Labelmerge

.gitignore

@@ -2,3 +2,11 @@
 test/data/derivatives/.snakemake/
 test/data/derivatives/config/
 test/data/derivatives/.snakebids
+
+# Tar files
+*.tar
+
+# Ignore files that are available in tar
+**/zona_bb_subcortex/MNI152
+**/zona_bb_subcortex/MNI2009b
+**/zona_bb_subcortex/transforms

dbsc/config/snakebids.yml

@@ -153,29 +153,28 @@ parse_args:
 
 # Workflow specific config
 # Spaces available (MNI152, MNINlin2009bAsym)
-Space: MNI152
+Space: MNI152NLin6Asym
 
 zona_bb_subcortex:
-  MNI152:
-    dir: 'resources/MNI152'
-    T1w: 'resources/MNI152/sub-SNSX32NLin2020Asym_space-MNI152_T1w.nii.gz'
-    seg: 'resources/MNI152/sub-SNSX32NLin2020Asym_space-MNI152_ZonaBBSubCorSeg.nii.gz'
-    exclude: 'resources/MNI152/sub-SNSX32NLin2020Asym_space-MNI152_desc-exclude_ROI.nii.gz'
-  MNI2009:
-    dir: 'resources/MNI2009b'
-    T1w: 'resources/MNI2009b/sub-SNSX32NLin2020Asym_space-MNI152_T1w.nii.gz'
-    seg: 'resources/MNI2009b/sub-SNSX32NLin2020Asym_space-MNINlin2009bAsym_ZonaBBSubCorSeg.nii.gz'
-    exclude: 'resources/MNI2009b/sub-SNSX32NLin2020Asym_space-MNINlin2009bAsym_desc-exclude_ROI.nii.gz'
+  tsv: 'resources/zona_bb_subcortex/desc-ZonaBBSubcor_dseg.tsv'
+  MNI152NLin6Asym:
+    dir: 'resources/zona_bb_subcortex/MNI152NLin6Asym/'
+    T1w: 'tpl-MNI152NLin6Asym_res-04_desc-brain_T1w.nii.gz'
+    seg:  'sub-SNSX32NLin2020Asym_space-MNI152NLin6Asym_desc-ZonaBBSubcor_dseg.nii.gz'
+  MNI152NLin2009bAsym:
+    dir: 'resources/zona_bb_subcortex/MNI152NLin2009bAsym/'
+    seg: 'sub-SNSX32NLin2020Asym_space-MNI152NLin2009bAsym_desc-ZonaBBSubcor_dseg.nii.gz'
 
 # NOTE: This may not be needed with labelmerge
 freesurfer:
-  labels: 'resources/freesurfer/fs_labels.csv'
+  tsv: 'resources/freesurfer/desc-FreesurferThal_dseg.tsv'
 
 # Containers
 # NOTE: Update from latest to use specific tags
 singularity:
   freesurfer: "docker://pwighton/freesurfer:7.2.0"
   neuroglia-core: "docker://khanlab/neuroglia-core:latest"
   mrtrix: "docker://brainlife/mrtrix:3.0.3"
+  labelmerge: "docker://kaitj/labelmerge:v0.1.0"
 
 fs_license: /path/to/fs/license

dbsc/resources/freesurfer/desc-FreesurferThal_dseg.tsv

@@ -0,0 +1,53 @@
+index	name
+8108	Left LD
+8208	Right LD
+8109	Left LGN
+8209	Right LGN
+8115	Left MGN
+8215	Right MGN
+8121	Left PuI
+8221	Right PuI
+8123	Left PuM
+8223	Right PuM
+8111	Left L-Sg
+8211	Right L-Sg
+8133	Left VPL
+8233	Right VPL
+8106	Left CM
+8206	Right CM
+8128	Left VLa
+8228	Right VLa
+8120	Left PuA
+8220	Right PuA
+8113	Left MDm
+8213	Right MDm
+8118	Left Pf
+8218	Right Pf
+8127	Left VAmc
+8227	Right VAmc
+8112	Left MDl
+8212	Right MDl
+8104	Left CeM
+8204	Right CeM
+8126	Left VA
+8226	Right VA
+8116	Left MV(Re)
+8216	Right MV(Re)
+8125	Left R
+8225	Right R
+8130	Left VM
+8230	Right VM
+8105	Left CL
+8205	Right CL
+8122	Left PuL
+8222	Right PuL
+8119	Left Pt
+8219	Right Pt
+8103	Left AV
+8203	Right AV
+8117	Left Pc
+8217	Right Pc
+8129	Left VLp
+8229	Right VLp
+8110	Left LP
+8210	Right LP

dbsc/resources/zona_bb_subcortex/desc-ZonaBBSubcor_dseg.tsv

@@ -0,0 +1,25 @@
+index	name
+1	Left RN
+2	Right RN
+3	Left SN
+4	Right SN
+5	Left STn
+6	Right STn
+7	Left Caudate
+8	Right Caudate
+9	Left Putamen
+10	Right Putamen
+11	Left GPe
+12	Right GPe
+13	Left GPi
+14	Right GPi
+15	Left Thalamus
+16	Right Thalalmus
+17	Left Hippocampus
+18	Right Hippocampus
+19	Left NAc
+20	Right NAc
+21	Left Amygdala
+22	Right Amygdala
+23	Left ZI
+24	Right ZI

dbsc/workflow/Snakefile

@@ -42,7 +42,9 @@ include: "rules/mrtpipelines.smk"
 
 rule all:
     input:
-        expand(
+        files=expand(
             rules.filtered_tck2connectome.output.sl_assignment,
             subject=config["input_lists"]["T1w"]["subject"],
         ),
+        fs_tsv=rules.cp_fs_tsv.output.fs_tsv,
+        zona_tsv=rules.cp_zona_tsv.output.zona_tsv,

dbsc/workflow/rules/freesurfer.smk

@@ -15,6 +15,22 @@ bids_fs_out = partial(
 # B. Fischl, A. van der Kouwe, C. Destrieux, E. Halgren, F. Ségonne, D.H. Salat, E. Busa, L.J. Seidman, J. Goldstein, D. Kennedy, V. Caviness, N. Makris, B. Rosen, A.M. Dale. Automatically parcellating the human cerebral cortex. Cereb. Cortex, 14 (2004), pp. 11-22, 10.1093/cercor/bhg087
 
 
+rule cp_fs_tsv:
+    """Copy tsv to freesurfer dir
+    """
+    input:
+        fs_tsv=str(
+            Path(workflow.basedir).parent / Path(config["freesurfer"]["tsv"])
+        ),
+    output:
+        fs_tsv=expand(
+            "{freesurfer_dir}/desc-FreesurferThal_dseg.tsv",
+            freesurfer_dir=freesurfer_dir,
+        ),
+    shell:
+        "cp -v {input.fs_tsv} {output.fs_tsv}"
+
+
 rule thalamic_segmentation:
     """Perform thalamus segmentation
 

dbsc/workflow/rules/mrtpipelines.smk

@@ -140,6 +140,7 @@ rule dwi2response:
 
 rule responsemean:
     """Compute average response function"""
+    # DOUBLE CHECK
     input:
         subject_rf=expand(
             bids_response_out(
@@ -317,7 +318,7 @@ rule tckgen:
         mask=rules.nii2mif.output.mask,
         cortical_ribbon=rules.fs_xfm_to_native.output.ribbon,
         convex_hull=rules.create_convex_hull.output.convex_hull,
-        subcortical_seg=rules.add_brainstem_new_seg.output.seg,
+        subcortical_seg=rules.add_brainstem.output.mask,
     params:
         step=config["step"],
         sl=config["sl_count"],
@@ -367,7 +368,7 @@ rule tck2connectome:
     input:
         weights=rules.tcksift2.output.weights,
         tck=rules.tckgen.output.tck,
-        subcortical_seg=rules.add_brainstem_new_seg.output.seg,
+        subcortical_seg=rules.add_brainstem.output.mask,
     params:
         radius=config["radial_search"],
     output:
@@ -417,11 +418,9 @@ rule connectome2tck:
         "connectome2tck -nthreads {threads} -nodes {params.nodes} -exclusive -filters_per_edge -tck_weights_in {input.node_weights} -prefix_tck_weights_out {output.edge_weight} {input.tck} {input.sl_assignment} {output.edge_tck} "
 
 
-# NOTE: Use labelmerge split segs here?
 rule create_roi_mask:
-    # EXPAND OVER NODE1 IN RULE ALL
     input:
-        subcortical_seg=rules.add_brainstem_new_seg.output.seg,
+        subcortical_seg=rules.add_brainstem.output.mask,
     output:
         roi_mask=temp(
             bids_anat_out(
@@ -450,7 +449,7 @@ rule create_exclude_mask:
         ),
         lZI=bids_anat_out(desc="21", suffix="mask.mif"),
         rZI=bids_anat_out(desc="22", suffix="mask.mif"),
-        subcortical_seg=rules.add_brainstem_new_seg.output.seg,
+        subcortical_seg=rules.add_brainstem.output.mask,
     output:
         filter_mask=temp(
             bids_anat_out(
@@ -472,7 +471,7 @@ rule filter_tck:
         filter_mask=rules.create_exclude_mask.output.filter_mask,
         tck=rules.connectome2tck.output.edge_tck,
         weights=rules.tck2connectome.output.node_weights,
-        subcortical_seg=rules.add_brainstem_new_seg.output.seg,
+        subcortical_seg=rules.add_brainstem.output.mask,
     output:
         filtered_tck=temp(
             bids_tractography_out(
@@ -537,7 +536,7 @@ rule filtered_tck2connectome:
     input:
         weights=rules.combine_filtered.output.combined_weights,
         tck=rules.combine_filtered.output.combined_tck,
-        subcortical_seg=rules.add_brainstem_new_seg.output.seg,
+        subcortical_seg=rules.add_brainstem.output.mask,
     params:
         radius=config["radial_search"],
     output: