add labelmerge placeholder

- Adds in rule for labelmerge (needs updating with container and proper
command)
- Update resources with correct names and paths
- Add tsv to rule all for copying from resource to bids folders for
labelmerge

dbsc/config/snakebids.yml

@@ -145,17 +145,18 @@ parse_args:
 Space: MNI152NLin6Asym
 
 zona_bb_subcortex:
+  tsv: 'resources/zona_bb_subcortex/desc-ZonaBBSubcor_dseg.tsv'
   MNI152NLin6Asym:
-    dir: 'resources/MNI152NLin6Asym/'
-    T1w: 'resources/MNI152NLin6Asym/tpl-MNI152NLin6Asm_res-04_desc-brain_T1w.nii.gz'
-    seg: 'resources/MNI152NLin6Asym/sub-SNSX32NLin2020Asym_space-MNI152NLin6Asym_desc-ZonaBBSubcor_dseg.nii.gz'
+    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/MNI152NLin2009bAsym/'
-    seg: 'resources/MNI152NLin2009bAsym/sub-SNSX32NLin2020Asym_space-MNI152NLin2009bAsym_desc-ZonaBBSubcor_dseg.nii.gz'
+    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:
-  tsv: 'resources/freesurfer/desc-Freesurfer_dseg.tsv'
+  tsv: 'resources/freesurfer/desc-FreesurferThal_dseg.tsv'
 
 # Containers
 # NOTE: Update from latest to use specific tags

dbsc/workflow/Snakefile

@@ -49,10 +49,10 @@ rule all:
             subject=config["input_lists"]["dwi"]["subject"],
         ),
         fs_tsv=str(
-            Path(config["output_dir"]) / "freesurfer" / config["freesurfer"]["tsv"]
+            Path(config["output_dir"]) / "freesurfer" / "desc-FreesurferThal_dseg.tsv"
         ),
         zona_tsv=str(
             Path(config["output_dir"])
             / "zona_bb_subcortex"
-            / config["zona_bb_subcortex"]["tsv"]
+            / "desc-ZonaBBSubcor_dseg.tsv"
         ),

dbsc/workflow/rules/zona_bb_subcortex.smk

@@ -40,18 +40,20 @@ rule cp_zona_tsv:
     output:
         zona_tsv=f"{zona_dir}/desc-ZonaBBSubcor_dseg.tsv",
     shell:
-        "cp -v {input.fs_tsv} {output.fs_tsv}"
+        "cp -v {input.zona_tsv} {output.zona_tsv}"
 
 
 rule xfm2native:
     """Transform from Zona template space to subject native space"""
     input:
         seg=str(
             Path(workflow.basedir).parent
+            / Path(config["zona_bb_subcortex"][config["Space"]]["dir"])
             / Path(config["zona_bb_subcortex"][config["Space"]]["seg"])
         ),
         seg_anat=str(
             Path(workflow.basedir).parent
+            / Path(config["zona_bb_subcortex"][config["Space"]]["dir"])
             / Path(config["zona_bb_subcortex"][config["Space"]]["T1w"])
         ),
         ref=config["input_path"]["T1w"],
@@ -135,9 +137,6 @@ rule rm_bb_thal:
         "fslmaths {output.seg} -add {output.non_thal} {output.seg}"
 
 
-# NEED TO PIPE FROM rm_bb_thal with labelmerge and PIPE TO binarize
-# Alternative option is to have a second target rule that performs everything
-# below with participant2 and everything above with participant1
 rule labelmerge:
     input:
         seg=expand(
@@ -154,8 +153,8 @@ rule labelmerge:
         fs_dir=str(Path(config["output_dir"]) / "freesurfer"),
         zona_desc="ZonaBBSubcor",
         fs_desc="FreesurferThal",
-    output:
         labelmerge_dir=directory(labelmerge_dir),
+    output:
         seg=expand(
             bids_labelmerge(
                 subject="{subject}",
@@ -177,10 +176,9 @@ rule labelmerge:
     # ADD CONTAINER
     shell:
         # TO BE UPDATED WITH APPROPRIATE COMMAND
-        "run.py {params.zona_dir} {output.labelmerge_dir} --overlay_bids_dir {params.fs_dir} --overlay_desc {params.fs_desc} --base_desc {params.zona_desc}"
+        "run.py {params.zona_dir} {params.labelmerge_dir} --overlay_bids_dir {params.fs_dir} --overlay_desc {params.fs_desc} --base_desc {params.zona_desc}"
 
 
-# Placeholder desc entity
 rule binarize:
     input:
         seg=bids_labelmerge(
@@ -200,30 +198,29 @@ rule binarize:
         "fslmaths {input.seg} -bin {output.mask}"
 
 
-# Placeholder desc entity
 rule add_brainstem:
     input:
         mask=rules.binarize.output.mask,
         aparcaseg=rules.fs_xfm_to_native.output.aparcaseg,
     output:
         mask=bids_anat(
-            root=rules.labelmerge.output.labelmerge_dir,
+            root=labelmerge_dir,
             space="T1w",
             desc="labelmergeStem",
             suffix="mask.nii.gz",
         ),
     container:
         config["singularity"]["neuroglia-core"]
     shell:
-        "fslmaths {input.aparcaseg} -thr 16 -uthr 16 -bin -max {input.seg} {output.seg}"
+        "fslmaths {input.aparcaseg} -thr 16 -uthr 16 -bin -max {input.mask} {output.mask}"
 
 
 rule create_convex_hull:
     input:
         bin_seg=rules.add_brainstem.output.mask,
     output:
         convex_hull=bids_anat(
-            root=rules.labelmerge.output.labelmerge_dir,
+            root=labelmerge_dir,
             space="T1w",
             desc="ConvexHull",
             suffix="mask.nii.gz",