RH_SomMotA_19 +RH_SomMotA_20 +RH_SomMotB_S2_1 +RH_SomMotB_S2_2 +RH_SomMotB_S2_3 +RH_SomMotB_S2_4 +RH_SomMotB_S2_5 +RH_SomMotB_S2_6 +RH_SomMotB_S2_7 +RH_SomMotB_S2_8 +RH_SomMotB_S2_9 +RH_SomMotB_S2_10 +RH_SomMotB_S2_11 +RH_SomMotB_S2_12 +RH_SomMotB_S2_13 +RH_SomMotB_S2_14 +RH_SomMotB_S2_15 +RH_DorsAttnA_TempOcc_1 +RH_DorsAttnA_TempOcc_2 +RH_DorsAttnA_TempOcc_3 +RH_DorsAttnA_TempOcc_4 +RH_DorsAttnA_TempOcc_5 +RH_DorsAttnA_SPL_1 +RH_DorsAttnA_SPL_2 +RH_DorsAttnA_SPL_3 +RH_DorsAttnA_SPL_4 +RH_DorsAttnA_SPL_5 +RH_DorsAttnA_SPL_6 +RH_DorsAttnA_SPL_7 +RH_DorsAttnA_SPL_8 +RH_DorsAttnA_SPL_9 +RH_DorsAttnB_TempOcc_1 +RH_DorsAttnB_PostC_1 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+RH_DefaultA_PFCm_5 +RH_DefaultA_PFCm_6 +RH_DefaultB_Temp_1 +RH_DefaultB_Temp_2 +RH_DefaultB_AntTemp_1 +RH_DefaultB_PFCd_1 +RH_DefaultB_PFCd_2 +RH_DefaultB_PFCd_3 +RH_DefaultB_PFCd_4 +RH_DefaultB_PFCd_5 +RH_DefaultB_PFCv_1 +RH_DefaultB_PFCv_2 +RH_DefaultB_PFCv_3 +RH_DefaultC_IPL_1 +RH_DefaultC_IPL_2 +RH_DefaultC_Rsp_1 +RH_DefaultC_Rsp_2 +RH_DefaultC_PHC_1 +RH_DefaultC_PHC_2 +RH_TempPar_1 +RH_TempPar_2 +RH_TempPar_3 +RH_TempPar_4 +RH_TempPar_5 +RH_TempPar_6 +RH_TempPar_7 +RH_TempPar_8 +RH_TempPar_9 +RH_TempPar_10 diff --git a/aslprep/data/niftiatlas/schaefer400x17/schaefer400x17Reference.bib b/aslprep/data/niftiatlas/schaefer400x17/schaefer400x17Reference.bib new file mode 100755 index 000000000..5da2c8744 --- /dev/null +++ b/aslprep/data/niftiatlas/schaefer400x17/schaefer400x17Reference.bib @@ -0,0 +1,24 @@ +@article{Schaefer_2017, + doi = {10.1093/cercor/bhx179}, + url = {https://doi.org/10.1093%2Fcercor%2Fbhx179}, + year = 2017, + month = {jul}, + publisher = {Oxford University Press ({OUP})}, + pages = {1--20}, + author = {Alexander Schaefer and Ru Kong and Evan M. Gordon and Timothy O. Laumann and Xi-Nian Zuo and Avram J. Holmes and Simon B. Eickhoff and B.T. Thomas Yeo}, + title = {Local-Global Parcellation of the Human Cerebral Cortex from Intrinsic Functional Connectivity {MRI}}, + journal = {Cerebral Cortex} +} +@article{Thomas_Yeo_2011, + doi = {10.1152/jn.00338.2011}, + url = {https://doi.org/10.1152%2Fjn.00338.2011}, + year = 2011, + month = {jun}, + publisher = {American Physiological Society}, + volume = {106}, + number = {3}, + pages = {1125--1165}, + author = {B. T. Thomas Yeo and F. M. Krienen and J. Sepulcre and M. R. Sabuncu and D. Lashkari and M. Hollinshead and J. L. Roffman and J. W. Smoller and L. Zollei and J. R. Polimeni and B. Fischl and H. Liu and R. L. Buckner}, + title = {The organization of the human cerebral cortex estimated by intrinsic functional connectivity}, + journal = {Journal of Neurophysiology} +} diff --git a/aslprep/data/niftiatlas/schaefer400x7/schaefer400x7CommunityAffiliation.1D b/aslprep/data/niftiatlas/schaefer400x7/schaefer400x7CommunityAffiliation.1D new file mode 100755 index 000000000..c749fcdca --- /dev/null +++ b/aslprep/data/niftiatlas/schaefer400x7/schaefer400x7CommunityAffiliation.1D @@ -0,0 +1,400 @@ +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +1 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +2 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +3 +4 +4 +4 +4 +4 +4 +4 +4 +4 +4 +4 +4 +4 +4 +4 +4 +4 +4 +4 +4 +4 +4 +5 +5 +5 +5 +5 +5 +5 +5 +5 +5 +5 +5 +5 +6 +6 +6 +6 +6 +6 +6 +6 +6 +6 +6 +6 +6 +6 +6 +6 +6 +6 +6 +6 +6 +6 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 +7 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+visual +somatomotor +dorsalAttention +salienceVentralAttention +limbic +frontoparietalControl +default diff --git a/aslprep/data/niftiatlas/schaefer400x7/schaefer400x7MNI.nii.gz b/aslprep/data/niftiatlas/schaefer400x7/schaefer400x7MNI.nii.gz new file mode 100755 index 000000000..ec9f94bf9 Binary files /dev/null and b/aslprep/data/niftiatlas/schaefer400x7/schaefer400x7MNI.nii.gz differ diff --git a/aslprep/data/niftiatlas/schaefer400x7/schaefer400x7NodeIndex.1D b/aslprep/data/niftiatlas/schaefer400x7/schaefer400x7NodeIndex.1D new file mode 100755 index 000000000..7b5d34d5c --- /dev/null +++ b/aslprep/data/niftiatlas/schaefer400x7/schaefer400x7NodeIndex.1D @@ -0,0 +1,400 @@ +1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +13 +14 +15 +16 +17 +18 +19 +20 +21 +22 +23 +24 +25 +26 +27 +28 +29 +30 +31 +32 +33 +34 +35 +36 +37 +38 +39 +40 +41 +42 +43 +44 +45 +46 +47 +48 +49 +50 +51 +52 +53 +54 +55 +56 +57 +58 +59 +60 +61 +62 +63 +64 +65 +66 +67 +68 +69 +70 +71 +72 +73 +74 +75 +76 +77 +78 +79 +80 +81 +82 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+RH_SomMot_26 +RH_SomMot_27 +RH_SomMot_28 +RH_SomMot_29 +RH_SomMot_30 +RH_SomMot_31 +RH_SomMot_32 +RH_SomMot_33 +RH_SomMot_34 +RH_SomMot_35 +RH_SomMot_36 +RH_SomMot_37 +RH_SomMot_38 +RH_SomMot_39 +RH_SomMot_40 +RH_DorsAttn_Post_1 +RH_DorsAttn_Post_2 +RH_DorsAttn_Post_3 +RH_DorsAttn_Post_4 +RH_DorsAttn_Post_5 +RH_DorsAttn_Post_6 +RH_DorsAttn_Post_7 +RH_DorsAttn_Post_8 +RH_DorsAttn_Post_9 +RH_DorsAttn_Post_10 +RH_DorsAttn_Post_11 +RH_DorsAttn_Post_12 +RH_DorsAttn_Post_13 +RH_DorsAttn_Post_14 +RH_DorsAttn_Post_15 +RH_DorsAttn_Post_16 +RH_DorsAttn_Post_17 +RH_DorsAttn_Post_18 +RH_DorsAttn_Post_19 +RH_DorsAttn_FEF_1 +RH_DorsAttn_FEF_2 +RH_DorsAttn_FEF_3 +RH_DorsAttn_PrCv_1 +RH_SalVentAttn_TempOccPar_1 +RH_SalVentAttn_TempOccPar_2 +RH_SalVentAttn_TempOccPar_3 +RH_SalVentAttn_TempOccPar_4 +RH_SalVentAttn_TempOccPar_5 +RH_SalVentAttn_TempOccPar_6 +RH_SalVentAttn_TempOccPar_7 +RH_SalVentAttn_PrC_1 +RH_SalVentAttn_FrOper_1 +RH_SalVentAttn_FrOper_2 +RH_SalVentAttn_FrOper_3 +RH_SalVentAttn_FrOper_4 +RH_SalVentAttn_FrOper_5 +RH_SalVentAttn_FrOper_6 +RH_SalVentAttn_FrOper_7 +RH_SalVentAttn_FrOper_8 +RH_SalVentAttn_PFCl_1 +RH_SalVentAttn_Med_1 +RH_SalVentAttn_Med_2 +RH_SalVentAttn_Med_3 +RH_SalVentAttn_Med_4 +RH_SalVentAttn_Med_5 +RH_SalVentAttn_Med_6 +RH_SalVentAttn_Med_7 +RH_SalVentAttn_Med_8 +RH_Limbic_OFC_1 +RH_Limbic_OFC_2 +RH_Limbic_OFC_3 +RH_Limbic_OFC_4 +RH_Limbic_OFC_5 +RH_Limbic_OFC_6 +RH_Limbic_TempPole_1 +RH_Limbic_TempPole_2 +RH_Limbic_TempPole_3 +RH_Limbic_TempPole_4 +RH_Limbic_TempPole_5 +RH_Limbic_TempPole_6 +RH_Limbic_TempPole_7 +RH_Cont_Par_1 +RH_Cont_Par_2 +RH_Cont_Par_3 +RH_Cont_Par_4 +RH_Cont_Par_5 +RH_Cont_Par_6 +RH_Cont_Temp_1 +RH_Cont_Temp_2 +RH_Cont_PFCv_1 +RH_Cont_PFCl_1 +RH_Cont_PFCl_2 +RH_Cont_PFCl_3 +RH_Cont_PFCl_4 +RH_Cont_PFCl_5 +RH_Cont_PFCl_6 +RH_Cont_PFCl_7 +RH_Cont_PFCl_8 +RH_Cont_PFCl_9 +RH_Cont_PFCl_10 +RH_Cont_PFCl_11 +RH_Cont_PFCl_12 +RH_Cont_PFCl_13 +RH_Cont_PFCl_14 +RH_Cont_PFCl_15 +RH_Cont_pCun_1 +RH_Cont_pCun_2 +RH_Cont_Cing_1 +RH_Cont_Cing_2 +RH_Cont_PFCmp_1 +RH_Cont_PFCmp_2 +RH_Default_Par_1 +RH_Default_Par_2 +RH_Default_Par_3 +RH_Default_Par_4 +RH_Default_Par_5 +RH_Default_Temp_1 +RH_Default_Temp_2 +RH_Default_Temp_3 +RH_Default_Temp_4 +RH_Default_Temp_5 +RH_Default_Temp_6 +RH_Default_Temp_7 +RH_Default_Temp_8 +RH_Default_PFCv_1 +RH_Default_PFCv_2 +RH_Default_PFCv_3 +RH_Default_PFCv_4 +RH_Default_PFCm_1 +RH_Default_PFCm_2 +RH_Default_PFCm_3 +RH_Default_PFCm_4 +RH_Default_PFCm_5 +RH_Default_PFCm_6 +RH_Default_PFCm_7 +RH_Default_PFCm_8 +RH_Default_PFCm_9 +RH_Default_PFCm_10 +RH_Default_PFCm_11 +RH_Default_PFCm_12 +RH_Default_PFCm_13 +RH_Default_PCC_1 +RH_Default_PCC_2 +RH_Default_PCC_3 +RH_Default_PCC_4 +RH_Default_PCC_5 +RH_Default_PCC_6 +RH_Default_PCC_7 +RH_Default_PCC_8 +RH_Default_PCC_9 diff --git a/aslprep/data/niftiatlas/schaefer400x7/schaefer400x7Reference.bib b/aslprep/data/niftiatlas/schaefer400x7/schaefer400x7Reference.bib new file mode 100755 index 000000000..5da2c8744 --- /dev/null +++ b/aslprep/data/niftiatlas/schaefer400x7/schaefer400x7Reference.bib @@ -0,0 +1,24 @@ +@article{Schaefer_2017, + doi = {10.1093/cercor/bhx179}, + url = {https://doi.org/10.1093%2Fcercor%2Fbhx179}, + year = 2017, + month = {jul}, + publisher = {Oxford University Press ({OUP})}, + pages = {1--20}, + author = {Alexander Schaefer and Ru Kong and Evan M. Gordon and Timothy O. Laumann and Xi-Nian Zuo and Avram J. Holmes and Simon B. Eickhoff and B.T. Thomas Yeo}, + title = {Local-Global Parcellation of the Human Cerebral Cortex from Intrinsic Functional Connectivity {MRI}}, + journal = {Cerebral Cortex} +} +@article{Thomas_Yeo_2011, + doi = {10.1152/jn.00338.2011}, + url = {https://doi.org/10.1152%2Fjn.00338.2011}, + year = 2011, + month = {jun}, + publisher = {American Physiological Society}, + volume = {106}, + number = {3}, + pages = {1125--1165}, + author = {B. T. Thomas Yeo and F. M. Krienen and J. Sepulcre and M. R. Sabuncu and D. Lashkari and M. Hollinshead and J. L. Roffman and J. W. Smoller and L. Zollei and J. R. Polimeni and B. Fischl and H. Liu and R. L. Buckner}, + title = {The organization of the human cerebral cortex estimated by intrinsic functional connectivity}, + journal = {Journal of Neurophysiology} +} diff --git a/aslprep/interfaces/ants.py b/aslprep/interfaces/ants.py new file mode 100644 index 000000000..234d83c31 --- /dev/null +++ b/aslprep/interfaces/ants.py @@ -0,0 +1,49 @@ +"""ANTS interfaces.""" +from nipype.interfaces.base import traits +from nipype.utils.filemanip import fname_presuffix +from niworkflows.interfaces.fixes import ( + FixHeaderApplyTransforms, + _FixTraitApplyTransformsInputSpec, +) + + +class _ApplyTransformsInputSpec(_FixTraitApplyTransformsInputSpec): + # Nipype's version doesn't have GenericLabel + interpolation = traits.Enum( + "Linear", + "NearestNeighbor", + "CosineWindowedSinc", + "WelchWindowedSinc", + "HammingWindowedSinc", + "LanczosWindowedSinc", + "MultiLabel", + "Gaussian", + "BSpline", + "GenericLabel", + argstr="%s", + usedefault=True, + ) + + +class ApplyTransforms(FixHeaderApplyTransforms): + """A modified version of FixHeaderApplyTransforms from niworkflows. + + The niworkflows version of ApplyTransforms "fixes the resampled image header + to match the xform of the reference image". + This modification overrides the allowed interpolation values, + since FixHeaderApplyTransforms doesn't support GenericLabel, + which is preferred over MultiLabel. + """ + + input_spec = _ApplyTransformsInputSpec + + def _run_interface(self, runtime): + # Run normally + self.inputs.output_image = fname_presuffix( + self.inputs.input_image, + suffix="_trans.nii.gz", + newpath=runtime.cwd, + use_ext=False, + ) + runtime = super(ApplyTransforms, self)._run_interface(runtime) + return runtime diff --git a/aslprep/interfaces/cbf_computation.py b/aslprep/interfaces/cbf_computation.py index 3254adfc0..50e5f38b0 100644 --- a/aslprep/interfaces/cbf_computation.py +++ b/aslprep/interfaces/cbf_computation.py @@ -7,7 +7,6 @@ import pandas as pd from nibabel.processing import smooth_image from nilearn import image, maskers -from nipype.interfaces.ants import ApplyTransforms from nipype.interfaces.base import ( BaseInterfaceInputSpec, File, @@ -21,11 +20,11 @@ from nipype.utils.filemanip import fname_presuffix from aslprep import config +from aslprep.interfaces.ants import ApplyTransforms from aslprep.utils.misc import ( _getcbfscore, _scrubcbf, estimate_labeling_efficiency, - parcellate_cbf, pcasl_or_pasl, ) from aslprep.utils.qc import ( @@ -1235,43 +1234,6 @@ def _run_interface(self, runtime): return runtime -class _ParcellateCBFInputSpec(BaseInterfaceInputSpec): - in_cbf = File(exists=True, mandatory=True, desc="cbf img") - atlasfile = File(exists=True, mandatory=True, desc="data") - atlasdata = File(exists=True, mandatory=True, desc="data") - atlaslabel = File(exists=True, mandatory=True, desc="data") - - -class _ParcellateCBFOutputSpec(TraitedSpec): - atlascsv = File(exists=False, desc="harvard output csv") - - -class ParcellateCBF(SimpleInterface): - """Parcellate CBF time series according to a given atlas.""" - - input_spec = _ParcellateCBFInputSpec - output_spec = _ParcellateCBFOutputSpec - - def _run_interface(self, runtime): - self._results["atlascsv"] = fname_presuffix( - self.inputs.in_cbf, - suffix="atlas.csv", - newpath=runtime.cwd, - use_ext=False, - ) - roiquant = parcellate_cbf( - roi_label=self.inputs.atlaslabel, - roi_file=self.inputs.atlasfile, - cbfmap=self.inputs.in_cbf, - ) - data1 = pd.read_table(self.inputs.atlasdata, header=None, index_col=None, sep="\t") - bb = list(data1.values.tolist()) - flattened = [val for sublist in bb for val in sublist] - datat = pd.DataFrame([flattened, roiquant]) - datat.to_csv(self._results["atlascsv"], header=None, index=None) - return runtime - - def regmotoasl(asl, m0file, m02asl): """Calculate mean M0 image and mean ASL image, then FLIRT M0 image to ASL space. @@ -1300,22 +1262,24 @@ def refine_ref_mask(t1w_mask, ref_asl_mask, t12ref_transform, tmp_mask, refined_ TODO: This should not be a function. It uses interfaces, so it should be a workflow. """ - b1 = ApplyTransforms() - b1.inputs.dimension = 3 - b1.inputs.float = True - b1.inputs.input_image = t1w_mask - b1.inputs.interpolation = "NearestNeighbor" - b1.inputs.reference_image = ref_asl_mask - b1.inputs.transforms = t12ref_transform - b1.inputs.input_image_type = 3 - b1.inputs.output_image = tmp_mask - b1.run() - - mat1 = MultiImageMaths() - mat1.inputs.in_file = tmp_mask - mat1.inputs.op_string = " -mul %s -bin" - mat1.inputs.operand_files = ref_asl_mask - mat1.inputs.out_file = refined_mask - mat1.run() - - return refined_mask + warp_t1w_mask_to_asl = ApplyTransforms( + dimension=3, + float=True, + input_image=t1w_mask, + interpolation="NearestNeighbor", + reference_image=ref_asl_mask, + transforms=[t12ref_transform], + input_image_type=3, + output_image=tmp_mask, + ) + results = warp_t1w_mask_to_asl.run() + + modify_asl_mask = MultiImageMaths( + in_file=results.outputs.output_image, + op_string="-mul %s -bin", + operand_files=ref_asl_mask, + out_file=refined_mask, + ) + results = modify_asl_mask.run() + + return results.outputs.out_file diff --git a/aslprep/interfaces/parcellation.py b/aslprep/interfaces/parcellation.py new file mode 100644 index 000000000..89a3cf56b --- /dev/null +++ b/aslprep/interfaces/parcellation.py @@ -0,0 +1,193 @@ +# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- +# vi: set ft=python sts=4 ts=4 sw=4 et: +"""Handling functional connectvity.""" +import nibabel as nb +import numpy as np +import pandas as pd +from nilearn.maskers import NiftiLabelsMasker +from nipype.interfaces.base import ( + BaseInterfaceInputSpec, + File, + SimpleInterface, + TraitedSpec, + traits, +) +from nipype.utils.filemanip import fname_presuffix + +from aslprep import config + + +class _ParcellateCBFInputSpec(BaseInterfaceInputSpec): + in_file = File(exists=True, mandatory=True, desc="File to be parcellated.") + mask = File(exists=True, mandatory=True, desc="brain mask file") + atlas = File(exists=True, mandatory=True, desc="atlas file") + atlas_labels = File(exists=True, mandatory=True, desc="atlas labels file") + min_coverage = traits.Float( + default=0.5, + usedefault=True, + desc=( + "Coverage threshold to apply to parcels. " + "Any parcels with lower coverage than the threshold will be replaced with NaNs. " + "Must be a value between zero and one. " + "Default is 0.5." + ), + ) + + +class _ParcellateCBFOutputSpec(TraitedSpec): + timeseries = File(exists=True, mandatory=True, desc="Parcellated time series file.") + coverage = File(exists=True, mandatory=True, desc="Parcel-wise coverage file.") + + +class ParcellateCBF(SimpleInterface): + """Extract timeseries and compute connectivity matrices. + + Write out time series using Nilearn's NiftiLabelMasker + Then write out functional correlation matrix of + timeseries using numpy. + """ + + input_spec = _ParcellateCBFInputSpec + output_spec = _ParcellateCBFOutputSpec + + def _run_interface(self, runtime): + in_file = self.inputs.in_file + mask = self.inputs.mask + atlas = self.inputs.atlas + atlas_labels = self.inputs.atlas_labels + min_coverage = self.inputs.min_coverage + + node_labels_df = pd.read_table(atlas_labels, index_col="index") + node_labels_df.sort_index(inplace=True) # ensure index is in order + + # Explicitly remove label corresponding to background (index=0), if present. + if 0 in node_labels_df.index: + config.loggers.interface.warning( + "Index value of 0 found in atlas labels file. " + "Will assume this describes the background and ignore it." + ) + node_labels_df = node_labels_df.drop(index=[0]) + + node_labels = node_labels_df["name"].tolist() + + self._results["timeseries"] = fname_presuffix( + "timeseries.tsv", + newpath=runtime.cwd, + use_ext=True, + ) + self._results["coverage"] = fname_presuffix( + "coverage.tsv", + newpath=runtime.cwd, + use_ext=True, + ) + + # Before anything, we need to measure coverage + atlas_img = nb.load(atlas) + atlas_data = atlas_img.get_fdata() + atlas_data_bin = (atlas_data > 0).astype(np.float32) + atlas_img_bin = nb.Nifti1Image(atlas_data_bin, atlas_img.affine, atlas_img.header) + + sum_masker_masked = NiftiLabelsMasker( + labels_img=atlas, + labels=node_labels, + mask_img=mask, + smoothing_fwhm=None, + standardize=False, + strategy="sum", + resampling_target=None, # they should be in the same space/resolution already + ) + sum_masker_unmasked = NiftiLabelsMasker( + labels_img=atlas, + labels=node_labels, + smoothing_fwhm=None, + standardize=False, + strategy="sum", + resampling_target=None, # they should be in the same space/resolution already + ) + n_voxels_in_masked_parcels = sum_masker_masked.fit_transform(atlas_img_bin) + n_voxels_in_parcels = sum_masker_unmasked.fit_transform(atlas_img_bin) + parcel_coverage = np.squeeze(n_voxels_in_masked_parcels / n_voxels_in_parcels) + coverage_thresholded = parcel_coverage < min_coverage + + n_nodes = len(node_labels) + n_found_nodes = coverage_thresholded.size + n_bad_nodes = np.sum(parcel_coverage == 0) + n_poor_parcels = np.sum( + np.logical_and(parcel_coverage > 0, parcel_coverage < min_coverage) + ) + n_partial_parcels = np.sum( + np.logical_and(parcel_coverage >= min_coverage, parcel_coverage < 1) + ) + + if n_found_nodes != n_nodes: + config.loggers.interface.warning( + f"{n_nodes - n_found_nodes}/{n_nodes} of parcels not found in atlas file." + ) + + if n_bad_nodes: + config.loggers.interface.warning( + f"{n_bad_nodes}/{n_nodes} of parcels have 0% coverage." + ) + + if n_poor_parcels: + config.loggers.interface.warning( + f"{n_poor_parcels}/{n_nodes} of parcels have <50% coverage. " + "These parcels' time series will be replaced with zeros." + ) + + if n_partial_parcels: + config.loggers.interface.warning( + f"{n_partial_parcels}/{n_nodes} of parcels have at least one uncovered " + "voxel, but have enough good voxels to be useable. " + "The bad voxels will be ignored and the parcels' time series will be " + "calculated from the remaining voxels." + ) + + masker = NiftiLabelsMasker( + labels_img=atlas, + labels=node_labels, + mask_img=mask, + smoothing_fwhm=None, + standardize=False, + resampling_target=None, # they should be in the same space/resolution already + ) + + # Use nilearn for time_series + timeseries_arr = masker.fit_transform(in_file) + assert timeseries_arr.shape[1] == n_found_nodes + + # Apply the coverage mask + timeseries_arr[:, coverage_thresholded] = np.nan + + # Region indices in the atlas may not be sequential, so we map them to sequential ints. + seq_mapper = {idx: i for i, idx in enumerate(node_labels_df.index.tolist())} + + if n_found_nodes != n_nodes: # parcels lost by warping/downsampling atlas + # Fill in any missing nodes in the timeseries array with NaNs. + new_timeseries_arr = np.full( + (timeseries_arr.shape[0], n_nodes), + fill_value=np.nan, + dtype=timeseries_arr.dtype, + ) + for col in range(timeseries_arr.shape[1]): + label_col = seq_mapper[masker.labels_[col]] + new_timeseries_arr[:, label_col] = timeseries_arr[:, col] + + timeseries_arr = new_timeseries_arr + + # Fill in any missing nodes in the coverage array with zero. + new_parcel_coverage = np.zeros(n_nodes, dtype=parcel_coverage.dtype) + for row in range(parcel_coverage.shape[0]): + label_row = seq_mapper[masker.labels_[row]] + new_parcel_coverage[label_row] = parcel_coverage[row] + + parcel_coverage = new_parcel_coverage + + # The time series file is tab-delimited, with node names included in the first row. + timeseries_df = pd.DataFrame(data=timeseries_arr, columns=node_labels) + coverage_df = pd.DataFrame(data=parcel_coverage, index=node_labels, columns=["coverage"]) + + timeseries_df.to_csv(self._results["timeseries"], sep="\t", na_rep="n/a", index=False) + coverage_df.to_csv(self._results["coverage"], sep="\t", index_label="Node") + + return runtime diff --git a/aslprep/tests/data/expected_outputs_examples_pasl_multipld.txt b/aslprep/tests/data/expected_outputs_examples_pasl_multipld.txt index 740d07acf..82a5e42b8 100644 --- a/aslprep/tests/data/expected_outputs_examples_pasl_multipld.txt +++ b/aslprep/tests/data/expected_outputs_examples_pasl_multipld.txt @@ -8,45 +8,85 @@ aslprep/sub-01.html aslprep/sub-01/ses-BAS1 aslprep/sub-01/ses-BAS1/perf aslprep/sub-01/ses-BAS1/perf/sub-01_ses-BAS1_aslref.nii.gz +aslprep/sub-01/ses-BAS1/perf/sub-01_ses-BAS1_atlas-Glasser_cbf.tsv +aslprep/sub-01/ses-BAS1/perf/sub-01_ses-BAS1_atlas-Glasser_desc-basilGM_cbf.tsv +aslprep/sub-01/ses-BAS1/perf/sub-01_ses-BAS1_atlas-Glasser_desc-basil_cbf.tsv +aslprep/sub-01/ses-BAS1/perf/sub-01_ses-BAS1_atlas-Glasser_desc-score_cbf.tsv +aslprep/sub-01/ses-BAS1/perf/sub-01_ses-BAS1_atlas-Glasser_desc-scrub_cbf.tsv +aslprep/sub-01/ses-BAS1/perf/sub-01_ses-BAS1_atlas-Gordon_cbf.tsv +aslprep/sub-01/ses-BAS1/perf/sub-01_ses-BAS1_atlas-Gordon_desc-basilGM_cbf.tsv 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+aslprep/sub-01/perf/sub-01_from-scanner_to-T1w_mode-image_xfm.txt \ No newline at end of file diff --git a/aslprep/tests/data/expected_outputs_examples_pcasl_singlepld_ge.txt b/aslprep/tests/data/expected_outputs_examples_pcasl_singlepld_ge.txt index 6afff1ee2..760a4f8bb 100644 --- a/aslprep/tests/data/expected_outputs_examples_pcasl_singlepld_ge.txt +++ b/aslprep/tests/data/expected_outputs_examples_pcasl_singlepld_ge.txt @@ -8,21 +8,45 @@ aslprep/sub-103.html aslprep/sub-103/ses-ge3d aslprep/sub-103/ses-ge3d/perf aslprep/sub-103/ses-ge3d/perf/sub-103_ses-ge3d_aslref.nii.gz -aslprep/sub-103/ses-ge3d/perf/sub-103_ses-ge3d_atlas-HarvardOxford_desc-mean_basil.csv -aslprep/sub-103/ses-ge3d/perf/sub-103_ses-ge3d_atlas-HarvardOxford_desc-mean_cbf.csv -aslprep/sub-103/ses-ge3d/perf/sub-103_ses-ge3d_atlas-HarvardOxford_desc-mean_pvc.csv -aslprep/sub-103/ses-ge3d/perf/sub-103_ses-ge3d_atlas-schaefer200x17_desc-mean_basil.csv 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+aslprep/sub-103/ses-ge3d/perf/sub-103_ses-ge3d_atlas-subcortical_cbf.tsv +aslprep/sub-103/ses-ge3d/perf/sub-103_ses-ge3d_atlas-subcortical_desc-basilGM_cbf.tsv +aslprep/sub-103/ses-ge3d/perf/sub-103_ses-ge3d_atlas-subcortical_desc-basil_cbf.tsv aslprep/sub-103/ses-ge3d/perf/sub-103_ses-ge3d_cbf.nii.gz aslprep/sub-103/ses-ge3d/perf/sub-103_ses-ge3d_desc-basil_cbf.nii.gz aslprep/sub-103/ses-ge3d/perf/sub-103_ses-ge3d_desc-bat_cbf.nii.gz @@ -35,4 +59,4 @@ aslprep/sub-103/ses-ge3d/perf/sub-103_ses-ge3d_desc-pvGM_cbf.nii.gz aslprep/sub-103/ses-ge3d/perf/sub-103_ses-ge3d_desc-pvWM_cbf.nii.gz aslprep/sub-103/ses-ge3d/perf/sub-103_ses-ge3d_desc-qualitycontrol_cbf.csv aslprep/sub-103/ses-ge3d/perf/sub-103_ses-ge3d_from-T1w_to-scanner_mode-image_xfm.txt -aslprep/sub-103/ses-ge3d/perf/sub-103_ses-ge3d_from-scanner_to-T1w_mode-image_xfm.txt +aslprep/sub-103/ses-ge3d/perf/sub-103_ses-ge3d_from-scanner_to-T1w_mode-image_xfm.txt \ No newline at end of file diff --git a/aslprep/tests/data/expected_outputs_examples_pcasl_singlepld_philips.txt b/aslprep/tests/data/expected_outputs_examples_pcasl_singlepld_philips.txt index 052a46e0f..f41704f73 100644 --- a/aslprep/tests/data/expected_outputs_examples_pcasl_singlepld_philips.txt +++ b/aslprep/tests/data/expected_outputs_examples_pcasl_singlepld_philips.txt @@ -8,31 +8,71 @@ aslprep/sub-103.html aslprep/sub-103/ses-philips2d aslprep/sub-103/ses-philips2d/perf aslprep/sub-103/ses-philips2d/perf/sub-103_ses-philips2d_aslref.nii.gz -aslprep/sub-103/ses-philips2d/perf/sub-103_ses-philips2d_atlas-HarvardOxford_desc-mean_basil.csv -aslprep/sub-103/ses-philips2d/perf/sub-103_ses-philips2d_atlas-HarvardOxford_desc-mean_cbf.csv -aslprep/sub-103/ses-philips2d/perf/sub-103_ses-philips2d_atlas-HarvardOxford_desc-mean_pvc.csv -aslprep/sub-103/ses-philips2d/perf/sub-103_ses-philips2d_atlas-HarvardOxford_desc-mean_score.csv 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aslprep/sub-103/ses-siemens3d/perf/sub-103_ses-siemens3d_desc-bat_cbf.nii.gz @@ -49,4 +89,4 @@ aslprep/sub-103/ses-siemens3d/perf/sub-103_ses-siemens3d_desc-qualitycontrol_cbf aslprep/sub-103/ses-siemens3d/perf/sub-103_ses-siemens3d_desc-score_cbf.nii.gz aslprep/sub-103/ses-siemens3d/perf/sub-103_ses-siemens3d_desc-scrub_cbf.nii.gz aslprep/sub-103/ses-siemens3d/perf/sub-103_ses-siemens3d_from-T1w_to-scanner_mode-image_xfm.txt -aslprep/sub-103/ses-siemens3d/perf/sub-103_ses-siemens3d_from-scanner_to-T1w_mode-image_xfm.txt +aslprep/sub-103/ses-siemens3d/perf/sub-103_ses-siemens3d_from-scanner_to-T1w_mode-image_xfm.txt \ No newline at end of file diff --git a/aslprep/tests/data/expected_outputs_test_001.txt b/aslprep/tests/data/expected_outputs_test_001.txt index 215853c98..e37d8b866 100644 --- a/aslprep/tests/data/expected_outputs_test_001.txt +++ b/aslprep/tests/data/expected_outputs_test_001.txt @@ -7,45 +7,113 @@ aslprep/sub-01 aslprep/sub-01.html aslprep/sub-01/perf 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generate_reports -from aslprep.tests.utils import check_generated_files, get_test_data_path +from aslprep.tests.utils import ( + check_generated_files, + download_test_data, + get_test_data_path, +) nipype_config.enable_debug_mode() @pytest.mark.examples_pasl_multipld -def test_examples_pasl_multipld(datasets, output_dir, working_dir): +def test_examples_pasl_multipld(data_dir, output_dir, working_dir): """Run aslprep on the asl_003 ASL-BIDS examples dataset. This dataset has 10 control-label pairs at 10 different PLDs, along with a separate M0 scan. @@ -26,12 +30,12 @@ def test_examples_pasl_multipld(datasets, output_dir, working_dir): TEST_NAME = "examples_pasl_multipld" PARTICIPANT_LABEL = "01" - data_dir = datasets[TEST_NAME] + dataset_dir = download_test_data(TEST_NAME, data_dir) out_dir = os.path.join(output_dir, TEST_NAME) work_dir = os.path.join(working_dir, TEST_NAME) parameters = [ - data_dir, + dataset_dir, out_dir, "participant", f"--participant-label={PARTICIPANT_LABEL}", @@ -42,14 +46,14 @@ def test_examples_pasl_multipld(datasets, output_dir, working_dir): "--scorescrub", "--basil", "--use-syn-sdc", - f"--anat-derivatives={os.path.join(data_dir, 'derivatives/smriprep')}", + f"--anat-derivatives={os.path.join(dataset_dir, 'derivatives/smriprep')}", ] _run_and_fail(parameters) @pytest.mark.examples_pcasl_multipld -def test_examples_pcasl_multipld(datasets, output_dir, working_dir): +def test_examples_pcasl_multipld(data_dir, output_dir, working_dir): """Run aslprep on the asl_004 ASL-BIDS examples dataset. This dataset has 48 control-label pairs at 6 different PLDs, along with a separate M0 scan. @@ -59,12 +63,12 @@ def test_examples_pcasl_multipld(datasets, output_dir, working_dir): TEST_NAME = "examples_pcasl_multipld" PARTICIPANT_LABEL = "01" - data_dir = datasets[TEST_NAME] + dataset_dir = download_test_data(TEST_NAME, data_dir) out_dir = os.path.join(output_dir, TEST_NAME) work_dir = os.path.join(working_dir, TEST_NAME) parameters = [ - data_dir, + dataset_dir, out_dir, "participant", f"--participant-label={PARTICIPANT_LABEL}", @@ -75,14 +79,14 @@ def test_examples_pcasl_multipld(datasets, output_dir, working_dir): "--scorescrub", "--basil", "--use-syn-sdc", - f"--anat-derivatives={os.path.join(data_dir, 'derivatives/smriprep')}", + f"--anat-derivatives={os.path.join(dataset_dir, 'derivatives/smriprep')}", ] _run_and_fail(parameters) @pytest.mark.examples_pcasl_singlepld_ge -def test_examples_pcasl_singlepld_ge(datasets, output_dir, working_dir): +def test_examples_pcasl_singlepld_ge(data_dir, output_dir, working_dir): """Run aslprep on the asl_001 ASL-BIDS examples dataset. This test uses a GE session with two volumes: one deltam and one M0. @@ -90,14 +94,14 @@ def test_examples_pcasl_singlepld_ge(datasets, output_dir, working_dir): TEST_NAME = "examples_pcasl_singlepld_ge" PARTICIPANT_LABEL = "103" - data_dir = datasets["examples_pcasl_singlepld"] + dataset_dir = download_test_data("examples_pcasl_singlepld", data_dir) out_dir = os.path.join(output_dir, TEST_NAME) work_dir = os.path.join(working_dir, TEST_NAME) test_data_dir = get_test_data_path() filter_file = os.path.join(test_data_dir, f"{TEST_NAME}_filter.json") parameters = [ - data_dir, + dataset_dir, out_dir, "participant", f"--participant-label={PARTICIPANT_LABEL}", @@ -109,14 +113,14 @@ def test_examples_pcasl_singlepld_ge(datasets, output_dir, working_dir): "--scorescrub", "--basil", "--use-syn-sdc", - f"--anat-derivatives={os.path.join(data_dir, 'derivatives/smriprep')}", + f"--anat-derivatives={os.path.join(dataset_dir, 'derivatives/smriprep')}", ] _run_and_generate(TEST_NAME, PARTICIPANT_LABEL, parameters, out_dir) @pytest.mark.examples_pcasl_singlepld_philips -def test_examples_pcasl_singlepld_philips(datasets, output_dir, working_dir): +def test_examples_pcasl_singlepld_philips(data_dir, output_dir, working_dir): """Run aslprep on the asl_002 ASL-BIDS examples datasets. This test a Philips session. @@ -124,14 +128,14 @@ def test_examples_pcasl_singlepld_philips(datasets, output_dir, working_dir): TEST_NAME = "examples_pcasl_singlepld_philips" PARTICIPANT_LABEL = "103" - data_dir = datasets["examples_pcasl_singlepld"] + dataset_dir = download_test_data("examples_pcasl_singlepld", data_dir) out_dir = os.path.join(output_dir, TEST_NAME) work_dir = os.path.join(working_dir, TEST_NAME) test_data_dir = get_test_data_path() filter_file = os.path.join(test_data_dir, f"{TEST_NAME}_filter.json") parameters = [ - data_dir, + dataset_dir, out_dir, "participant", f"--participant-label={PARTICIPANT_LABEL}", @@ -143,14 +147,14 @@ def test_examples_pcasl_singlepld_philips(datasets, output_dir, working_dir): "--scorescrub", "--basil", "--use-syn-sdc", - f"--anat-derivatives={os.path.join(data_dir, 'derivatives/smriprep')}", + f"--anat-derivatives={os.path.join(dataset_dir, 'derivatives/smriprep')}", ] _run_and_generate(TEST_NAME, PARTICIPANT_LABEL, parameters, out_dir) @pytest.mark.examples_pcasl_singlepld_siemens -def test_examples_pcasl_singlepld_siemens(datasets, output_dir, working_dir): +def test_examples_pcasl_singlepld_siemens(data_dir, output_dir, working_dir): """Run aslprep on the asl_005 ASL-BIDS examples datasets. This test a Siemens session. @@ -158,14 +162,14 @@ def test_examples_pcasl_singlepld_siemens(datasets, output_dir, working_dir): TEST_NAME = "examples_pcasl_singlepld_siemens" PARTICIPANT_LABEL = "103" - data_dir = datasets["examples_pcasl_singlepld"] + dataset_dir = download_test_data("examples_pcasl_singlepld", data_dir) out_dir = os.path.join(output_dir, TEST_NAME) work_dir = os.path.join(working_dir, TEST_NAME) test_data_dir = get_test_data_path() filter_file = os.path.join(test_data_dir, f"{TEST_NAME}_filter.json") parameters = [ - data_dir, + dataset_dir, out_dir, "participant", f"--participant-label={PARTICIPANT_LABEL}", @@ -177,42 +181,45 @@ def test_examples_pcasl_singlepld_siemens(datasets, output_dir, working_dir): "--scorescrub", "--basil", "--use-syn-sdc", - f"--anat-derivatives={os.path.join(data_dir, 'derivatives/smriprep')}", + f"--anat-derivatives={os.path.join(dataset_dir, 'derivatives/smriprep')}", ] _run_and_generate(TEST_NAME, PARTICIPANT_LABEL, parameters, out_dir) @pytest.mark.test_001 -def test_test_001(datasets, output_dir, working_dir): +def test_test_001(data_dir, output_dir, working_dir): """Run aslprep on sub-01 data.""" TEST_NAME = "test_001" PARTICIPANT_LABEL = "01" - data_dir = datasets[TEST_NAME] + dataset_dir = download_test_data(TEST_NAME, data_dir) out_dir = os.path.join(output_dir, TEST_NAME) work_dir = os.path.join(working_dir, TEST_NAME) parameters = [ - data_dir, + dataset_dir, out_dir, "participant", f"--participant-label={PARTICIPANT_LABEL}", f"-w={work_dir}", "--nthreads=2", "--omp-nthreads=2", - "--output-spaces=asl", + "--output-spaces", + "asl", + "T1w", + "MNI152NLin2009cAsym", "--scorescrub", "--basil", "--use-syn-sdc", - f"--anat-derivatives={os.path.join(data_dir, 'derivatives/smriprep')}", + f"--anat-derivatives={os.path.join(dataset_dir, 'derivatives/smriprep')}", ] _run_and_generate(TEST_NAME, PARTICIPANT_LABEL, parameters, out_dir) @pytest.mark.test_002 -def test_test_002(datasets, output_dir, working_dir): +def test_test_002(data_dir, output_dir, working_dir): """Run aslprep on sub-10R01383. This dataset contains PCASL data from a GE scanner. @@ -221,40 +228,42 @@ def test_test_002(datasets, output_dir, working_dir): TEST_NAME = "test_002" PARTICIPANT_LABEL = "10R01383" - data_dir = datasets[TEST_NAME] + dataset_dir = download_test_data(TEST_NAME, data_dir) out_dir = os.path.join(output_dir, TEST_NAME) work_dir = os.path.join(working_dir, TEST_NAME) parameters = [ - data_dir, + dataset_dir, out_dir, "participant", f"--participant-label={PARTICIPANT_LABEL}", f"-w={work_dir}", "--nthreads=2", "--omp-nthreads=2", - "--output-spaces=asl", + "--output-spaces", + "asl", + "MNI152NLin2009cAsym", "--scorescrub", "--basil", "--use-syn-sdc", - f"--anat-derivatives={os.path.join(data_dir, 'derivatives/smriprep')}", + f"--anat-derivatives={os.path.join(dataset_dir, 'derivatives/smriprep')}", ] _run_and_generate(TEST_NAME, PARTICIPANT_LABEL, parameters, out_dir) @pytest.mark.test_003 -def test_test_003(datasets, output_dir, working_dir): +def test_test_003(data_dir, output_dir, working_dir): """Run aslprep on sub-A00086748.""" TEST_NAME = "test_003" PARTICIPANT_LABEL = "A00086748" - data_dir = datasets[TEST_NAME] + dataset_dir = download_test_data(TEST_NAME, data_dir) out_dir = os.path.join(output_dir, TEST_NAME) work_dir = os.path.join(working_dir, TEST_NAME) parameters = [ - data_dir, + dataset_dir, out_dir, "participant", f"--participant-label={PARTICIPANT_LABEL}", @@ -265,7 +274,7 @@ def test_test_003(datasets, output_dir, working_dir): "--scorescrub", "--basil", "--use-syn-sdc", - f"--anat-derivatives={os.path.join(data_dir, 'derivatives/smriprep')}", + f"--anat-derivatives={os.path.join(dataset_dir, 'derivatives/smriprep')}", ] _run_and_generate(TEST_NAME, PARTICIPANT_LABEL, parameters, out_dir) diff --git a/aslprep/tests/utils.py b/aslprep/tests/utils.py index 795dd052b..40df3e557 100644 --- a/aslprep/tests/utils.py +++ b/aslprep/tests/utils.py @@ -12,6 +12,8 @@ import requests from bids.layout import BIDSLayout +from aslprep import config + def download_test_data(dset, data_dir=None): """Download test data.""" @@ -38,11 +40,13 @@ def download_test_data(dset, data_dir=None): out_dir = os.path.join(data_dir, dset) if os.path.isdir(out_dir): - print( + config.loggers.utils.info( f"Dataset {dset} already exists. " "If you need to re-download the data, please delete the folder." ) return out_dir + else: + config.loggers.utils.info(f"Downloading {dset} to {out_dir}") os.makedirs(out_dir, exist_ok=True) with requests.get(URLS[dset], stream=True) as req: diff --git a/aslprep/utils/atlas.py b/aslprep/utils/atlas.py new file mode 100644 index 000000000..d20ab5b26 --- /dev/null +++ b/aslprep/utils/atlas.py @@ -0,0 +1,144 @@ +"""Functions for working with atlases.""" + + +def get_atlas_names(): + """Get a list of atlases to be used for parcellation and functional connectivity analyses. + + The actual list of files for the atlases is loaded from a different function. + + NOTE: This is a Node function. + + Returns + ------- + :obj:`list` of :obj:`str` + List of atlases. + """ + return [ + "Schaefer117", + "Schaefer217", + "Schaefer317", + "Schaefer417", + "Schaefer517", + "Schaefer617", + "Schaefer717", + "Schaefer817", + "Schaefer917", + "Schaefer1017", + "Glasser", + "Gordon", + "subcortical", + ] + + +def get_atlas_nifti(atlas_name): + """Select atlas by name from aslprep/data using pkgrf. + + All atlases are in MNI space. + + NOTE: This is a Node function. + + Parameters + ---------- + atlas_name : {"Schaefer117", "Schaefer217", "Schaefer317", "Schaefer417", \ + "Schaefer517", "Schaefer617", "Schaefer717", "Schaefer817", \ + "Schaefer917", "Schaefer1017", "Glasser", "Gordon", \ + "subcortical"} + The name of the NIFTI atlas to fetch. + + Returns + ------- + atlas_file : :obj:`str` + Path to the atlas file. + """ + from pkg_resources import resource_filename as pkgrf + + if atlas_name[:8] == "Schaefer": + if atlas_name[8:12] == "1017": + atlas_file = pkgrf( + "aslprep", + "data/niftiatlas/Schaefer2018_1000Parcels_17Networks_order_FSLMNI152_2mm.nii", + ) + else: + atlas_file = pkgrf( + "aslprep", + ( + "data/niftiatlas/" + f"Schaefer2018_{atlas_name[8]}00Parcels_17Networks_order_FSLMNI152_2mm.nii" + ), + ) + atlas_labels_file = atlas_file.replace("_FSLMNI152_2mm.nii", "_info.tsv") + + elif atlas_name == "Glasser": + atlas_file = pkgrf("aslprep", "data/niftiatlas/glasser360/glasser360MNI.nii.gz") + atlas_labels_file = pkgrf("aslprep", "data/niftiatlas/Glasser_360Parcels_info.tsv") + elif atlas_name == "Gordon": + atlas_file = pkgrf("aslprep", "data/niftiatlas/gordon333/gordon333MNI.nii.gz") + atlas_labels_file = pkgrf("aslprep", "data/niftiatlas/Gordon_333Parcels_info.tsv") + elif atlas_name == "subcortical": + atlas_file = pkgrf( + "aslprep", + "data/niftiatlas/TianSubcortical/Tian_Subcortex_S3_3T.nii.gz", + ) + atlas_labels_file = pkgrf("aslprep", "data/niftiatlas/Tian_info.tsv") + else: + raise RuntimeError(f'Atlas "{atlas_name}" not available') + + return atlas_file, atlas_labels_file + + +def get_atlas_cifti(atlas_name): + """Select atlas by name from aslprep/data. + + All atlases are in 91K space. + + NOTE: This is a Node function. + + Parameters + ---------- + atlas_name : {"Schaefer117", "Schaefer217", "Schaefer317", "Schaefer417", \ + "Schaefer517", "Schaefer617", "Schaefer717", "Schaefer817", \ + "Schaefer917", "Schaefer1017", "Glasser", "Gordon", \ + "subcortical"} + The name of the CIFTI atlas to fetch. + + Returns + ------- + atlas_file : :obj:`str` + Path to the atlas file. + """ + from pkg_resources import resource_filename as pkgrf + + if atlas_name[:8] == "Schaefer": + if atlas_name[8:12] == "1017": + atlas_file = pkgrf( + "aslprep", + "data/ciftiatlas/Schaefer2018_1000Parcels_17Networks_order.dlabel.nii", + ) + else: + atlas_file = pkgrf( + "aslprep", + ( + "data/ciftiatlas/" + f"Schaefer2018_{atlas_name[8]}00Parcels_17Networks_order.dlabel.nii" + ), + ) + atlas_labels_file = atlas_file.replace(".dlabel.nii", "_info.tsv") + elif atlas_name == "Glasser": + atlas_file = pkgrf( + "aslprep", + "data/ciftiatlas/glasser_space-fsLR_den-32k_desc-atlas.dlabel.nii", + ) + atlas_labels_file = pkgrf("aslprep", "data/ciftiatlas/Glasser_360Parcels_info.tsv") + elif atlas_name == "Gordon": + atlas_file = pkgrf( + "aslprep", + "data/ciftiatlas/gordon_space-fsLR_den-32k_desc-atlas.dlabel.nii", + ) + atlas_labels_file = pkgrf("aslprep", "data/ciftiatlas/Gordon_333Parcels_info.tsv") + elif atlas_name == "subcortical": + atlas_file = pkgrf("aslprep", "data/ciftiatlas/Tian_Subcortex_S3_3T_32k.dlabel.nii") + atlas_labels_file = pkgrf("aslprep", "data/ciftiatlas/Tian_info.tsv") + else: + raise RuntimeError(f'Atlas "{atlas_name}" not available') + + return atlas_file, atlas_labels_file diff --git a/aslprep/utils/confounds.py b/aslprep/utils/confounds.py index 26a8fffc1..7a58146fc 100644 --- a/aslprep/utils/confounds.py +++ b/aslprep/utils/confounds.py @@ -2,6 +2,7 @@ import os import re +import numpy as np import pandas as pd from nipype.interfaces.base import isdefined @@ -23,11 +24,23 @@ def _camel_to_snake(name): def _adjust_indices(left_df, right_df): """Force missing values to appear at the beginning of the DataFrame instead of the end.""" - index_diff = len(left_df.index) - len(right_df.index) + index_diff = left_df.shape[0] - right_df.shape[0] if index_diff > 0: - right_df.index = range(index_diff, len(right_df.index) + index_diff) + # right_df is shorter + empty_df = pd.DataFrame( + np.full((np.abs(index_diff), right_df.shape[1]), np.nan), + columns=right_df.columns, + ) + right_df = pd.concat((empty_df, right_df), axis=0).reset_index(drop=True) elif index_diff < 0: - left_df.index = range(-index_diff, len(left_df.index) - index_diff) + # left_df is shorter + empty_df = pd.DataFrame( + np.full((np.abs(index_diff), left_df.shape[1]), np.nan), + columns=left_df.columns, + ) + left_df = pd.concat((empty_df, left_df), axis=0).reset_index(drop=True) + + return left_df, right_df def _gather_confounds( @@ -39,7 +52,11 @@ def _gather_confounds( motion=None, newpath=None, ): - """Load confounds from the filenames, concatenate together horizontally, and save new file.""" + """Load confounds from the filenames, concatenate together horizontally, and save new file. + + For some confounds (e.g., FD), the number of rows in the file will be one less than the + number of volumes. This will be adjusted automatically in this function. + """ all_files = [] confounds_list = [] for confound, name in ( @@ -63,7 +80,7 @@ def _gather_confounds( columns={column_name: _camel_to_snake(_less_breakable(column_name))}, inplace=True ) - _adjust_indices(confounds_data, new) + confounds_data, new = _adjust_indices(confounds_data, new) confounds_data = pd.concat((confounds_data, new), axis=1) if newpath is None: diff --git a/aslprep/utils/misc.py b/aslprep/utils/misc.py index d49d4c382..c9133f52e 100644 --- a/aslprep/utils/misc.py +++ b/aslprep/utils/misc.py @@ -8,7 +8,6 @@ import nibabel as nb import numpy as np -from pkg_resources import resource_filename as pkgrf from scipy.stats import median_abs_deviation @@ -728,51 +727,6 @@ def _scrubcbf(cbf_ts, gm, wm, csf, mask, wfun="huber", thresh=0.7): return newcbf -def get_atlas(atlasname): - """Find atlas file and metadata associated with a given atlas name.""" - if atlasname == "HarvardOxford": - atlasfile = pkgrf("aslprep", "data/atlas/HarvardOxford/HarvardOxfordMNI.nii.gz") - atlasdata = pkgrf("aslprep", "data/atlas/HarvardOxford/HarvardOxfordNodeNames.txt") - atlaslabel = pkgrf("aslprep", "data/atlas/HarvardOxford/HarvardOxfordNodeIndex.1D") - elif atlasname == "schaefer200x7": - atlasfile = pkgrf("aslprep", "data/atlas/schaefer200x7/schaefer200x7MNI.nii.gz") - atlasdata = pkgrf("aslprep", "data/atlas/schaefer200x7/schaefer200x7NodeNames.txt") - atlaslabel = pkgrf("aslprep", "data/atlas/schaefer200x7/schaefer200x7NodeIndex.1D") - elif atlasname == "schaefer200x17": - atlasfile = pkgrf("aslprep", "data/atlas/schaefer200x17/schaefer200x17MNI.nii.gz") - atlasdata = pkgrf("aslprep", "data/atlas/schaefer200x17/schaefer200x17NodeNames.txt") - atlaslabel = pkgrf("aslprep", "data/atlas/schaefer200x17/schaefer200x17NodeIndex.1D") - elif atlasname == "schaefer400x7": - atlasfile = pkgrf("aslprep", "data/atlas/schaefer400x7/schaefer400x7MNI.nii.gz") - atlasdata = pkgrf("aslprep", "data/atlas/schaefer400x7/schaefer400x7NodeNames.txt") - atlaslabel = pkgrf("aslprep", "data/atlas/schaefer200x17/schaefer200x17NodeIndex.1D") - elif atlasname == "schaefer400x17": - atlasfile = pkgrf("aslprep", "data/atlas/schaefer400x17/schaefer400x17MNI.nii.gz") - atlasdata = pkgrf("aslprep", "data/atlas/schaefer400x17/schaefer400x17NodeNames.txt") - atlaslabel = pkgrf("aslprep", "data/atlas/schaefer400x17/schaefer400x17NodeIndex.1D") - else: - raise RuntimeError("atlas not available") - return atlasfile, atlasdata, atlaslabel - - -def parcellate_cbf(roi_file, roi_label, cbfmap): - """Parcellate CBF data using atlas. - - TODO: Replace with NiftiLabelsMasker. - """ - data = nb.load(cbfmap).get_fdata() - roi = nb.load(roi_file).get_fdata() - roi_labels = np.loadtxt(roi_label) - if data.shape != roi.shape: - raise ValueError("Image-shapes do not match") - - mean_vals = [] - for roi_label in roi_labels: - mean_vals.append(np.mean(data[roi == roi_label])) - - return mean_vals - - def estimate_labeling_efficiency(metadata): """Estimate labeling efficiency based on the available metadata. diff --git a/aslprep/workflows/asl/base.py b/aslprep/workflows/asl/base.py index 292aaa541..b7cf79b20 100644 --- a/aslprep/workflows/asl/base.py +++ b/aslprep/workflows/asl/base.py @@ -17,7 +17,7 @@ from aslprep.utils.bids import collect_run_data from aslprep.utils.meepi import combine_meepi_source from aslprep.utils.misc import _create_mem_gb, _get_series_len, _get_wf_name -from aslprep.workflows.asl.cbf import init_cbf_compt_wf, init_cbfroiquant_wf +from aslprep.workflows.asl.cbf import init_cbf_compt_wf, init_parcellate_cbf_wf from aslprep.workflows.asl.confounds import init_asl_confs_wf, init_carpetplot_wf from aslprep.workflows.asl.hmc import init_asl_hmc_wf from aslprep.workflows.asl.outputs import init_asl_derivatives_wf @@ -284,15 +284,16 @@ def init_asl_preproc_wf(asl_file): spaces=spaces, scorescrub=scorescrub, basil=basil, + output_confounds=True, ) # fmt:off workflow.connect([ (outputnode, asl_derivatives_wf, [ + ("asl_native", "inputnode.asl_native"), ("asl_t1", "inputnode.asl_t1"), - ("asl_t1_ref", "inputnode.asl_t1_ref"), + ("asl_t1_ref", "inputnode.aslref_t1"), ("asl_mask_t1", "inputnode.asl_mask_t1"), - ("asl_native", "inputnode.asl_native"), ("confounds", "inputnode.confounds"), ("confounds_metadata", "inputnode.confounds_metadata"), ]), @@ -658,9 +659,7 @@ def init_asl_preproc_wf(asl_file): # Map final asl mask into T1w space (if required) nonstd_spaces = set(spaces.get_nonstandard()) if nonstd_spaces.intersection(("T1w", "anat")): - from aslprep.niworkflows.interfaces.fixes import ( - FixHeaderApplyTransforms as ApplyTransforms, - ) + from aslprep.interfaces.ants import ApplyTransforms aslmask_to_t1w = pe.Node( ApplyTransforms(interpolation="MultiLabel"), name="aslmask_to_t1w", mem_gb=0.1 @@ -721,14 +720,14 @@ def init_asl_preproc_wf(asl_file): workflow.connect([ (asl_asl_trans_wf, outputnode, [("outputnode.asl", "asl_native")]), (asl_asl_trans_wf, asl_derivatives_wf, [ - ("outputnode.asl_ref", "inputnode.asl_native_ref"), + ("outputnode.asl_ref", "inputnode.aslref_native"), ]), (refine_mask, asl_derivatives_wf, [ ("out_mask", "inputnode.asl_mask_native"), ]), (compt_cbf_wf, asl_derivatives_wf, [ - ("outputnode.out_cbf", "inputnode.cbf"), - ("outputnode.out_mean", "inputnode.meancbf"), + ("outputnode.out_cbf", "inputnode.cbf_native"), + ("outputnode.out_mean", "inputnode.meancbf_native"), ]), ]) # fmt:on @@ -737,9 +736,9 @@ def init_asl_preproc_wf(asl_file): # fmt:off workflow.connect([ (compt_cbf_wf, asl_derivatives_wf, [ - ("outputnode.out_score", "inputnode.score"), - ("outputnode.out_avgscore", "inputnode.avgscore"), - ("outputnode.out_scrub", "inputnode.scrub"), + ("outputnode.out_score", "inputnode.score_native"), + ("outputnode.out_avgscore", "inputnode.avgscore_native"), + ("outputnode.out_scrub", "inputnode.scrub_native"), ]), ]) # fmt:on @@ -748,10 +747,10 @@ def init_asl_preproc_wf(asl_file): # fmt:off workflow.connect([ (compt_cbf_wf, asl_derivatives_wf, [ - ("outputnode.out_cbfb", "inputnode.basil"), - ("outputnode.out_cbfpv", "inputnode.pv"), - ("outputnode.out_cbfpvwm", "inputnode.pvwm"), - ("outputnode.out_att", "inputnode.att"), + ("outputnode.out_cbfb", "inputnode.basil_native"), + ("outputnode.out_cbfpv", "inputnode.pv_native"), + ("outputnode.out_cbfpvwm", "inputnode.pvwm_native"), + ("outputnode.out_att", "inputnode.att_native"), ]), ]) # fmt:on @@ -834,7 +833,7 @@ def init_asl_preproc_wf(asl_file): (asl_std_trans_wf, asl_derivatives_wf, [ ("outputnode.template", "inputnode.template"), ("outputnode.spatial_reference", "inputnode.spatial_reference"), - ("outputnode.asl_std_ref", "inputnode.asl_std_ref"), + ("outputnode.asl_std_ref", "inputnode.aslref_std"), ("outputnode.asl_std", "inputnode.asl_std"), ("outputnode.asl_mask_std", "inputnode.asl_mask_std"), ("outputnode.cbf_std", "inputnode.cbf_std"), @@ -942,56 +941,59 @@ def init_asl_preproc_wf(asl_file): ]) # fmt:on - if spaces.get_spaces(nonstandard=False, dim=(3,)): - carpetplot_wf = init_carpetplot_wf( - mem_gb=mem_gb["resampled"], - metadata=metadata, - # cifti_output=config.workflow.cifti_output, - name="carpetplot_wf", - ) + carpetplot_wf = init_carpetplot_wf( + mem_gb=mem_gb["resampled"], + metadata=metadata, + # cifti_output=config.workflow.cifti_output, + name="carpetplot_wf", + ) - # Xform to 'MNI152NLin2009cAsym' is always computed. - carpetplot_select_std = pe.Node( - KeySelect(fields=["std2anat_xfm"], key="MNI152NLin2009cAsym"), - name="carpetplot_select_std", - run_without_submitting=True, - ) + # xform to 'MNI152NLin2009cAsym' is always computed, so this should always be available. + select_xform_MNI152NLin2009cAsym_to_t1w = pe.Node( + KeySelect(fields=["std2anat_xfm"], key="MNI152NLin2009cAsym"), + name="carpetplot_select_std", + run_without_submitting=True, + ) - # fmt:off - workflow.connect([ - (inputnode, carpetplot_select_std, [ - ("std2anat_xfm", "std2anat_xfm"), - ("template", "keys"), - ]), - (carpetplot_select_std, carpetplot_wf, [("std2anat_xfm", "inputnode.std2anat_xfm")]), - (asl_asl_trans_wf if not multiecho else asl_t2s_wf, carpetplot_wf, [ - ("outputnode.asl", "inputnode.asl"), - ]), - (refine_mask, carpetplot_wf, [("out_mask", "inputnode.asl_mask")]), - (asl_reg_wf, carpetplot_wf, [("outputnode.itk_t1_to_asl", "inputnode.t1_asl_xform")]), - (asl_confounds_wf, carpetplot_wf, [ - ("outputnode.confounds_file", "inputnode.confounds_file"), - ]), - ]) - # fmt:on + # fmt:off + workflow.connect([ + (inputnode, select_xform_MNI152NLin2009cAsym_to_t1w, [ + ("std2anat_xfm", "std2anat_xfm"), + ("template", "keys"), + ]), + (select_xform_MNI152NLin2009cAsym_to_t1w, carpetplot_wf, [ + ("std2anat_xfm", "inputnode.std2anat_xfm"), + ]), + (asl_asl_trans_wf if not multiecho else asl_t2s_wf, carpetplot_wf, [ + ("outputnode.asl", "inputnode.asl"), + ]), + (refine_mask, carpetplot_wf, [("out_mask", "inputnode.asl_mask")]), + (asl_reg_wf, carpetplot_wf, [("outputnode.itk_t1_to_asl", "inputnode.t1_asl_xform")]), + (asl_confounds_wf, carpetplot_wf, [ + ("outputnode.confounds_file", "inputnode.confounds_file"), + ]), + ]) + # fmt:on - cbfroiqu = init_cbfroiquant_wf( + parcellate_cbf_wf = init_parcellate_cbf_wf( basil=basil, scorescrub=scorescrub, - name="cbf_roiquant", + name="parcellate_cbf_wf", ) + # fmt:off workflow.connect([ - (asl_asl_trans_wf, cbfroiqu, [("outputnode.asl_mask", "inputnode.aslmask")]), - (inputnode, cbfroiqu, [("std2anat_xfm", "inputnode.std2anat_xfm")]), - (asl_reg_wf, cbfroiqu, [("outputnode.itk_t1_to_asl", "inputnode.t1_asl_xform")]), - (compt_cbf_wf, cbfroiqu, [("outputnode.out_mean", "inputnode.cbf")]), - (cbfroiqu, asl_derivatives_wf, [ - ("outputnode.cbf_hvoxf", "inputnode.cbf_hvoxf"), - ("outputnode.cbf_sc207", "inputnode.cbf_sc207"), - ("outputnode.cbf_sc217", "inputnode.cbf_sc217"), - ("outputnode.cbf_sc407", "inputnode.cbf_sc407"), - ("outputnode.cbf_sc417", "inputnode.cbf_sc417"), + (select_xform_MNI152NLin2009cAsym_to_t1w, parcellate_cbf_wf, [ + ("std2anat_xfm", "inputnode.MNI152NLin2009cAsym_to_anat_xform"), + ]), + (asl_asl_trans_wf, parcellate_cbf_wf, [("outputnode.asl_mask", "inputnode.asl_mask")]), + (asl_reg_wf, parcellate_cbf_wf, [ + ("outputnode.itk_t1_to_asl", "inputnode.anat_to_asl_xform"), + ]), + (compt_cbf_wf, parcellate_cbf_wf, [("outputnode.out_mean", "inputnode.mean_cbf")]), + (parcellate_cbf_wf, asl_derivatives_wf, [ + ("outputnode.atlas_names", "inputnode.atlas_names"), + ("outputnode.mean_cbf_parcellated", "inputnode.mean_cbf_parcellated"), ]), ]) # fmt:on @@ -999,21 +1001,13 @@ def init_asl_preproc_wf(asl_file): if scorescrub: # fmt:off workflow.connect([ - (compt_cbf_wf, cbfroiqu, [ - ("outputnode.out_avgscore", "inputnode.score"), - ("outputnode.out_scrub", "inputnode.scrub"), + (compt_cbf_wf, parcellate_cbf_wf, [ + ("outputnode.out_avgscore", "inputnode.mean_cbf_score"), + ("outputnode.out_scrub", "inputnode.mean_cbf_scrub"), ]), - (cbfroiqu, asl_derivatives_wf, [ - ("outputnode.score_hvoxf", "inputnode.score_hvoxf"), - ("outputnode.score_sc207", "inputnode.score_sc207"), - ("outputnode.score_sc217", "inputnode.score_sc217"), - ("outputnode.score_sc407", "inputnode.score_sc407"), - ("outputnode.score_sc417", "inputnode.score_sc417"), - ("outputnode.scrub_hvoxf", "inputnode.scrub_hvoxf"), - ("outputnode.scrub_sc207", "inputnode.scrub_sc207"), - ("outputnode.scrub_sc217", "inputnode.scrub_sc217"), - ("outputnode.scrub_sc407", "inputnode.scrub_sc407"), - ("outputnode.scrub_sc417", "inputnode.scrub_sc417"), + (parcellate_cbf_wf, asl_derivatives_wf, [ + ("outputnode.mean_cbf_score_parcellated", "inputnode.mean_cbf_score_parcellated"), + ("outputnode.mean_cbf_scrub_parcellated", "inputnode.mean_cbf_scrub_parcellated"), ]), ]) # fmt:on @@ -1021,21 +1015,16 @@ def init_asl_preproc_wf(asl_file): if basil: # fmt:off workflow.connect([ - (compt_cbf_wf, cbfroiqu, [ - ("outputnode.out_cbfb", "inputnode.basil"), - ("outputnode.out_cbfpv", "inputnode.pvc"), + (compt_cbf_wf, parcellate_cbf_wf, [ + ("outputnode.out_cbfb", "inputnode.mean_cbf_basil"), + ("outputnode.out_cbfpv", "inputnode.mean_cbf_gm_basil"), ]), - (cbfroiqu, asl_derivatives_wf, [ - ("outputnode.basil_hvoxf", "inputnode.basil_hvoxf"), - ("outputnode.basil_sc207", "inputnode.basil_sc207"), - ("outputnode.basil_sc217", "inputnode.basil_sc217"), - ("outputnode.basil_sc407", "inputnode.basil_sc407"), - ("outputnode.basil_sc417", "inputnode.basil_sc417"), - ("outputnode.pvc_hvoxf", "inputnode.pvc_hvoxf"), - ("outputnode.pvc_sc207", "inputnode.pvc_sc207"), - ("outputnode.pvc_sc217", "inputnode.pvc_sc217"), - ("outputnode.pvc_sc407", "inputnode.pvc_sc407"), - ("outputnode.pvc_sc417", "inputnode.pvc_sc417"), + (parcellate_cbf_wf, asl_derivatives_wf, [ + ("outputnode.mean_cbf_basil_parcellated", "inputnode.mean_cbf_basil_parcellated"), + ( + "outputnode.mean_cbf_gm_basil_parcellated", + "inputnode.mean_cbf_gm_basil_parcellated", + ), ]), ]) # fmt:on diff --git a/aslprep/workflows/asl/cbf.py b/aslprep/workflows/asl/cbf.py index f2afebf52..1e6ef111f 100644 --- a/aslprep/workflows/asl/cbf.py +++ b/aslprep/workflows/asl/cbf.py @@ -5,27 +5,22 @@ from nipype.interfaces import utility as niu from nipype.interfaces.fsl import Info, MultiImageMaths from nipype.pipeline import engine as pe +from templateflow.api import get as get_template from aslprep import config +from aslprep.interfaces.ants import ApplyTransforms from aslprep.interfaces.cbf_computation import ( BASILCBF, ComputeCBF, ExtractCBF, ExtractCBForDeltaM, - ParcellateCBF, RefineMask, ScoreAndScrubCBF, ) +from aslprep.interfaces.parcellation import ParcellateCBF from aslprep.niworkflows.engine.workflows import LiterateWorkflow as Workflow -from aslprep.niworkflows.interfaces.fixes import ( - FixHeaderApplyTransforms as ApplyTransforms, -) -from aslprep.utils.misc import ( - estimate_labeling_efficiency, - get_atlas, - get_tis, - pcasl_or_pasl, -) +from aslprep.utils.atlas import get_atlas_names, get_atlas_nifti +from aslprep.utils.misc import estimate_labeling_efficiency, get_tis, pcasl_or_pasl def init_cbf_compt_wf( @@ -698,17 +693,70 @@ def _getfiledir(file): return workflow -def init_cbfroiquant_wf(scorescrub=False, basil=False, name="cbf_roiquant"): +def init_parcellate_cbf_wf( + min_coverage=0.5, + scorescrub=False, + basil=False, + mem_gb=0.1, + omp_nthreads=1, + name="parcellate_cbf_wf", +): """Parcellate CBF results using a set of atlases. + Atlases are in MNI152NLin6Asym space, but ASLPrep is not guaranteed to generate + MNI152NLin6Asym-space derivatives. + However, it *is* guaranteed to generate MNI152NLin2009cAsym derivatives, + so this workflow warps the atlases to asl reference space via the path: + MNI152NLin6Asym --> MNI152NLin2009cAsym --> anat --> asl. + Workflow Graph .. workflow:: :graph2use: orig :simple_form: yes - from aslprep.workflows.asl.cbf import init_cbfroiquant_wf + from aslprep.workflows.asl.cbf import init_parcellate_cbf_wf + + wf = init_parcellate_cbf_wf() - wf = init_cbfroiquant_wf() + Parameters + ---------- + min_coverage + scorescrub + basil + mem_gb + omp_nthreads + name + Default is "parcellate_cbf_wf". + + Inputs + ------ + mean_cbf : str + mean_cbf_score : Undefined or str + mean_cbf_scrub : Undefined or str + mean_cbf_basil : Undefined or str + mean_cbf_gm_basil : Undefined or str + asl_mask : str + anat_to_asl_xform : str + MNI152NLin2009cAsym_to_anat_xform : str + The transform from MNI152NLin2009cAsym to the subject's anatomical space. + + Outputs + ------- + atlas_names : list of str + A list of atlases used for parcellating the CBF results. + The list of atlas names is generated by :func:`aslprep.utils.atlas.get_atlas_names`. + The atlases include: "Schaefer117", "Schaefer217", "Schaefer317", "Schaefer417", + "Schaefer517", "Schaefer617", "Schaefer717", "Schaefer817", "Schaefer917", + "Schaefer1017", "Glasser", "Gordon", and "subcortical" (Tian). + mean_cbf_parcellated : list of str + mean_cbf_score_parcellated : Undefined or list of str + Only defined if ``scorescrub`` is True. + mean_cbf_scrub_parcellated : Undefined or list of str + Only defined if ``scorescrub`` is True. + mean_cbf_basil_parcellated : Undefined or list of str + Only defined if ``basil`` is True. + mean_cbf_gm_basil_parcellated : Undefined or list of str + Only defined if ``basil`` is True. """ workflow = Workflow(name=name) @@ -720,14 +768,14 @@ def init_cbfroiquant_wf(scorescrub=False, basil=False, name="cbf_roiquant"): inputnode = pe.Node( niu.IdentityInterface( fields=[ - "cbf", - "score", - "scrub", - "basil", - "pvc", - "aslmask", - "t1_asl_xform", - "std2anat_xfm", + "mean_cbf", + "mean_cbf_score", + "mean_cbf_scrub", + "mean_cbf_basil", + "mean_cbf_gm_basil", + "asl_mask", + "anat_to_asl_xform", + "MNI152NLin2009cAsym_to_anat_xform", ] ), name="inputnode", @@ -735,262 +783,116 @@ def init_cbfroiquant_wf(scorescrub=False, basil=False, name="cbf_roiquant"): outputnode = pe.Node( niu.IdentityInterface( fields=[ - "cbf_hvoxf", - "score_hvoxf", - "scrub_hvoxf", - "basil_hvoxf", - "pvc_hvoxf", - "cbf_sc207", - "score_sc207", - "scrub_sc207", - "basil_sc207", - "pvc_sc207", - "cbf_sc217", - "score_sc217", - "scrub_sc217", - "basil_sc217", - "pvc_sc217", - "cbf_sc407", - "score_sc407", - "scrub_sc407", - "basil_sc407", - "pvc_sc407", - "cbf_sc417", - "score_sc417", - "scrub_sc417", - "basil_sc417", - "pvc_sc417", - ] + "atlas_names", + "mean_cbf_parcellated", + "mean_cbf_score_parcellated", + "mean_cbf_scrub_parcellated", + "mean_cbf_basil_parcellated", + "mean_cbf_gm_basil_parcellated", + ], ), name="outputnode", ) - hvoxfile, hvoxdata, hvoxlabel = get_atlas(atlasname="HarvardOxford") - sc207file, sc207data, sc207label = get_atlas(atlasname="schaefer200x7") - sc217file, sc217data, sc217label = get_atlas(atlasname="schaefer200x17") - sc407file, sc407data, sc407label = get_atlas(atlasname="schaefer400x7") - sc417file, sc417data, sc417label = get_atlas(atlasname="schaefer400x17") - - mrg_xfms = pe.Node(niu.Merge(2), name="mrg_xfms") - hvoftrans = pe.Node( - ApplyTransforms( - float=True, - input_image=hvoxfile, - dimension=3, - default_value=0, - interpolation="NearestNeighbor", - ), - name="hvoftrans", + atlas_name_grabber = pe.Node( + niu.Function(output_names=["atlas_names"], function=get_atlas_names), + name="atlas_name_grabber", ) - sc207trans = pe.Node( - ApplyTransforms( - float=True, - input_image=sc207file, - dimension=3, - default_value=0, - interpolation="NearestNeighbor", - ), - name="sc207trans", - ) - sc217trans = pe.Node( - ApplyTransforms( - float=True, - input_image=sc217file, - dimension=3, - default_value=0, - interpolation="NearestNeighbor", + + # fmt:off + workflow.connect([(atlas_name_grabber, outputnode, [("atlas_names", "atlas_names")])]) + # fmt:on + + # get atlases via pkgrf + atlas_file_grabber = pe.MapNode( + niu.Function( + input_names=["atlas_name"], + output_names=["atlas_file", "atlas_labels_file"], + function=get_atlas_nifti, ), - name="sc217trans", + name="atlas_file_grabber", + iterfield=["atlas_name"], ) - sc407trans = pe.Node( - ApplyTransforms( - float=True, - input_image=sc407file, - dimension=3, - default_value=0, - interpolation="NearestNeighbor", + + # fmt:off + workflow.connect([(atlas_name_grabber, atlas_file_grabber, [("atlas_names", "atlas_name")])]) + # fmt:on + + # Atlases are in MNI152NLin6Asym + MNI152NLin6Asym_to_MNI152NLin2009cAsym = str( + get_template( + template="MNI152NLin2009cAsym", + mode="image", + suffix="xfm", + extension=".h5", + **{"from": "MNI152NLin6Asym"}, ), - name="sc407trans", ) - sc417trans = pe.Node( + + # Prepare to warp atlases from MNI152NLin6Asym to ASL reference space. + # One of the output spaces selected by the user *may* be MNI152NLin6Asym, + # but MNI152NLin2009cAsym is always used, so it's safer to go: + # MNI152NLin6Asym --> MNI152NLin2009cAsym --> anat --> asl + merge_xforms = pe.Node(niu.Merge(3), name="merge_xforms") + merge_xforms.inputs.in1 = MNI152NLin6Asym_to_MNI152NLin2009cAsym + + # fmt:off + workflow.connect([ + (inputnode, merge_xforms, [ + ("MNI152NLin2009cAsym_to_anat_xform", "in2"), + ("anat_to_asl_xform", "in3"), + ]), + ]) + # fmt:on + + # Using the generated transforms, apply them to get everything in the correct MNI form + warp_atlases_to_asl_space = pe.MapNode( ApplyTransforms( - float=True, - input_image=sc417file, + interpolation="GenericLabel", + input_image_type=3, dimension=3, - default_value=0, - interpolation="NearestNeighbor", ), - name="sc417trans", + name="warp_atlases_to_asl_space", + iterfield=["input_image"], + mem_gb=mem_gb, + n_procs=omp_nthreads, ) - cbfroihv = pe.Node(ParcellateCBF(atlaslabel=hvoxlabel, atlasdata=hvoxdata), name="cbfroihv") - cbfroi207 = pe.Node(ParcellateCBF(atlaslabel=sc207label, atlasdata=sc207data), name="cbf207") - cbfroi217 = pe.Node(ParcellateCBF(atlaslabel=sc217label, atlasdata=sc217data), name="cbf217") - cbfroi407 = pe.Node(ParcellateCBF(atlaslabel=sc407label, atlasdata=sc407data), name="cbf407") - cbfroi417 = pe.Node(ParcellateCBF(atlaslabel=sc417label, atlasdata=sc417data), name="cbf417") - if scorescrub: - scorehv = pe.Node(ParcellateCBF(atlaslabel=hvoxlabel, atlasdata=hvoxdata), name="scorehv") - score207 = pe.Node( - ParcellateCBF(atlaslabel=sc207label, atlasdata=sc207data), - name="score207", - ) - score217 = pe.Node( - ParcellateCBF(atlaslabel=sc217label, atlasdata=sc217data), - name="score217", - ) - score407 = pe.Node( - ParcellateCBF(atlaslabel=sc407label, atlasdata=sc407data), - name="score407", - ) - score417 = pe.Node( - ParcellateCBF(atlaslabel=sc417label, atlasdata=sc417data), - name="score417", - ) - scrubhv = pe.Node(ParcellateCBF(atlaslabel=hvoxlabel, atlasdata=hvoxdata), name="scrubhv") - scrub207 = pe.Node( - ParcellateCBF(atlaslabel=sc207label, atlasdata=sc207data), - name="scrub207", - ) - scrub217 = pe.Node( - ParcellateCBF(atlaslabel=sc217label, atlasdata=sc217data), - name="scrub217", - ) - scrub407 = pe.Node( - ParcellateCBF(atlaslabel=sc407label, atlasdata=sc407data), - name="scrub407", - ) - scrub417 = pe.Node( - ParcellateCBF(atlaslabel=sc417label, atlasdata=sc417data), - name="scrub417", - ) - - if basil: - basilhv = pe.Node(ParcellateCBF(atlaslabel=hvoxlabel, atlasdata=hvoxdata), name="basilhv") - basil207 = pe.Node( - ParcellateCBF(atlaslabel=sc207label, atlasdata=sc207data), - name="basil207", - ) - basil217 = pe.Node( - ParcellateCBF(atlaslabel=sc217label, atlasdata=sc217data), - name="basil217", - ) - basil407 = pe.Node( - ParcellateCBF(atlaslabel=sc407label, atlasdata=sc407data), - name="basil407", - ) - basil417 = pe.Node( - ParcellateCBF(atlaslabel=sc417label, atlasdata=sc417data), - name="basil417", - ) - pvchv = pe.Node(ParcellateCBF(atlaslabel=hvoxlabel, atlasdata=hvoxdata), name="pvchv") - pvc207 = pe.Node(ParcellateCBF(atlaslabel=sc207label, atlasdata=sc207data), name="pvc207") - pvc217 = pe.Node(ParcellateCBF(atlaslabel=sc217label, atlasdata=sc217data), name="pvc217") - pvc407 = pe.Node(ParcellateCBF(atlaslabel=sc407label, atlasdata=sc407data), name="pvc407") - pvc417 = pe.Node(ParcellateCBF(atlaslabel=sc417label, atlasdata=sc417data), name="pvc417") - # fmt:off workflow.connect([ - (inputnode, mrg_xfms, [ - ("t1_asl_xform", "in2"), - ("std2anat_xfm", "in1"), - ]), - (inputnode, hvoftrans, [("aslmask", "reference_image")]), - (mrg_xfms, hvoftrans, [("out", "transforms")]), - (inputnode, sc207trans, [("aslmask", "reference_image")]), - (mrg_xfms, sc207trans, [("out", "transforms")]), - (inputnode, sc217trans, [("aslmask", "reference_image")]), - (mrg_xfms, sc217trans, [("out", "transforms")]), - (inputnode, sc407trans, [("aslmask", "reference_image")]), - (mrg_xfms, sc407trans, [("out", "transforms")]), - (inputnode, sc417trans, [("aslmask", "reference_image")]), - (mrg_xfms, sc417trans, [("out", "transforms")]), - (hvoftrans, cbfroihv, [("output_image", "atlasfile")]), - (sc207trans, cbfroi207, [("output_image", "atlasfile")]), - (sc217trans, cbfroi217, [("output_image", "atlasfile")]), - (sc407trans, cbfroi407, [("output_image", "atlasfile")]), - (sc417trans, cbfroi417, [("output_image", "atlasfile")]), - (inputnode, cbfroihv, [("cbf", "in_cbf")]), - (inputnode, cbfroi207, [("cbf", "in_cbf")]), - (inputnode, cbfroi217, [("cbf", "in_cbf")]), - (inputnode, cbfroi407, [("cbf", "in_cbf")]), - (inputnode, cbfroi417, [("cbf", "in_cbf")]), - (cbfroihv, outputnode, [("atlascsv", "cbf_hvoxf")]), - (cbfroi207, outputnode, [("atlascsv", "cbf_sc207")]), - (cbfroi217, outputnode, [("atlascsv", "cbf_sc217")]), - (cbfroi407, outputnode, [("atlascsv", "cbf_sc407")]), - (cbfroi417, outputnode, [("atlascsv", "cbf_sc417")]), + (inputnode, warp_atlases_to_asl_space, [("asl_mask", "reference_image")]), + (atlas_file_grabber, warp_atlases_to_asl_space, [("atlas_file", "input_image")]), + (merge_xforms, warp_atlases_to_asl_space, [("out", "transforms")]), ]) # fmt:on + cbf_types = ["mean_cbf"] if scorescrub: - # fmt:off - workflow.connect([ - (hvoftrans, scorehv, [("output_image", "atlasfile")]), - (hvoftrans, scrubhv, [("output_image", "atlasfile")]), - (sc207trans, score207, [("output_image", "atlasfile")]), - (sc207trans, scrub207, [("output_image", "atlasfile")]), - (sc217trans, score217, [("output_image", "atlasfile")]), - (sc217trans, scrub217, [("output_image", "atlasfile")]), - (sc407trans, score407, [("output_image", "atlasfile")]), - (sc407trans, scrub407, [("output_image", "atlasfile")]), - (sc417trans, score417, [("output_image", "atlasfile")]), - (sc417trans, scrub417, [("output_image", "atlasfile")]), - (inputnode, scorehv, [("score", "in_cbf")]), - (inputnode, scrubhv, [("scrub", "in_cbf")]), - (inputnode, score207, [("score", "in_cbf")]), - (inputnode, scrub207, [("scrub", "in_cbf")]), - (inputnode, score217, [("score", "in_cbf")]), - (inputnode, scrub217, [("scrub", "in_cbf")]), - (inputnode, score407, [("score", "in_cbf")]), - (inputnode, scrub407, [("scrub", "in_cbf")]), - (inputnode, score417, [("score", "in_cbf")]), - (inputnode, scrub417, [("scrub", "in_cbf")]), - (scorehv, outputnode, [("atlascsv", "score_hvoxf")]), - (score207, outputnode, [("atlascsv", "score_sc207")]), - (score217, outputnode, [("atlascsv", "score_sc217")]), - (score407, outputnode, [("atlascsv", "score_sc407")]), - (score417, outputnode, [("atlascsv", "score_sc417")]), - (scrubhv, outputnode, [("atlascsv", "scrub_hvoxf")]), - (scrub207, outputnode, [("atlascsv", "scrub_sc207")]), - (scrub217, outputnode, [("atlascsv", "scrub_sc217")]), - (scrub407, outputnode, [("atlascsv", "scrub_sc407")]), - (scrub417, outputnode, [("atlascsv", "scrub_sc417")]), - ]) - # fmt:on + cbf_types += ["mean_cbf_score", "mean_cbf_scrub"] if basil: + cbf_types += ["mean_cbf_basil", "mean_cbf_gm_basil"] + + for cbf_type in cbf_types: + parcellate_cbf = pe.MapNode( + ParcellateCBF(min_coverage=min_coverage), + name=f"parcellate_{cbf_type}", + iterfield=["atlas", "atlas_labels"], + mem_gb=mem_gb, + ) + # fmt:off workflow.connect([ - (hvoftrans, basilhv, [("output_image", "atlasfile")]), - (hvoftrans, pvchv, [("output_image", "atlasfile")]), - (sc207trans, pvc207, [("output_image", "atlasfile")]), - (sc207trans, basil207, [("output_image", "atlasfile")]), - (sc217trans, pvc217, [("output_image", "atlasfile")]), - (sc217trans, basil217, [("output_image", "atlasfile")]), - (sc407trans, pvc407, [("output_image", "atlasfile")]), - (sc407trans, basil407, [("output_image", "atlasfile")]), - (sc417trans, pvc417, [("output_image", "atlasfile")]), - (sc417trans, basil417, [("output_image", "atlasfile")]), - (inputnode, basilhv, [("basil", "in_cbf")]), - (inputnode, pvchv, [("pvc", "in_cbf")]), - (inputnode, basil207, [("basil", "in_cbf")]), - (inputnode, pvc207, [("pvc", "in_cbf")]), - (inputnode, basil217, [("basil", "in_cbf")]), - (inputnode, pvc217, [("pvc", "in_cbf")]), - (inputnode, basil407, [("basil", "in_cbf")]), - (inputnode, pvc407, [("pvc", "in_cbf")]), - (inputnode, basil417, [("basil", "in_cbf")]), - (inputnode, pvc417, [("pvc", "in_cbf")]), - (basilhv, outputnode, [("atlascsv", "basil_hvoxf")]), - (basil207, outputnode, [("atlascsv", "basil_sc207")]), - (basil217, outputnode, [("atlascsv", "basil_sc217")]), - (basil407, outputnode, [("atlascsv", "basil_sc407")]), - (basil417, outputnode, [("atlascsv", "basil_sc417")]), - (pvchv, outputnode, [("atlascsv", "pvc_hvoxf")]), - (pvc207, outputnode, [("atlascsv", "pvc_sc207")]), - (pvc217, outputnode, [("atlascsv", "pvc_sc217")]), - (pvc407, outputnode, [("atlascsv", "pvc_sc407")]), - (pvc417, outputnode, [("atlascsv", "pvc_sc417")]), + (inputnode, parcellate_cbf, [ + (cbf_type, "in_file"), + ("asl_mask", "mask"), + ]), + (atlas_file_grabber, parcellate_cbf, [("atlas_labels_file", "atlas_labels")]), + (warp_atlases_to_asl_space, parcellate_cbf, [("output_image", "atlas")]), + (parcellate_cbf, outputnode, [ + ("timeseries", f"{cbf_type}_parcellated"), + ("coverage", f"{cbf_type}_coverage"), + ]), ]) # fmt:on diff --git a/aslprep/workflows/asl/confounds.py b/aslprep/workflows/asl/confounds.py index 0d53e5ffe..3295807c6 100644 --- a/aslprep/workflows/asl/confounds.py +++ b/aslprep/workflows/asl/confounds.py @@ -8,10 +8,8 @@ from aslprep.config import DEFAULT_MEMORY_MIN_GB from aslprep.interfaces import ASLSummary, DerivativesDataSink, GatherConfounds +from aslprep.interfaces.ants import ApplyTransforms from aslprep.niworkflows.engine.workflows import LiterateWorkflow as Workflow -from aslprep.niworkflows.interfaces.fixes import ( - FixHeaderApplyTransforms as ApplyTransforms, -) from aslprep.niworkflows.interfaces.utils import AddTSVHeader diff --git a/aslprep/workflows/asl/ge_utils.py b/aslprep/workflows/asl/ge_utils.py index 6bfd0efe7..0a895eedb 100644 --- a/aslprep/workflows/asl/ge_utils.py +++ b/aslprep/workflows/asl/ge_utils.py @@ -7,11 +7,9 @@ from aslprep import config from aslprep.interfaces import DerivativesDataSink +from aslprep.interfaces.ants import ApplyTransforms from aslprep.interfaces.ge import GeReferenceFile from aslprep.niworkflows.engine.workflows import LiterateWorkflow as Workflow -from aslprep.niworkflows.interfaces.fixes import ( - FixHeaderApplyTransforms as ApplyTransforms, -) from aslprep.niworkflows.interfaces.masks import SimpleShowMaskRPT from aslprep.niworkflows.interfaces.utility import KeySelect from aslprep.niworkflows.interfaces.utils import GenerateSamplingReference @@ -229,9 +227,6 @@ def init_asl_t1_getrans_wf( ) """ from aslprep.niworkflows.engine.workflows import LiterateWorkflow as Workflow - from aslprep.niworkflows.interfaces.fixes import ( - FixHeaderApplyTransforms as ApplyTransforms, - ) workflow = Workflow(name=name) inputnode = pe.Node( diff --git a/aslprep/workflows/asl/gecbf.py b/aslprep/workflows/asl/gecbf.py index 19a6e8f34..406f2f26b 100644 --- a/aslprep/workflows/asl/gecbf.py +++ b/aslprep/workflows/asl/gecbf.py @@ -10,16 +10,17 @@ from aslprep.interfaces.reports import FunctionalSummary from aslprep.niworkflows.engine.workflows import LiterateWorkflow as Workflow from aslprep.niworkflows.interfaces.nibabel import ApplyMask +from aslprep.niworkflows.interfaces.utility import KeySelect from aslprep.utils.bids import collect_run_data from aslprep.utils.misc import _create_mem_gb, _get_wf_name -from aslprep.workflows.asl.cbf import init_cbfroiquant_wf, init_gecbf_compt_wf +from aslprep.workflows.asl.cbf import init_gecbf_compt_wf, init_parcellate_cbf_wf from aslprep.workflows.asl.ge_utils import ( init_asl_geref_wf, init_asl_gereg_wf, init_asl_gestd_trans_wf, init_asl_t1_getrans_wf, ) -from aslprep.workflows.asl.outputs import init_geasl_derivatives_wf +from aslprep.workflows.asl.outputs import init_asl_derivatives_wf from aslprep.workflows.asl.plotting import init_gecbfplot_wf from aslprep.workflows.asl.qc import init_cbfgeqc_compt_wf @@ -286,23 +287,24 @@ def init_asl_gepreproc_wf(asl_file): ) # summary.inputs.dummy_scans = 0 - asl_derivatives_wf = init_geasl_derivatives_wf( + asl_derivatives_wf = init_asl_derivatives_wf( bids_root=layout.root, metadata=metadata, output_dir=output_dir, scorescrub=scorescrub, basil=basil, spaces=spaces, + output_confounds=False, # GE workflow doesn't generate volume-wise confounds ) # fmt:off workflow.connect([ (inputnode, asl_derivatives_wf, [("asl_file", "inputnode.source_file")]), (outputnode, asl_derivatives_wf, [ + ("asl_native", "inputnode.asl_native"), ("asl_t1", "inputnode.asl_t1"), - ("asl_t1_ref", "inputnode.asl_t1_ref"), + ("asl_t1_ref", "inputnode.aslref_t1"), ("asl_mask_t1", "inputnode.asl_mask_t1"), - ("asl_native", "inputnode.asl_native"), ]), ]) # fmt:on @@ -475,9 +477,7 @@ def init_asl_gepreproc_wf(asl_file): if nonstd_spaces.intersection(("T1w", "anat")): t1cbfspace = True - from aslprep.niworkflows.interfaces.fixes import ( - FixHeaderApplyTransforms as ApplyTransforms, - ) + from aslprep.interfaces.ants import ApplyTransforms aslmask_to_t1w = pe.Node( ApplyTransforms(interpolation="MultiLabel"), @@ -574,12 +574,12 @@ def init_asl_gepreproc_wf(asl_file): workflow.connect([ (inputnode, outputnode, [("asl_file", "asl_native")]), (gen_ref_wf, asl_derivatives_wf, [ - ("outputnode.raw_ref_image", "inputnode.asl_native_ref"), + ("outputnode.raw_ref_image", "inputnode.aslref_native"), ]), (refine_mask, asl_derivatives_wf, [("out_mask", "inputnode.asl_mask_native")]), (cbf_compt_wf, asl_derivatives_wf, [ - ("outputnode.out_cbf", "inputnode.cbf"), - ("outputnode.out_mean", "inputnode.meancbf"), + ("outputnode.out_cbf", "inputnode.cbf_native"), + ("outputnode.out_mean", "inputnode.meancbf_native"), ]), ]) # fmt:on @@ -588,9 +588,9 @@ def init_asl_gepreproc_wf(asl_file): # fmt:off workflow.connect([ (cbf_compt_wf, asl_derivatives_wf, [ - ("outputnode.out_score", "inputnode.score"), - ("outputnode.out_avgscore", "inputnode.avgscore"), - ("outputnode.out_scrub", "inputnode.scrub"), + ("outputnode.out_score", "inputnode.score_native"), + ("outputnode.out_avgscore", "inputnode.avgscore_native"), + ("outputnode.out_scrub", "inputnode.scrub_native"), ]), ]) # fmt:on @@ -599,10 +599,10 @@ def init_asl_gepreproc_wf(asl_file): # fmt:off workflow.connect([ (cbf_compt_wf, asl_derivatives_wf, [ - ("outputnode.out_cbfb", "inputnode.basil"), - ("outputnode.out_cbfpv", "inputnode.pv"), - ("outputnode.out_cbfpvwm", "inputnode.pvwm"), - ("outputnode.out_att", "inputnode.att"), + ("outputnode.out_cbfb", "inputnode.basil_native"), + ("outputnode.out_cbfpv", "inputnode.pv_native"), + ("outputnode.out_cbfpvwm", "inputnode.pvwm_native"), + ("outputnode.out_att", "inputnode.att_native"), ]), ]) # fmt:on @@ -678,7 +678,7 @@ def init_asl_gepreproc_wf(asl_file): (std_gereg_wf, asl_derivatives_wf, [ ("outputnode.template", "inputnode.template"), ("outputnode.spatial_reference", "inputnode.spatial_reference"), - ("outputnode.asl_std_ref", "inputnode.asl_std_ref"), + ("outputnode.asl_std_ref", "inputnode.aslref_std"), ("outputnode.asl_std", "inputnode.asl_std"), ("outputnode.asl_mask_std", "inputnode.asl_mask_std"), ("outputnode.cbf_std", "inputnode.cbf_std"), @@ -710,24 +710,41 @@ def init_asl_gepreproc_wf(asl_file): ]) # fmt:on - cbfroiqu = init_cbfroiquant_wf( + # xform to 'MNI152NLin2009cAsym' is always computed, so this should always be available. + select_xform_MNI152NLin2009cAsym_to_t1w = pe.Node( + KeySelect(fields=["std2anat_xfm"], key="MNI152NLin2009cAsym"), + name="carpetplot_select_std", + run_without_submitting=True, + ) + + # fmt:off + workflow.connect([ + (inputnode, select_xform_MNI152NLin2009cAsym_to_t1w, [ + ("std2anat_xfm", "std2anat_xfm"), + ("template", "keys"), + ]), + ]) + # fmt:on + + parcellate_cbf_wf = init_parcellate_cbf_wf( scorescrub=scorescrub, basil=basil, - name="cbf_roiquant", + name="parcellate_cbf_wf", ) # fmt:off workflow.connect([ - (refine_mask, cbfroiqu, [("out_mask", "inputnode.aslmask")]), - (inputnode, cbfroiqu, [("std2anat_xfm", "inputnode.std2anat_xfm")]), - (asl_reg_wf, cbfroiqu, [("outputnode.itk_t1_to_asl", "inputnode.t1_asl_xform")]), - (cbf_compt_wf, cbfroiqu, [("outputnode.out_mean", "inputnode.cbf")]), - (cbfroiqu, asl_derivatives_wf, [ - ("outputnode.cbf_hvoxf", "inputnode.cbf_hvoxf"), - ("outputnode.cbf_sc207", "inputnode.cbf_sc207"), - ("outputnode.cbf_sc217", "inputnode.cbf_sc217"), - ("outputnode.cbf_sc407", "inputnode.cbf_sc407"), - ("outputnode.cbf_sc417", "inputnode.cbf_sc417"), + (select_xform_MNI152NLin2009cAsym_to_t1w, parcellate_cbf_wf, [ + ("std2anat_xfm", "inputnode.MNI152NLin2009cAsym_to_anat_xform"), + ]), + (refine_mask, parcellate_cbf_wf, [("out_mask", "inputnode.asl_mask")]), + (asl_reg_wf, parcellate_cbf_wf, [ + ("outputnode.itk_t1_to_asl", "inputnode.anat_to_asl_xform"), + ]), + (cbf_compt_wf, parcellate_cbf_wf, [("outputnode.out_mean", "inputnode.mean_cbf")]), + (parcellate_cbf_wf, asl_derivatives_wf, [ + ("outputnode.atlas_names", "inputnode.atlas_names"), + ("outputnode.mean_cbf_parcellated", "inputnode.mean_cbf_parcellated"), ]), ]) # fmt:on @@ -735,21 +752,13 @@ def init_asl_gepreproc_wf(asl_file): if scorescrub: # fmt:off workflow.connect([ - (cbf_compt_wf, cbfroiqu, [ - ("outputnode.out_avgscore", "inputnode.score"), - ("outputnode.out_scrub", "inputnode.scrub"), + (cbf_compt_wf, parcellate_cbf_wf, [ + ("outputnode.out_avgscore", "inputnode.mean_cbf_score"), + ("outputnode.out_scrub", "inputnode.mean_cbf_scrub"), ]), - (cbfroiqu, asl_derivatives_wf, [ - ("outputnode.score_hvoxf", "inputnode.score_hvoxf"), - ("outputnode.score_sc207", "inputnode.score_sc207"), - ("outputnode.score_sc217", "inputnode.score_sc217"), - ("outputnode.score_sc407", "inputnode.score_sc407"), - ("outputnode.score_sc417", "inputnode.score_sc417"), - ("outputnode.scrub_hvoxf", "inputnode.scrub_hvoxf"), - ("outputnode.scrub_sc207", "inputnode.scrub_sc207"), - ("outputnode.scrub_sc217", "inputnode.scrub_sc217"), - ("outputnode.scrub_sc407", "inputnode.scrub_sc407"), - ("outputnode.scrub_sc417", "inputnode.scrub_sc417"), + (parcellate_cbf_wf, asl_derivatives_wf, [ + ("outputnode.mean_cbf_score_parcellated", "inputnode.mean_cbf_score_parcellated"), + ("outputnode.mean_cbf_scrub_parcellated", "inputnode.mean_cbf_scrub_parcellated"), ]), ]) # fmt:on @@ -757,21 +766,16 @@ def init_asl_gepreproc_wf(asl_file): if basil: # fmt:off workflow.connect([ - (cbf_compt_wf, cbfroiqu, [ - ("outputnode.out_cbfb", "inputnode.basil"), - ("outputnode.out_cbfpv", "inputnode.pvc"), + (cbf_compt_wf, parcellate_cbf_wf, [ + ("outputnode.out_cbfb", "inputnode.mean_cbf_basil"), + ("outputnode.out_cbfpv", "inputnode.mean_cbf_gm_basil"), ]), - (cbfroiqu, asl_derivatives_wf, [ - ("outputnode.basil_hvoxf", "inputnode.basil_hvoxf"), - ("outputnode.basil_sc207", "inputnode.basil_sc207"), - ("outputnode.basil_sc217", "inputnode.basil_sc217"), - ("outputnode.basil_sc407", "inputnode.basil_sc407"), - ("outputnode.basil_sc417", "inputnode.basil_sc417"), - ("outputnode.pvc_hvoxf", "inputnode.pvc_hvoxf"), - ("outputnode.pvc_sc207", "inputnode.pvc_sc207"), - ("outputnode.pvc_sc217", "inputnode.pvc_sc217"), - ("outputnode.pvc_sc407", "inputnode.pvc_sc407"), - ("outputnode.pvc_sc417", "inputnode.pvc_sc417"), + (parcellate_cbf_wf, asl_derivatives_wf, [ + ("outputnode.mean_cbf_basil_parcellated", "inputnode.mean_cbf_basil_parcellated"), + ( + "outputnode.mean_cbf_gm_basil_parcellated", + "inputnode.mean_cbf_gm_basil_parcellated", + ), ]), ]) # fmt:on diff --git a/aslprep/workflows/asl/outputs.py b/aslprep/workflows/asl/outputs.py index 54d0f337e..3e68f0425 100644 --- a/aslprep/workflows/asl/outputs.py +++ b/aslprep/workflows/asl/outputs.py @@ -5,7 +5,7 @@ from nipype.pipeline import engine as pe from smriprep.workflows.outputs import _bids_relative -from aslprep.config import DEFAULT_MEMORY_MIN_GB +from aslprep import config from aslprep.interfaces import DerivativesDataSink from aslprep.niworkflows.engine.workflows import LiterateWorkflow as Workflow from aslprep.niworkflows.interfaces.utility import KeySelect @@ -16,6 +16,7 @@ def init_asl_derivatives_wf( metadata, output_dir, spaces, + output_confounds=True, scorescrub=False, basil=False, name="asl_derivatives_wf", @@ -48,76 +49,64 @@ def init_asl_derivatives_wf( inputnode = pe.Node( niu.IdentityInterface( fields=[ - "asl_mask_std", - "asl_mask_t1", - "asl_std", - "itk_asl_to_t1", - "itk_t1_to_asl", - "asl_std_ref", - "asl_t1", - "asl_t1_ref", - "asl_native", - "asl_native_ref", - "asl_mask_native", - "confounds", - "confounds_metadata", "source_file", "template", "spatial_reference", - "cbf", - "meancbf", - "score", - "avgscore", - "scrub", - "basil", - "pv", - "pvwm", + "qc_file", + # Preprocessed ASL files + "asl_native", + "asl_t1", + "asl_std", + "aslref_native", + "aslref_t1", + "aslref_std", + "asl_mask_native", + "asl_mask_t1", + "asl_mask_std", + # Transforms + "itk_asl_to_t1", + "itk_t1_to_asl", + # Standard CBF outputs + "cbf_native", "cbf_t1", - "meancbf_t1", - "att_t1", - "score_t1", - "avgscore_t1", - "scrub_t1", - "basil_t1", - "pv_t1", - "pvwm_t1", "cbf_std", + "meancbf_native", + "meancbf_t1", "meancbf_std", + # SCORE/SCRUB outputs + "score_native", + "score_t1", "score_std", + "avgscore_native", + "avgscore_t1", "avgscore_std", + "scrub_native", + "scrub_t1", "scrub_std", + # BASIL outputs + "basil_native", + "basil_t1", "basil_std", + "pv_native", + "pv_t1", "pv_std", + "pvwm_native", + "pvwm_t1", "pvwm_std", - "att", + "att_native", + "att_t1", "att_std", - "qc_file", - "cbf_hvoxf", - "score_hvoxf", - "scrub_hvoxf", - "basil_hvoxf", - "pvc_hvoxf", - "cbf_sc207", - "score_sc207", - "scrub_sc207", - "basil_sc207", - "pvc_sc207", - "cbf_sc217", - "score_sc217", - "scrub_sc217", - "basil_sc217", - "pvc_sc217", - "cbf_sc407", - "score_sc407", - "scrub_sc407", - "basil_sc407", - "pvc_sc407", - "cbf_sc417", - "score_sc417", - "scrub_sc417", - "basil_sc417", - "pvc_sc417", - ] + # Parcellated CBF outputs + "atlas_names", + "mean_cbf_parcellated", + "mean_cbf_score_parcellated", + "mean_cbf_scrub_parcellated", + "mean_cbf_basil_parcellated", + "mean_cbf_gm_basil_parcellated", + # non-GE outputs + "confounds", + "confounds_metadata", + ], ), name="inputnode", ) @@ -125,41 +114,47 @@ def init_asl_derivatives_wf( raw_sources = pe.Node(niu.Function(function=_bids_relative), name="raw_sources") raw_sources.inputs.bids_root = bids_root - ds_confounds = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="confounds", - suffix="regressors", - ), - name="ds_confounds", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) # fmt:off - workflow.connect([ - (inputnode, raw_sources, [("source_file", "in_files")]), - (inputnode, ds_confounds, [ - ("source_file", "source_file"), - ("confounds", "in_file"), - ("confounds_metadata", "meta_dict"), - ]), - ]) + workflow.connect([(inputnode, raw_sources, [("source_file", "in_files")])]) # fmt:on - qcfile = pe.Node( + if output_confounds: + ds_confounds = pe.Node( + DerivativesDataSink( + base_directory=output_dir, + desc="confounds", + suffix="regressors", + ), + name="ds_confounds", + run_without_submitting=True, + mem_gb=config.DEFAULT_MEMORY_MIN_GB, + ) + + # fmt:off + workflow.connect([ + (inputnode, ds_confounds, [ + ("source_file", "source_file"), + ("confounds", "in_file"), + ("confounds_metadata", "meta_dict"), + ]), + ]) + # fmt:on + + ds_qcfile = pe.Node( DerivativesDataSink( base_directory=output_dir, desc="qualitycontrol", suffix="cbf", compress=False, ), - name="qcfile", + name="ds_qcfile", run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, + mem_gb=config.DEFAULT_MEMORY_MIN_GB, ) + # fmt:off workflow.connect([ - (inputnode, qcfile, [ + (inputnode, ds_qcfile, [ ("source_file", "source_file"), ("qc_file", "in_file"), ]), @@ -170,23 +165,23 @@ def init_asl_derivatives_wf( ds_t1w_to_asl_xform = pe.Node( DerivativesDataSink( base_directory=output_dir, - to="T1w", + to="scanner", mode="image", suffix="xfm", extension=".txt", dismiss_entities=("echo",), - **{"from": "scanner"}, + **{"from": "T1w"}, ), name="ds_t1w_to_asl_xform", run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, + mem_gb=config.DEFAULT_MEMORY_MIN_GB, ) # fmt:off workflow.connect([ (inputnode, ds_t1w_to_asl_xform, [ ("source_file", "source_file"), - ("itk_asl_to_t1", "in_file"), + ("itk_t1_to_asl", "in_file"), ]), ]) # fmt:on @@ -195,2524 +190,261 @@ def init_asl_derivatives_wf( DerivativesDataSink( base_directory=output_dir, dismiss_entities=("echo",), - to="scanner", + to="T1w", mode="image", suffix="xfm", extension=".txt", - **{"from": "T1w"}, + **{"from": "scanner"}, ), name="ds_asl_to_t1w_xform", run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, + mem_gb=config.DEFAULT_MEMORY_MIN_GB, ) # fmt:off workflow.connect([ (inputnode, ds_asl_to_t1w_xform, [ ("source_file", "source_file"), - ("itk_t1_to_asl", "in_file"), + ("itk_asl_to_t1", "in_file"), ]), ]) # fmt:on - cbf_hvoxf = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="HarvardOxford", - desc="mean", - suffix="cbf", - compress=False, - ), - name="cbf_hvoxf", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - cbf_sc207 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer200x7", - desc="mean", - suffix="cbf", - compress=False, - ), - name="cbf_sc207", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - cbf_sc217 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer200x17", - desc="mean", - suffix="cbf", - compress=False, - ), - name="cbf_sc217", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - cbf_sc407 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer400x7", - desc="mean", - suffix="cbf", - compress=False, - ), - name="cbf_sc407", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - cbf_sc417 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer400x17", - desc="mean", - suffix="cbf", - compress=False, - ), - name="cbf_sc417", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) + # Parcellated data + PARCELLATED_INPUT_FIELDS = { + "mean_cbf_parcellated": {}, + "mean_cbf_score_parcellated": { + "desc": "score", + }, + "mean_cbf_scrub_parcellated": { + "desc": "scrub", + }, + "mean_cbf_basil_parcellated": { + "desc": "basil", + }, + "mean_cbf_gm_basil_parcellated": { + "desc": "basilGM", + }, + } + parcellated_inputs = ["mean_cbf_parcellated"] + if scorescrub: + parcellated_inputs += ["mean_cbf_score_parcellated", "mean_cbf_scrub_parcellated"] - # fmt:off - workflow.connect([ - (inputnode, cbf_hvoxf, [ - ("source_file", "source_file"), - ("cbf_hvoxf", "in_file"), - ]), - (inputnode, cbf_sc207, [ - ("source_file", "source_file"), - ("cbf_sc207", "in_file"), - ]), - (inputnode, cbf_sc217, [ - ("source_file", "source_file"), - ("cbf_sc217", "in_file"), - ]), - (inputnode, cbf_sc407, [ - ("source_file", "source_file"), - ("cbf_sc407", "in_file"), - ]), - (inputnode, cbf_sc417, [ - ("source_file", "source_file"), - ("cbf_sc417", "in_file"), - ]), - ]) - # fmt:on + if basil: + parcellated_inputs += ["mean_cbf_basil_parcellated", "mean_cbf_gm_basil_parcellated"] - if scorescrub: - score_hvoxf = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="HarvardOxford", - desc="mean", - suffix="score", - compress=False, - ), - name="score_hvoxf", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - scrub_hvoxf = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="HarvardOxford", - desc="mean", - suffix="scrub", - compress=False, - ), - name="scrub_hvoxf", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - score_sc207 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer200x7", - desc="mean", - suffix="score", - compress=False, - ), - name="score_sc207", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - scrub_sc207 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer200x7", - desc="mean", - suffix="scrub", - compress=False, - ), - name="scrub_sc207", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - score_sc217 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer200x17", - desc="mean", - suffix="score", - compress=False, - ), - name="score_sc217", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - scrub_sc217 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer200x17", - desc="mean", - suffix="scrub", - compress=False, - ), - name="scrub_sc217", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - score_sc407 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer400x7", - desc="mean", - suffix="score", - compress=False, - ), - name="score_sc407", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - scrub_sc407 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer400x7", - desc="mean", - suffix="scrub", - compress=False, - ), - name="scrub_sc407", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - score_sc417 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer400x17", - desc="mean", - suffix="score", - compress=False, - ), - name="score_sc417", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - scrub_sc417 = pe.Node( + for parcellated_input in parcellated_inputs: + ds_parcellated_input = pe.MapNode( DerivativesDataSink( base_directory=output_dir, - atlas="schaefer400x17", - desc="mean", - suffix="scrub", + suffix="cbf", compress=False, + **PARCELLATED_INPUT_FIELDS[parcellated_input], ), - name="scrub_sc417", + name=f"ds_{parcellated_input}", run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, + mem_gb=config.DEFAULT_MEMORY_MIN_GB, + iterfield=["atlas", "in_file"], ) # fmt:off workflow.connect([ - (inputnode, score_hvoxf, [ - ("source_file", "source_file"), - ("score_hvoxf", "in_file"), - ]), - (inputnode, scrub_hvoxf, [ - ("source_file", "source_file"), - ("scrub_hvoxf", "in_file"), - ]), - (inputnode, score_sc217, [ - ("source_file", "source_file"), - ("score_sc217", "in_file"), - ]), - (inputnode, score_sc207, [ - ("source_file", "source_file"), - ("score_sc207", "in_file"), - ]), - (inputnode, scrub_sc207, [ - ("source_file", "source_file"), - ("scrub_sc207", "in_file"), - ]), - (inputnode, scrub_sc217, [ + (inputnode, ds_parcellated_input, [ ("source_file", "source_file"), - ("scrub_sc217", "in_file"), - ]), - (inputnode, score_sc417, [ - ("source_file", "source_file"), - ("score_sc417", "in_file"), - ]), - (inputnode, scrub_sc417, [ - ("source_file", "source_file"), - ("scrub_sc417", "in_file"), - ]), - (inputnode, score_sc407, [ - ("source_file", "source_file"), - ("score_sc407", "in_file"), - ]), - (inputnode, scrub_sc407, [ - ("source_file", "source_file"), - ("scrub_sc407", "in_file"), + ("atlas_names", "atlas"), + (parcellated_input, "in_file"), ]), ]) # fmt:on + # Now prepare to write out primary imaging derivatives + timeseries_metadata = { + "SkullStripped": False, + "RepetitionTime": metadata.get("RepetitionTime"), + "RepetitionTimePreparation": metadata.get("RepetitionTimePreparation"), + "TaskName": metadata.get("TaskName"), + } + + BASE_INPUT_FIELDS = { + "asl": { + "desc": "preproc", + "suffix": "asl", + **timeseries_metadata, + }, + "aslref": { + "suffix": "aslref", + "dismiss_entities": ("echo",), + }, + "asl_mask": { + "desc": "brain", + "suffix": "mask", + "dismiss_entities": ("echo",), + }, + "cbf": { + "suffix": "cbf", + }, + "meancbf": { + "desc": "mean", + "suffix": "cbf", + }, + "score": { + "desc": "score", + "suffix": "cbf", + }, + "avgscore": { + "desc": "meanScore", + "suffix": "cbf", + }, + "scrub": { + "desc": "scrub", + "suffix": "cbf", + }, + "basil": { + "desc": "basil", + "suffix": "cbf", + }, + "pv": { + "desc": "pvGM", + "suffix": "cbf", + }, + "pvwm": { + "desc": "pvWM", + "suffix": "cbf", + }, + "att": { + "desc": "bat", + "suffix": "cbf", + }, + } + + base_inputs = ["asl", "aslref", "asl_mask", "cbf", "meancbf"] + if scorescrub: + base_inputs += ["score", "avgscore", "scrub"] + if basil: - basil_hvoxf = pe.Node( + base_inputs += ["basil", "pv", "pvwm", "att"] + + # Native-space derivatives + if nonstd_spaces.intersection(("func", "run", "asl", "sbref")): + for base_input in base_inputs: + base_input_native = f"{base_input}_native" + ds_base_input_native = pe.Node( + DerivativesDataSink( + base_directory=output_dir, + compress=True, + **BASE_INPUT_FIELDS[base_input], + ), + name=f"ds_{base_input_native}", + run_without_submitting=True, + mem_gb=config.DEFAULT_MEMORY_MIN_GB, + ) + + # fmt:off + workflow.connect([ + (inputnode, ds_base_input_native, [ + ("source_file", "source_file"), + (base_input_native, "in_file"), + ]), + ]) + # fmt:on + + # The mask file gets one extra bit of metadata. + if base_input == "asl_mask": + # fmt:off + workflow.connect([(raw_sources, ds_base_input_native, [("out", "RawSources")])]) + # fmt:on + + # T1w-space derivatives + if nonstd_spaces.intersection(("T1w", "anat")): + for base_input in base_inputs: + base_input_t1 = f"{base_input}_t1" + ds_base_input_t1 = pe.Node( + DerivativesDataSink( + base_directory=output_dir, + compress=True, + space="T1w", + **BASE_INPUT_FIELDS[base_input], + ), + name=f"ds_{base_input_t1}", + run_without_submitting=True, + mem_gb=config.DEFAULT_MEMORY_MIN_GB, + ) + + # fmt:off + workflow.connect([ + (inputnode, ds_base_input_t1, [ + ("source_file", "source_file"), + (base_input_t1, "in_file"), + ]), + ]) + # fmt:on + + # The mask file gets one extra bit of metadata. + if base_input == "asl_mask": + # fmt:off + workflow.connect([(raw_sources, ds_base_input_t1, [("out", "RawSources")])]) + # fmt:on + + if getattr(spaces, "_cached") is None: + return workflow + + # Standard-space derivatives + from niworkflows.interfaces.space import SpaceDataSource + + spacesource = pe.Node(SpaceDataSource(), name="spacesource", run_without_submitting=True) + spacesource.iterables = ( + "in_tuple", + [(s.fullname, s.spec) for s in spaces.cached.get_standard(dim=(3,))], + ) + + select_std = pe.Node( + KeySelect(fields=[f"{base_input}_std" for base_input in base_inputs] + ["template"]), + name="select_std", + run_without_submitting=True, + mem_gb=config.DEFAULT_MEMORY_MIN_GB, + ) + + # fmt:off + workflow.connect([ + (inputnode, select_std, [ + ("template", "template"), + ("spatial_reference", "keys"), + ]), + (spacesource, select_std, [("uid", "key")]), + ]) + # fmt:on + + for base_input in base_inputs: + base_input_std = f"{base_input}_std" + ds_base_input_std = pe.Node( DerivativesDataSink( base_directory=output_dir, - atlas="HarvardOxford", - desc="mean", - suffix="basil", - compress=False, + compress=True, + **BASE_INPUT_FIELDS[base_input], ), - name="basil_hvoxf", + name=f"ds_{base_input_std}", run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - pvc_hvoxf = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="HarvardOxford", - desc="mean", - suffix="pvc", - compress=False, - ), - name="pvc_hvoxf", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - basil_sc207 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer200x7", - desc="mean", - suffix="basil", - compress=False, - ), - name="basil_sc207", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - pvc_sc207 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer200x7", - desc="mean", - suffix="pvc", - compress=False, - ), - name="pvc_sc207", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - basil_sc217 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer200x17", - desc="mean", - suffix="basil", - compress=False, - ), - name="basil_sc217", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - pvc_sc217 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer200x17", - desc="mean", - suffix="pvc", - compress=False, - ), - name="pvc_sc217", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - basil_sc407 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer400x7", - desc="mean", - suffix="basil", - compress=False, - ), - name="basil_sc407", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - pvc_sc407 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer400x7", - desc="mean", - suffix="pvc", - compress=False, - ), - name="pvc_sc407", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - basil_sc417 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer400x17", - desc="mean", - suffix="basil", - compress=False, - ), - name="basil_sc417", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - pvc_sc417 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer400x17", - desc="mean", - suffix="pvc", - compress=False, - ), - name="pvc_sc417", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - - # fmt:off - workflow.connect([ - (inputnode, basil_hvoxf, [ - ("source_file", "source_file"), - ("basil_hvoxf", "in_file"), - ]), - (inputnode, pvc_hvoxf, [ - ("source_file", "source_file"), - ("pvc_hvoxf", "in_file"), - ]), - (inputnode, basil_sc207, [ - ("source_file", "source_file"), - ("basil_sc207", "in_file"), - ]), - (inputnode, pvc_sc207, [ - ("source_file", "source_file"), - ("pvc_sc207", "in_file"), - ]), - (inputnode, basil_sc217, [ - ("source_file", "source_file"), - ("basil_sc217", "in_file"), - ]), - (inputnode, pvc_sc217, [ - ("source_file", "source_file"), - ("pvc_sc217", "in_file"), - ]), - (inputnode, basil_sc407, [ - ("source_file", "source_file"), - ("basil_sc407", "in_file"), - ]), - (inputnode, pvc_sc407, [ - ("source_file", "source_file"), - ("pvc_sc217", "in_file"), - ]), - (inputnode, basil_sc417, [ - ("source_file", "source_file"), - ("basil_sc417", "in_file"), - ]), - (inputnode, pvc_sc417, [ - ("source_file", "source_file"), - ("pvc_sc417", "in_file"), - ]), - ]) - # fmt:on - - if nonstd_spaces.intersection(("func", "run", "asl", "sbref")): - ds_asl_native = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="preproc", - compress=True, - SkullStripped=False, - RepetitionTime=metadata.get("RepetitionTime"), - RepetitionTimePreparation=metadata.get("RepetitionTimePreparation"), - TaskName=metadata.get("TaskName"), - ), - name="ds_asl_native", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - ds_asl_native_ref = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - suffix="aslref", - compress=True, - dismiss_entities=("echo",), - ), - name="ds_asl_native_ref", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - ds_asl_mask_native = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="brain", - suffix="mask", - compress=True, - dismiss_entities=("echo",), - ), - name="ds_asl_mask_native", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - cbfnative = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - suffix="cbf", - compress=True, - ), - name="cbfnative", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - meancbfnative = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="mean", - suffix="cbf", - compress=True, - ), - name="meancbfnative", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - - # fmt:off - workflow.connect([ - (inputnode, ds_asl_native, [ - ("source_file", "source_file"), - ("asl_native", "in_file"), - ]), - (inputnode, ds_asl_native_ref, [ - ("source_file", "source_file"), - ("asl_native_ref", "in_file"), - ]), - (inputnode, ds_asl_mask_native, [ - ("source_file", "source_file"), - ("asl_mask_native", "in_file"), - ]), - (inputnode, cbfnative, [ - ("source_file", "source_file"), - ("cbf", "in_file"), - ]), - (inputnode, meancbfnative, [ - ("source_file", "source_file"), - ("meancbf", "in_file"), - ]), - ]) - # fmt:on - - if scorescrub: - scorenative = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="score", - suffix="cbf", - compress=True, - ), - name="scorenative", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - meanscorenative = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="meanScore", - suffix="cbf", - compress=True, - ), - name="meanscorenative", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - - scrubnative = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="scrub", - suffix="cbf", - compress=True, - ), - name="scrubnative", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - - # fmt:off - workflow.connect([ - (inputnode, scorenative, [ - ("source_file", "source_file"), - ("score", "in_file"), - ]), - (inputnode, meanscorenative, [ - ("source_file", "source_file"), - ("avgscore", "in_file"), - ]), - (inputnode, scrubnative, [ - ("source_file", "source_file"), - ("scrub", "in_file"), - ]), - ]) - # fmt:on - - if basil: - basilnative = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="basil", - suffix="cbf", - compress=True, - ), - name="basilnative", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - pvnative = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="pvGM", - suffix="cbf", - compress=True, - ), - name="pvcnative", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - pvnativewm = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="pvWM", - suffix="cbf", - compress=True, - ), - name="pvcwmnative", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - attnative = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="bat", - suffix="cbf", - compress=True, - ), - name="attcnative", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - - # fmt:off - workflow.connect([ - (inputnode, basilnative, [ - ("source_file", "source_file"), - ("basil", "in_file"), - ]), - (inputnode, pvnative, [ - ("source_file", "source_file"), - ("pv", "in_file"), - ]), - (inputnode, pvnativewm, [ - ("source_file", "source_file"), - ("pvwm", "in_file"), - ]), - (inputnode, attnative, [ - ("source_file", "source_file"), - ("att", "in_file"), - ]), - (raw_sources, ds_asl_mask_native, [("out", "RawSources")]), - ]) - # fmt:on - - # Resample to T1w space - if nonstd_spaces.intersection(("T1w", "anat")): - ds_asl_t1 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - space="T1w", - desc="preproc", - compress=True, - SkullStripped=False, - RepetitionTime=metadata.get("RepetitionTime"), - RepetitionTimePreparation=metadata.get("RepetitionTimePreparation"), - TaskName=metadata.get("TaskName"), - dismiss_entities=("echo",), - ), - name="ds_asl_t1", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - ds_asl_t1_ref = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - space="T1w", - suffix="aslref", - compress=True, - dismiss_entities=("echo",), - ), - name="ds_asl_t1_ref", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - ds_asl_mask_t1 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - space="T1w", - desc="brain", - suffix="mask", - compress=True, - dismiss_entities=("echo",), - ), - name="ds_asl_mask_t1", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - cbfnativet1 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - space="T1w", - suffix="cbf", - compress=True, - ), - name="cbfnativet1", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - meancbfnativet1 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - space="T1w", - desc="mean", - suffix="cbf", - compress=True, - ), - name="meancbfnativet1", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - - # fmt:off - workflow.connect([ - (inputnode, ds_asl_t1, [ - ("source_file", "source_file"), - ("asl_t1", "in_file"), - ]), - (inputnode, ds_asl_t1_ref, [ - ("source_file", "source_file"), - ("asl_t1_ref", "in_file"), - ]), - (inputnode, ds_asl_mask_t1, [ - ("source_file", "source_file"), - ("asl_mask_t1", "in_file"), - ]), - (inputnode, cbfnativet1, [ - ("source_file", "source_file"), - ("cbf_t1", "in_file"), - ]), - (inputnode, meancbfnativet1, [ - ("source_file", "source_file"), - ("meancbf_t1", "in_file"), - ]), - ]) - # fmt:on - - if scorescrub: - scorenativet1 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - space="T1w", - desc="score", - suffix="cbf", - compress=True, - ), - name="scorenativet1", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - meanscorenativet1 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - space="T1w", - desc="meanScore", - suffix="cbf", - compress=True, - ), - name="meanscorenativet1", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - scrubnativet1 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - space="T1w", - desc="scrub", - suffix="cbf", - compress=True, - ), - name="scrubnativet1", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - - # fmt:off - workflow.connect([ - (inputnode, scorenativet1, [ - ("source_file", "source_file"), - ("score_t1", "in_file"), - ]), - (inputnode, meanscorenativet1, [ - ("source_file", "source_file"), - ("avgscore_t1", "in_file"), - ]), - (inputnode, scrubnativet1, [ - ("source_file", "source_file"), - ("scrub_t1", "in_file"), - ]), - ]) - # fmt:on - - if basil: - basilnativet1 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - space="T1w", - desc="basil", - suffix="cbf", - compress=True, - ), - name="basilnativet1", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - pvnativet1 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - space="T1w", - desc="pvGM", - suffix="cbf", - compress=True, - ), - name="pvcnativet1", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - pvnativetwm1 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - space="T1w", - desc="pvWM", - suffix="cbf", - compress=True, - ), - name="pvcnativet1wm", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - attnativet1 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - space="T1w", - desc="bat", - suffix="cbf", - compress=True, - ), - name="attnativet1", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - - # fmt:off - workflow.connect([ - (inputnode, basilnativet1, [ - ("source_file", "source_file"), - ("basil_t1", "in_file"), - ]), - (inputnode, pvnativet1, [ - ("source_file", "source_file"), - ("pv_t1", "in_file"), - ]), - (inputnode, pvnativetwm1, [ - ("source_file", "source_file"), - ("pvwm_t1", "in_file"), - ]), - (inputnode, attnativet1, [ - ("source_file", "source_file"), - ("att_t1", "in_file"), - ]), - ]) - # fmt:on - - # fmt:off - workflow.connect([(raw_sources, ds_asl_mask_t1, [("out", "RawSources")])]) - # fmt:on - - if getattr(spaces, "_cached") is None: - return workflow - - # Store resamplings in standard spaces when listed in --output-spaces - if spaces.cached.references: - from aslprep.niworkflows.interfaces.space import SpaceDataSource - - spacesource = pe.Node(SpaceDataSource(), name="spacesource", run_without_submitting=True) - spacesource.iterables = ( - "in_tuple", - [(s.fullname, s.spec) for s in spaces.cached.get_standard(dim=(3,))], - ) - out_names = [ - "template", - "asl_std", - "asl_std_ref", - "asl_mask_std", - "cbf_std", - "meancbf_std", - ] - if scorescrub: - out_names = out_names + ["score_std", "avgscore_std", "scrub_std"] - - if basil: - out_names = out_names + ["basil_std", "pv_std", "pvwm_std", "att_std"] - - select_std = pe.Node( - KeySelect(fields=out_names), - name="select_std", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - ds_asl_std = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="preproc", - compress=True, - SkullStripped=False, - RepetitionTime=metadata.get("RepetitionTime"), - RepetitionTimePreparation=metadata.get("RepetitionTimePreparation"), - TaskName=metadata.get("TaskName"), - dismiss_entities=("echo",), - ), - name="ds_asl_std", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - ds_asl_std_ref = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - suffix="aslref", - compress=True, - dismiss_entities=("echo",), - ), - name="ds_asl_std_ref", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - ds_asl_mask_std = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="brain", - suffix="mask", - compress=True, - dismiss_entities=("echo",), - ), - name="ds_asl_mask_std", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - cbfstd = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - suffix="cbf", - compress=True, - ), - name="cbfstd", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - meancbfstd = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="mean", - suffix="cbf", - compress=True, - ), - name="meancbfstd", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - - # fmt:off - workflow.connect([ - (inputnode, ds_asl_std, [("source_file", "source_file")]), - (inputnode, ds_asl_std_ref, [("source_file", "source_file")]), - (inputnode, ds_asl_mask_std, [("source_file", "source_file")]), - (inputnode, cbfstd, [("source_file", "source_file")]), - (inputnode, meancbfstd, [("source_file", "source_file")]), - (inputnode, select_std, [ - ("asl_std", "asl_std"), - ("asl_std_ref", "asl_std_ref"), - ("asl_mask_std", "asl_mask_std"), - ("cbf_std", "cbf_std"), - ("meancbf_std", "meancbf_std"), - ("template", "template"), - ("spatial_reference", "keys"), - ]), - (spacesource, select_std, [("uid", "key")]), - (select_std, ds_asl_std, [("asl_std", "in_file")]), - (spacesource, ds_asl_std, [ - ("space", "space"), - ("cohort", "cohort"), - ("resolution", "resolution"), - ("density", "density"), - ]), - (select_std, ds_asl_std_ref, [("asl_std_ref", "in_file")]), - (spacesource, ds_asl_std_ref, [ - ("space", "space"), - ("cohort", "cohort"), - ("resolution", "resolution"), - ("density", "density"), - ]), - (select_std, ds_asl_mask_std, [("asl_mask_std", "in_file")]), - (spacesource, ds_asl_mask_std, [ - ("space", "space"), - ("cohort", "cohort"), - ("resolution", "resolution"), - ("density", "density"), - ]), - (select_std, cbfstd, [("cbf_std", "in_file")]), - (spacesource, cbfstd, [ - ("space", "space"), - ("cohort", "cohort"), - ("resolution", "resolution"), - ("density", "density"), - ]), - (select_std, meancbfstd, [("meancbf_std", "in_file")]), - (spacesource, meancbfstd, [ - ("space", "space"), - ("cohort", "cohort"), - ("resolution", "resolution"), - ("density", "density"), - ]), - (raw_sources, ds_asl_mask_std, [("out", "RawSources")]), - ]) - # fmt:on - - if scorescrub: - scorestd = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="score", - suffix="cbf", - compress=True, - ), - name="scorestd", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - meanscorestd = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="meanScore", - suffix="cbf", - compress=True, - ), - name="meanscorestd", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - scrubstd = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="scrub", - suffix="cbf", - compress=True, - ), - name="scrubstd", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - - # fmt:off - workflow.connect([ - (inputnode, scorestd, [("source_file", "source_file")]), - (inputnode, meanscorestd, [("source_file", "source_file")]), - (inputnode, scrubstd, [("source_file", "source_file")]), - (inputnode, select_std, [ - ("score_std", "score_std"), - ("avgscore_std", "avgscore_std"), - ("scrub_std", "scrub_std"), - ]), - (select_std, scorestd, [("score_std", "in_file")]), - (spacesource, scorestd, [ - ("space", "space"), - ("cohort", "cohort"), - ("resolution", "resolution"), - ("density", "density"), - ]), - (select_std, meanscorestd, [("avgscore_std", "in_file")]), - (spacesource, meanscorestd, [ - ("space", "space"), - ("cohort", "cohort"), - ("resolution", "resolution"), - ("density", "density"), - ]), - (select_std, scrubstd, [("scrub_std", "in_file")]), - (spacesource, scrubstd, [ - ("space", "space"), - ("cohort", "cohort"), - ("resolution", "resolution"), - ("density", "density"), - ]), - ]) - # fmt:on - - if basil: - basilstd = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="basil", - suffix="cbf", - compress=True, - ), - name="basilstd", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - pvstd = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="pvGM", - suffix="cbf", - compress=True, - ), - name="pvcstd", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - pvstdwm = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="pvWM", - suffix="cbf", - compress=True, - ), - name="pvcstdwm", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - attstd = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="bat", - suffix="cbf", - compress=True, - ), - name="attstd", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - - # fmt:off - workflow.connect([ - (inputnode, basilstd, [("source_file", "source_file")]), - (inputnode, pvstd, [("source_file", "source_file")]), - (inputnode, pvstdwm, [("source_file", "source_file")]), - (inputnode, attstd, [("source_file", "source_file")]), - (inputnode, select_std, [ - ("basil_std", "basil_std"), - ("pv_std", "pv_std"), - ("pvwm_std", "pvwm_std"), - ("att_std", "att_std"), - ]), - (select_std, basilstd, [("basil_std", "in_file")]), - (spacesource, basilstd, [ - ("space", "space"), - ("cohort", "cohort"), - ("resolution", "resolution"), - ("density", "density"), - ]), - (select_std, pvstd, [("pv_std", "in_file")]), - (spacesource, pvstd, [ - ("space", "space"), - ("cohort", "cohort"), - ("resolution", "resolution"), - ("density", "density"), - ]), - (select_std, pvstdwm, [("pvwm_std", "in_file")]), - (spacesource, pvstdwm, [ - ("space", "space"), - ("cohort", "cohort"), - ("resolution", "resolution"), - ("density", "density"), - ]), - (select_std, attstd, [("att_std", "in_file")]), - (spacesource, attstd, [ - ("space", "space"), - ("cohort", "cohort"), - ("resolution", "resolution"), - ("density", "density"), - ]), - ]) - # fmt:on - - return workflow - - -def init_geasl_derivatives_wf( - bids_root, - metadata, - output_dir, - spaces, - scorescrub=False, - basil=False, - name="asl_derivatives_wf", -): - """Set up a battery of datasinks to store derivatives in the right location, for GE data. - - Parameters - ---------- - bids_root : :obj:`str` - Original BIDS dataset path. - cifti_output : :obj:`bool` - Whether the ``--cifti-output`` flag was set. - freesurfer : :obj:`bool` - Whether FreeSurfer anatomical processing was run. - metadata : :obj:`dict` - Metadata dictionary associated to the ASL run. - output_dir : :obj:`str` - Where derivatives should be written out to. - spaces : :py:class:`~niworkflows.utils.spaces.SpatialReferences` - A container for storing, organizing, and parsing spatial normalizations. Composed of - :py:class:`~niworkflows.utils.spaces.Reference` objects representing spatial references. - Each ``Reference`` contains a space, which is a string of either TemplateFlow template IDs - (e.g., ``MNI152Lin``, ``MNI152NLin6Asym``, ``MNIPediatricAsym``), nonstandard references - (e.g., ``T1w`` or ``anat``, ``sbref``, ``run``, etc.), or a custom template located in - the TemplateFlow root directory. Each ``Reference`` may also contain a spec, which is a - dictionary with template specifications (e.g., a specification of ``{'resolution': 2}`` - would lead to resampling on a 2mm resolution of the space). - name : :obj:`str` - This workflow's identifier (default: ``func_derivatives_wf``). - """ - nonstd_spaces = set(spaces.get_nonstandard()) - workflow = Workflow(name=name) - - inputnode = pe.Node( - niu.IdentityInterface( - fields=[ - "asl_mask_std", - "asl_mask_t1", - "asl_std", - "asl_std_ref", - "asl_t1", - "asl_t1_ref", - "asl_native", - "asl_native_ref", - "asl_mask_native", - "source_file", - "itk_asl_to_t1", - "itk_t1_to_asl", - "template", - "spatial_reference", - "cbf", - "meancbf", - "score", - "avgscore", - "scrub", - "basil", - "pv", - "pvwm", - "cbf_t1", - "meancbf_t1", - "att_t1", - "score_t1", - "avgscore_t1", - "scrub_t1", - "basil_t1", - "pv_t1", - "pvwm_t1", - "cbf_std", - "meancbf_std", - "score_std", - "avgscore_std", - "scrub_std", - "basil_std", - "pv_std", - "pvwm_std", - "att", - "att_std", - "qc_file", - "cbf_hvoxf", - "score_hvoxf", - "scrub_hvoxf", - "basil_hvoxf", - "pvc_hvoxf", - "cbf_sc207", - "score_sc207", - "scrub_sc207", - "basil_sc207", - "pvc_sc207", - "cbf_sc217", - "score_sc217", - "scrub_sc217", - "basil_sc217", - "pvc_sc217", - "cbf_sc407", - "score_sc407", - "scrub_sc407", - "basil_sc407", - "pvc_sc407", - "cbf_sc417", - "score_sc417", - "scrub_sc417", - "basil_sc417", - "pvc_sc417", - ], - ), - name="inputnode", - ) - - raw_sources = pe.Node(niu.Function(function=_bids_relative), name="raw_sources") - raw_sources.inputs.bids_root = bids_root - - # fmt:off - workflow.connect([(inputnode, raw_sources, [("source_file", "in_files")])]) - # fmt:on - - qcfile = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="qualitycontrol", - suffix="cbf", - compress=False, - ), - name="qcfile", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - # fmt:off - workflow.connect([ - (inputnode, qcfile, [ - ("source_file", "source_file"), - ("qc_file", "in_file"), - ]), - ]) - # fmt:on - - # write transform matrix file between asl native space and T1w - ds_t1w_to_asl_xform = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - to="scanner", - mode="image", - suffix="xfm", - extension=".txt", - dismiss_entities=("echo",), - **{"from": "T1w"}, - ), - name="ds_t1w_to_asl_xform", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - - # fmt:off - workflow.connect([ - (inputnode, ds_t1w_to_asl_xform, [ - ("source_file", "source_file"), - ("itk_asl_to_t1", "in_file"), - ]), - ]) - # fmt:on - - ds_asl_to_t1w_xform = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - to="T1w", - mode="image", - suffix="xfm", - extension=".txt", - dismiss_entities=("echo",), - **{"from": "scanner"}, - ), - name="ds_asl_to_t1w_xform", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - - # fmt:off - workflow.connect([ - (inputnode, ds_asl_to_t1w_xform, [ - ("source_file", "source_file"), - ("itk_t1_to_asl", "in_file"), - ]), - ]) - # fmt:on - - cbf_hvoxf = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="HarvardOxford", - desc="mean", - suffix="cbf", - compress=False, - ), - name="cbf_hvoxf", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - cbf_sc207 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer200x7", - desc="mean", - suffix="cbf", - compress=False, - ), - name="cbf_sc207", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - cbf_sc217 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer200x17", - desc="mean", - suffix="cbf", - compress=False, - ), - name="cbf_sc217", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - cbf_sc407 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer400x7", - desc="mean", - suffix="cbf", - compress=False, - ), - name="cbf_sc407", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - cbf_sc417 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer400x17", - desc="mean", - suffix="cbf", - compress=False, - ), - name="cbf_sc417", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - - # fmt:off - workflow.connect([ - (inputnode, cbf_hvoxf, [ - ("source_file", "source_file"), - ("cbf_hvoxf", "in_file"), - ]), - (inputnode, cbf_sc207, [ - ("source_file", "source_file"), - ("cbf_sc207", "in_file"), - ]), - (inputnode, cbf_sc217, [ - ("source_file", "source_file"), - ("cbf_sc217", "in_file"), - ]), - (inputnode, cbf_sc407, [ - ("source_file", "source_file"), - ("cbf_sc407", "in_file"), - ]), - (inputnode, cbf_sc417, [ - ("source_file", "source_file"), - ("cbf_sc417", "in_file"), - ]), - ]) - # fmt:on - - if scorescrub: - score_hvoxf = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="HarvardOxford", - desc="mean", - suffix="score", - compress=False, - ), - name="score_hvoxf", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - scrub_hvoxf = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="HarvardOxford", - desc="mean", - suffix="scrub", - compress=False, - ), - name="scrub_hvoxf", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - score_sc207 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer200x7", - desc="mean", - suffix="score", - compress=False, - ), - name="score_sc207", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - scrub_sc207 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer200x7", - desc="mean", - suffix="scrub", - compress=False, - ), - name="scrub_sc207", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - score_sc217 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer200x17", - desc="mean", - suffix="score", - compress=False, - ), - name="score_sc217", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - scrub_sc217 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer200x17", - desc="mean", - suffix="scrub", - compress=False, - ), - name="scrub_sc217", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - score_sc407 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer400x7", - desc="mean", - suffix="score", - compress=False, - ), - name="score_sc407", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - scrub_sc407 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer400x7", - desc="mean", - suffix="scrub", - compress=False, - ), - name="scrub_sc407", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - score_sc417 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer400x17", - desc="mean", - suffix="score", - compress=False, - ), - name="score_sc417", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - scrub_sc417 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer400x17", - desc="mean", - suffix="scrub", - compress=False, - ), - name="scrub_sc417", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - - # fmt:off - workflow.connect([ - (inputnode, score_hvoxf, [ - ("source_file", "source_file"), - ("score_hvoxf", "in_file"), - ]), - (inputnode, scrub_hvoxf, [ - ("source_file", "source_file"), - ("scrub_hvoxf", "in_file"), - ]), - (inputnode, score_sc217, [ - ("source_file", "source_file"), - ("score_sc217", "in_file"), - ]), - (inputnode, score_sc207, [ - ("source_file", "source_file"), - ("score_sc207", "in_file"), - ]), - (inputnode, scrub_sc207, [ - ("source_file", "source_file"), - ("scrub_sc207", "in_file"), - ]), - (inputnode, scrub_sc217, [ - ("source_file", "source_file"), - ("scrub_sc217", "in_file"), - ]), - (inputnode, score_sc417, [ - ("source_file", "source_file"), - ("score_sc417", "in_file"), - ]), - (inputnode, scrub_sc417, [ - ("source_file", "source_file"), - ("scrub_sc417", "in_file"), - ]), - (inputnode, score_sc407, [ - ("source_file", "source_file"), - ("score_sc407", "in_file"), - ]), - (inputnode, scrub_sc407, [ - ("source_file", "source_file"), - ("scrub_sc407", "in_file"), - ]), - ]) - # fmt:on - - if basil: - basil_hvoxf = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="HarvardOxford", - desc="mean", - suffix="basil", - compress=False, - ), - name="basil_hvoxf", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - pvc_hvoxf = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="HarvardOxford", - desc="mean", - suffix="pvc", - compress=False, - ), - name="pvc_hvoxf", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - basil_sc207 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer200x7", - desc="mean", - suffix="basil", - compress=False, - ), - name="basil_sc207", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - pvc_sc207 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer200x7", - desc="mean", - suffix="pvc", - compress=False, - ), - name="pvc_sc207", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - basil_sc217 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer200x17", - desc="mean", - suffix="basil", - compress=False, - ), - name="basil_sc217", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - pvc_sc217 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer200x17", - desc="mean", - suffix="pvc", - compress=False, - ), - name="pvc_sc217", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - basil_sc407 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer400x7", - desc="mean", - suffix="basil", - compress=False, - ), - name="basil_sc407", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - pvc_sc407 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer400x7", - desc="mean", - suffix="pvc", - compress=False, - ), - name="pvc_sc407", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - basil_sc417 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer400x17", - desc="mean", - suffix="basil", - compress=False, - ), - name="basil_sc417", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - pvc_sc417 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - atlas="schaefer400x17", - desc="mean", - suffix="pvc", - compress=False, - ), - name="pvc_sc417", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - - # fmt:off - workflow.connect([ - (inputnode, basil_hvoxf, [ - ("source_file", "source_file"), - ("basil_hvoxf", "in_file"), - ]), - (inputnode, pvc_hvoxf, [ - ("source_file", "source_file"), - ("pvc_hvoxf", "in_file"), - ]), - (inputnode, basil_sc207, [ - ("source_file", "source_file"), - ("basil_sc207", "in_file"), - ]), - (inputnode, pvc_sc207, [ - ("source_file", "source_file"), - ("pvc_sc207", "in_file"), - ]), - (inputnode, basil_sc217, [ - ("source_file", "source_file"), - ("basil_sc217", "in_file"), - ]), - (inputnode, pvc_sc217, [ - ("source_file", "source_file"), - ("pvc_sc217", "in_file"), - ]), - (inputnode, basil_sc407, [ - ("source_file", "source_file"), - ("basil_sc407", "in_file"), - ]), - (inputnode, pvc_sc407, [ - ("source_file", "source_file"), - ("pvc_sc217", "in_file"), - ]), - (inputnode, basil_sc417, [ - ("source_file", "source_file"), - ("basil_sc417", "in_file"), - ]), - (inputnode, pvc_sc417, [ - ("source_file", "source_file"), - ("pvc_sc417", "in_file"), - ]), - ]) - # fmt:on - - if nonstd_spaces.intersection(("func", "run", "asl", "sbref")): - ds_asl_native = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="preproc", - compress=True, - SkullStripped=False, - RepetitionTime=metadata.get("RepetitionTime"), - RepetitionTimePreparation=metadata.get("RepetitionTimePreparation"), - TaskName=metadata.get("TaskName"), - ), - name="ds_asl_native", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - ds_asl_native_ref = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - suffix="aslref", - compress=True, - dismiss_entities=("echo",), - ), - name="ds_asl_native_ref", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - ds_asl_mask_native = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="brain", - suffix="mask", - compress=True, - dismiss_entities=("echo",), - ), - name="ds_asl_mask_native", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - cbfnative = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - suffix="cbf", - compress=True, - ), - name="cbfnative", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - meancbfnative = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="mean", - suffix="cbf", - compress=True, - ), - name="meancbfnative", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - - # fmt:off - workflow.connect([ - (inputnode, ds_asl_native, [ - ("source_file", "source_file"), - ("asl_native", "in_file"), - ]), - (inputnode, ds_asl_native_ref, [ - ("source_file", "source_file"), - ("asl_native_ref", "in_file"), - ]), - (inputnode, ds_asl_mask_native, [ - ("source_file", "source_file"), - ("asl_mask_native", "in_file"), - ]), - (inputnode, cbfnative, [ - ("source_file", "source_file"), - ("cbf", "in_file"), - ]), - (inputnode, meancbfnative, [ - ("source_file", "source_file"), - ("meancbf", "in_file"), - ]), - ]) - # fmt:on - - if scorescrub: - scorenative = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="score", - suffix="cbf", - compress=True, - ), - name="scorenative", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - meanscorenative = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="meanScore", - suffix="cbf", - compress=True, - ), - name="meanscorenative", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - scrubnative = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="scrub", - suffix="cbf", - compress=True, - ), - name="scrubnative", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - - # fmt:off - workflow.connect([ - (inputnode, scorenative, [ - ("source_file", "source_file"), - ("score", "in_file"), - ]), - (inputnode, meanscorenative, [ - ("source_file", "source_file"), - ("avgscore", "in_file"), - ]), - (inputnode, scrubnative, [ - ("source_file", "source_file"), - ("scrub", "in_file"), - ]), - ]) - # fmt:on - - if basil: - basilnative = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="basil", - suffix="cbf", - compress=True, - ), - name="basilnative", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - pvnative = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="pvGM", - suffix="cbf", - compress=True, - ), - name="pvcnative", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - pvnativewm = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="pvWM", - suffix="cbf", - compress=True, - ), - name="pvcnativewm", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - attnative = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="bat", - suffix="cbf", - compress=True, - ), - name="attcnative", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - - # fmt:off - workflow.connect([ - (inputnode, basilnative, [ - ("source_file", "source_file"), - ("basil", "in_file"), - ]), - (inputnode, pvnative, [ - ("source_file", "source_file"), - ("pv", "in_file"), - ]), - (inputnode, pvnativewm, [ - ("source_file", "source_file"), - ("pvwm", "in_file"), - ]), - (inputnode, attnative, [ - ("source_file", "source_file"), - ("att", "in_file"), - ]), - (raw_sources, ds_asl_mask_native, [("out", "RawSources")]), - ]) - # fmt:on - - # Resample to T1w space - if nonstd_spaces.intersection(("T1w", "anat")): - ds_asl_t1 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - space="T1w", - desc="preproc", - compress=True, - SkullStripped=False, - RepetitionTime=metadata.get("RepetitionTime"), - RepetitionTimePreparation=metadata.get("RepetitionTimePreparation"), - TaskName=metadata.get("TaskName"), - dismiss_entities=("echo",), - ), - name="ds_asl_t1", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - ds_asl_t1_ref = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - space="T1w", - suffix="aslref", - compress=True, - dismiss_entities=("echo",), - ), - name="ds_asl_t1_ref", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - ds_asl_mask_t1 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - space="T1w", - desc="brain", - suffix="mask", - compress=True, - dismiss_entities=("echo",), - ), - name="ds_asl_mask_t1", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - cbfnativet1 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - suffix="cbf", - space="T1w", - compress=True, - ), - name="cbfnativet1", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - meancbfnativet1 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="mean", - suffix="cbf", - space="T1w", - compress=True, - ), - name="meancbfnativet1", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - - # fmt:off - workflow.connect([ - (inputnode, ds_asl_t1, [ - ("source_file", "source_file"), - ("asl_t1", "in_file"), - ]), - (inputnode, ds_asl_t1_ref, [ - ("source_file", "source_file"), - ("asl_t1_ref", "in_file"), - ]), - (inputnode, ds_asl_mask_t1, [ - ("source_file", "source_file"), - ("asl_mask_t1", "in_file"), - ]), - (inputnode, cbfnativet1, [ - ("source_file", "source_file"), - ("cbf_t1", "in_file"), - ]), - (inputnode, meancbfnativet1, [ - ("source_file", "source_file"), - ("meancbf_t1", "in_file"), - ]), - ]) - # fmt:on - - if scorescrub: - scorenativet1 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="score", - suffix="cbf", - space="T1w", - compress=True, - ), - name="scorenativet1", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - meanscorenativet1 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - suffix="cbf", - desc="meanScore", - space="T1w", - compress=True, - ), - name="meanscorenativet1", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - scrubnativet1 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="scrub", - suffix="cbf", - space="T1w", - compress=True, - ), - name="scrubnativet1", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - - # fmt:off - workflow.connect([ - (inputnode, scorenativet1, [ - ("source_file", "source_file"), - ("score_t1", "in_file"), - ]), - (inputnode, meanscorenativet1, [ - ("source_file", "source_file"), - ("avgscore_t1", "in_file"), - ]), - (inputnode, scrubnativet1, [ - ("source_file", "source_file"), - ("scrub_t1", "in_file"), - ]), - ]) - # fmt:on - - if basil: - basilnativet1 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="basil", - suffix="cbf", - space="T1w", - compress=True, - ), - name="basilnativet1", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - pvnativet1 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="pvGM", - suffix="cbf", - space="T1w", - compress=True, - ), - name="pvcnativet1", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - pvnativet1wm = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="pvWM", - suffix="cbf", - space="T1w", - compress=True, - ), - name="pvcnativet1wm", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - attnativet1 = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="bat", - suffix="cbf", - space="T1w", - compress=True, - ), - name="attnativet1", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - - # fmt:off - workflow.connect([ - (inputnode, basilnativet1, [ - ("source_file", "source_file"), - ("basil_t1", "in_file"), - ]), - (inputnode, pvnativet1, [ - ("source_file", "source_file"), - ("pv_t1", "in_file"), - ]), - (inputnode, pvnativet1wm, [ - ("source_file", "source_file"), - ("pvwm_t1", "in_file"), - ]), - (inputnode, attnativet1, [ - ("source_file", "source_file"), - ("att_t1", "in_file"), - ]), - ]) - # fmt:on - - # fmt:off - workflow.connect([(raw_sources, ds_asl_mask_t1, [("out", "RawSources")])]) - # fmt:on - - if getattr(spaces, "_cached") is None: - return workflow - - # Store resamplings in standard spaces when listed in --output-spaces - if spaces.cached.references: - from aslprep.niworkflows.interfaces.space import SpaceDataSource - - spacesource = pe.Node(SpaceDataSource(), name="spacesource", run_without_submitting=True) - spacesource.iterables = ( - "in_tuple", - [(s.fullname, s.spec) for s in spaces.cached.get_standard(dim=(3,))], - ) - - out_names = [ - "template", - "asl_std", - "asl_std_ref", - "asl_mask_std", - "cbf_std", - "meancbf_std", - ] - if scorescrub: - out_names = out_names + ["score_std", "avgscore_std", "scrub_std"] - - if basil: - out_names = out_names + ["basil_std", "pv_std", "pvwm_std", "att_std"] - - select_std = pe.Node( - KeySelect(fields=out_names), - name="select_std", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - ds_asl_std = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="preproc", - compress=True, - SkullStripped=False, - RepetitionTime=metadata.get("RepetitionTime"), - RepetitionTimePreparation=metadata.get("RepetitionTimePreparation"), - TaskName=metadata.get("TaskName"), - dismiss_entities=("echo",), - ), - name="ds_asl_std", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - ds_asl_std_ref = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - suffix="aslref", - compress=True, - dismiss_entities=("echo",), - ), - name="ds_asl_std_ref", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - ds_asl_mask_std = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="brain", - suffix="mask", - compress=True, - dismiss_entities=("echo",), - ), - name="ds_asl_mask_std", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - cbfstd = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - suffix="cbf", - compress=True, - ), - name="cbfstd", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - meancbfstd = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="mean", - suffix="cbf", - compress=True, - ), - name="meancbfstd", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, + mem_gb=config.DEFAULT_MEMORY_MIN_GB, ) # fmt:off workflow.connect([ - (inputnode, ds_asl_std, [("source_file", "source_file")]), - (inputnode, ds_asl_std_ref, [("source_file", "source_file")]), - (inputnode, ds_asl_mask_std, [("source_file", "source_file")]), - (inputnode, cbfstd, [("source_file", "source_file")]), - (inputnode, meancbfstd, [("source_file", "source_file")]), - (inputnode, select_std, [ - ("asl_std", "asl_std"), - ("asl_std_ref", "asl_std_ref"), - ("asl_mask_std", "asl_mask_std"), - ("cbf_std", "cbf_std"), - ("meancbf_std", "meancbf_std"), - ("template", "template"), - ("spatial_reference", "keys"), - ]), - (spacesource, select_std, [("uid", "key")]), - (select_std, ds_asl_std, [("asl_std", "in_file")]), - (spacesource, ds_asl_std, [ - ("space", "space"), - ("cohort", "cohort"), - ("resolution", "resolution"), - ("density", "density"), - ]), - (select_std, ds_asl_std_ref, [("asl_std_ref", "in_file")]), - (spacesource, ds_asl_std_ref, [ - ("space", "space"), - ("cohort", "cohort"), - ("resolution", "resolution"), - ("density", "density"), - ]), - (select_std, ds_asl_mask_std, [("asl_mask_std", "in_file")]), - (spacesource, ds_asl_mask_std, [ - ("space", "space"), - ("cohort", "cohort"), - ("resolution", "resolution"), - ("density", "density"), - ]), - (select_std, cbfstd, [("cbf_std", "in_file")]), - (spacesource, cbfstd, [ - ("space", "space"), - ("cohort", "cohort"), - ("resolution", "resolution"), - ("density", "density"), - ]), - (select_std, meancbfstd, [("meancbf_std", "in_file")]), - (spacesource, meancbfstd, [ + (inputnode, ds_base_input_std, [("source_file", "source_file")]), + (inputnode, select_std, [(base_input_std, base_input_std)]), + (select_std, ds_base_input_std, [(base_input_std, "in_file")]), + (spacesource, ds_base_input_std, [ ("space", "space"), ("cohort", "cohort"), ("resolution", "resolution"), ("density", "density"), ]), - (raw_sources, ds_asl_mask_std, [("out", "RawSources")]), ]) # fmt:on - if scorescrub: - scorestd = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="score", - suffix="cbf", - compress=True, - ), - name="scorestd", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - meanscorestd = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="meanScore", - suffix="cbf", - compress=True, - ), - name="meanscorestd", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - scrubstd = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="scrub", - suffix="cbf", - compress=True, - ), - name="scrubstd", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - - # fmt:off - workflow.connect([ - (inputnode, scorestd, [("source_file", "source_file")]), - (inputnode, meanscorestd, [("source_file", "source_file")]), - (inputnode, scrubstd, [("source_file", "source_file")]), - (inputnode, select_std, [ - ("score_std", "score_std"), - ("avgscore_std", "avgscore_std"), - ("scrub_std", "scrub_std"), - ]), - (select_std, scorestd, [("score_std", "in_file")]), - (spacesource, scorestd, [ - ("space", "space"), - ("cohort", "cohort"), - ("resolution", "resolution"), - ("density", "density"), - ]), - (select_std, meanscorestd, [("avgscore_std", "in_file")]), - (spacesource, meanscorestd, [ - ("space", "space"), - ("cohort", "cohort"), - ("resolution", "resolution"), - ("density", "density"), - ]), - (select_std, scrubstd, [("scrub_std", "in_file")]), - (spacesource, scrubstd, [ - ("space", "space"), - ("cohort", "cohort"), - ("resolution", "resolution"), - ("density", "density"), - ]), - ]) - # fmt:on - - if basil: - basilstd = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="basil", - suffix="cbf", - compress=True, - ), - name="basilstd", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - pvstd = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="pvGM", - suffix="cbf", - compress=True, - ), - name="pvcstd", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - pvstdwm = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="pvWM", - suffix="cbf", - compress=True, - ), - name="pvcstdwm", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - attstd = pe.Node( - DerivativesDataSink( - base_directory=output_dir, - desc="bat", - suffix="cbf", - compress=True, - ), - name="attstd", - run_without_submitting=True, - mem_gb=DEFAULT_MEMORY_MIN_GB, - ) - + # The mask file gets one extra bit of metadata. + if base_input == "asl_mask": # fmt:off - workflow.connect([ - (inputnode, basilstd, [("source_file", "source_file")]), - (inputnode, pvstd, [("source_file", "source_file")]), - (inputnode, pvstdwm, [("source_file", "source_file")]), - (inputnode, attstd, [("source_file", "source_file")]), - (inputnode, select_std, [ - ("basil_std", "basil_std"), - ("pv_std", "pv_std"), - ("pvwm_std", "pvwm_std"), - ("att_std", "att_std"), - ]), - (select_std, basilstd, [("basil_std", "in_file")]), - (spacesource, basilstd, [ - ("space", "space"), - ("cohort", "cohort"), - ("resolution", "resolution"), - ("density", "density"), - ]), - (select_std, pvstd, [("pv_std", "in_file")]), - (spacesource, pvstd, [ - ("space", "space"), - ("cohort", "cohort"), - ("resolution", "resolution"), - ("density", "density"), - ]), - (select_std, pvstdwm, [("pvwm_std", "in_file")]), - (spacesource, pvstdwm, [ - ("space", "space"), - ("cohort", "cohort"), - ("resolution", "resolution"), - ("density", "density"), - ]), - (select_std, attstd, [("att_std", "in_file")]), - (spacesource, attstd, [ - ("space", "space"), - ("cohort", "cohort"), - ("resolution", "resolution"), - ("density", "density"), - ]), - ]) + workflow.connect([(raw_sources, ds_base_input_std, [("out", "RawSources")])]) # fmt:on return workflow diff --git a/aslprep/workflows/asl/plotting.py b/aslprep/workflows/asl/plotting.py index aa4f3db15..dc7e36efd 100644 --- a/aslprep/workflows/asl/plotting.py +++ b/aslprep/workflows/asl/plotting.py @@ -7,11 +7,9 @@ from aslprep import config from aslprep.interfaces import DerivativesDataSink +from aslprep.interfaces.ants import ApplyTransforms from aslprep.interfaces.plotting import CBFSummary, CBFtsSummary from aslprep.niworkflows.engine.workflows import LiterateWorkflow as Workflow -from aslprep.niworkflows.interfaces.fixes import ( - FixHeaderApplyTransforms as ApplyTransforms, -) def init_cbfplot_wf( diff --git a/aslprep/workflows/asl/qc.py b/aslprep/workflows/asl/qc.py index 618bd4203..a0b20c8d0 100644 --- a/aslprep/workflows/asl/qc.py +++ b/aslprep/workflows/asl/qc.py @@ -6,11 +6,9 @@ from nipype.pipeline import engine as pe from templateflow.api import get as get_template +from aslprep.interfaces.ants import ApplyTransforms from aslprep.interfaces.cbf_computation import ComputeCBFQC, ComputeCBFQCforGE from aslprep.niworkflows.engine.workflows import LiterateWorkflow as Workflow -from aslprep.niworkflows.interfaces.fixes import ( - FixHeaderApplyTransforms as ApplyTransforms, -) from aslprep.utils.misc import _select_last_in_list diff --git a/aslprep/workflows/asl/registration.py b/aslprep/workflows/asl/registration.py index 94e2f1551..ce8b251b2 100644 --- a/aslprep/workflows/asl/registration.py +++ b/aslprep/workflows/asl/registration.py @@ -11,11 +11,9 @@ from aslprep import config from aslprep.interfaces import DerivativesDataSink +from aslprep.interfaces.ants import ApplyTransforms from aslprep.niworkflows.engine.workflows import LiterateWorkflow as Workflow from aslprep.niworkflows.func.util import init_asl_reference_wf -from aslprep.niworkflows.interfaces.fixes import ( - FixHeaderApplyTransforms as ApplyTransforms, -) from aslprep.niworkflows.interfaces.itk import MultiApplyTransforms from aslprep.niworkflows.interfaces.nilearn import Merge from aslprep.niworkflows.interfaces.registration import FLIRTRPT diff --git a/aslprep/workflows/asl/resampling.py b/aslprep/workflows/asl/resampling.py index 8e72ce07b..78fd3a454 100644 --- a/aslprep/workflows/asl/resampling.py +++ b/aslprep/workflows/asl/resampling.py @@ -8,11 +8,9 @@ from nipype.pipeline import engine as pe from aslprep.config import DEFAULT_MEMORY_MIN_GB +from aslprep.interfaces.ants import ApplyTransforms from aslprep.niworkflows.engine.workflows import LiterateWorkflow as Workflow from aslprep.niworkflows.func.util import init_asl_reference_wf -from aslprep.niworkflows.interfaces.fixes import ( - FixHeaderApplyTransforms as ApplyTransforms, -) from aslprep.niworkflows.interfaces.itk import MultiApplyTransforms from aslprep.niworkflows.interfaces.nilearn import Merge from aslprep.niworkflows.interfaces.surf import GiftiSetAnatomicalStructure diff --git a/docs/api.rst b/docs/api.rst index ca51953ec..8ff517114 100644 --- a/docs/api.rst +++ b/docs/api.rst @@ -34,6 +34,8 @@ Internal configuration system aslprep.workflows.asl.gecbf aslprep.workflows.asl.hmc aslprep.workflows.asl.outputs + aslprep.workflows.asl.plotting + aslprep.workflows.asl.qc aslprep.workflows.asl.registration aslprep.workflows.asl.resampling aslprep.workflows.asl.stc @@ -54,11 +56,13 @@ Internal configuration system :toctree: generated/ :template: module.rst + aslprep.interfaces.ants aslprep.interfaces.bids aslprep.interfaces.cbf_computation aslprep.interfaces.confounds aslprep.interfaces.ge aslprep.interfaces.multiecho + aslprep.interfaces.parcellation aslprep.interfaces.plotting aslprep.interfaces.reports @@ -77,6 +81,7 @@ Internal configuration system :toctree: generated/ :template: module.rst + aslprep.utils.atlas aslprep.utils.bids aslprep.utils.confounds aslprep.utils.meepi