Manualseg (#34)

* BF: incidentally found bug in subfield+tissue

Was combining nnunet tissue seg with subfields, instead of
post-processed tissue seg with subfields. Probably had a
minor effect on the final dseg, but fixed now anyways

* BF: updated autotop and snakefile for man segs

autotop rule for man segs needed updating, and the
nnunet rules file is now only included if manual segs
are not used.

* added test data for seg, removed space wildcard

* BF: arguments in wrong order

Co-authored-by: jordandekraker <[email protected]>

hippunfold/config/snakebids.yml

@@ -76,7 +76,6 @@ pybids_inputs:
     wildcards:
       - subject
       - session
-#      - space
 
 
 

hippunfold/workflow/Snakefile

@@ -9,6 +9,7 @@ configfile: 'config/snakebids.yml'
 limit_to_list = set()
 limit_to_list.add('T1w') #always need T1w
 
+
 for modality in config['modality']:
     if modality[:3] == 'seg': #if modality is segT2w, then add seg and T2w
         limit_to_list.add('seg')
@@ -89,9 +90,14 @@ def get_final_anat():
     anat = []
     for modality in config['modality']:
         mod_index = get_modality_key(modality)
+        if mod_index == 'seg':
+            modality_suffix = modality[3:]
+        else:
+            modality_suffix = modality
         anat = anat + \
-            expand(bids(root='results',datatype='seg_{modality}',desc='preproc',suffix='{modality}.nii.gz', space='cropT1w',hemi='{hemi}', **config['subj_wildcards']),
+            expand(bids(root='results',datatype='seg_{modality}',desc='preproc',suffix='{modality_suffix}.nii.gz', space='cropT1w',hemi='{hemi}', **config['subj_wildcards']),
                 modality=modality,
+                modality_suffix=modality_suffix,
                 hemi=['L','R'],
                 subject=config['input_lists'][mod_index]['subject'],
                 session=config['sessions'])
@@ -138,7 +144,10 @@ include: 'rules/preproc_t1.smk'
 #include rules only as they are needed..
 if 'segT1w' in config['modality'] or 'segT2w' in config['modality']:
     include: 'rules/preproc_seg.smk'
+else: 
+    include: 'rules/nnunet.smk'
 
+#if using manual segs, then don't use nnunet
 if 'segT2w' in config['modality'] or 'T2w' in config['modality']:
     include: 'rules/preproc_t2.smk'
 
@@ -147,6 +156,5 @@ if 'b500' in config['modality'] or 'b1000' in config['modality']:
 
 include: 'rules/autotop.smk'
 include: 'rules/gifti.smk'
-include: 'rules/nnunet.smk'
 include: 'rules/subfields.smk'
 include: 'rules/resample_final_to_crop_t1.smk'

hippunfold/workflow/rules/autotop.smk

@@ -35,8 +35,6 @@ def get_autotop_input (wildcards):
 
     return nii
 
-
-
 rule run_autotop:
     input:
         nii = get_autotop_input,
@@ -69,7 +67,7 @@ def get_autotop_inputseg_cmd (wildcards, input, output):
 
     if config['use_mcr'] == True:
         cmd = f"AUTOTOP_DIR={autotop_dir} {autotop_dir}/mcr_v97/run_AutoTops_TransformAndRollOut.sh /opt/mcr/v97 "\
-                f"{input.nii} {output.out_dir} '{input.seg}' {config['cnn_model'][wildcards.modality]}"
+                f"{input.nii} {output.out_dir} {config['cnn_model'][wildcards.modality]} {input.seg}"
     else:
         singularity_cmd = f"singularity exec -B {autotop_dir}:/src -e {config['singularity']['autotop']}" 
         set_matlab_lic = f"SINGULARITYENV_MLM_LICENSE_FILE={config['mlm_license_file']}"
@@ -78,7 +76,7 @@ def get_autotop_inputseg_cmd (wildcards, input, output):
 
         cmd = f"{set_matlab_lic} {set_java_home} {set_autotop_dir} {singularity_cmd} "\
                 f"{config['matlab_bin']} -batch \"addpath(genpath('{autotop_dir}')); "\
-                f"AutoTops_TransformAndRollOut('{input.nii}','{output.out_dir}','{config['cnn_model'][wildcards.modality]},'{input.seg}'')\""
+                f"AutoTops_TransformAndRollOut('{input.nii}','{output.out_dir}','{config['cnn_model'][wildcards.modality]}','{input.seg}')\""
     return cmd   
 
 rule run_autotop_inputseg:
@@ -90,11 +88,12 @@ rule run_autotop_inputseg:
     output:
         out_dir = directory(bids(root='work',**config['subj_wildcards'],suffix='autotop',desc='cropped',space='corobl',hemi='{hemi,Lflip|R}',modality='seg{modality}')),
         #subfields = bids(root='work',**config['subj_wildcards'],suffix='autotop/subfields-BigBrain.nii.gz',desc='cropped',space='corobl',hemi='{hemi,Lflip|R}',modality='seg{modality}'),
-        warp_unfold2native = bids(root='work',**config['subj_wildcards'],suffix='autotop/Warp_unfold2native.nii',desc='cropped',space='corobl',hemi='{hemi,Lflip|R}',modality='{modality}'),
-        warp_native2unfold= bids(root='work',**config['subj_wildcards'],suffix='autotop/Warp_native2unfold.nii',desc='cropped',space='corobl',hemi='{hemi,Lflip|R}',modality='{modality}'),
-        warpitk_unfold2native = bids(root='work',**config['subj_wildcards'],suffix='autotop/WarpITK_unfold2native.nii',desc='cropped',space='corobl',hemi='{hemi,Lflip|R}',modality='{modality}'),
-        warpitk_native2unfold= bids(root='work',**config['subj_wildcards'],suffix='autotop/WarpITK_native2unfold.nii',desc='cropped',space='corobl',hemi='{hemi,Lflip|R}',modality='{modality}'),
-        gii = expand(bids(root='work',suffix='autotop/{surfname}.unfoldedtemplate.surf.gii',desc='cropped', space='corobl',hemi='{{hemi}}',modality='seg{{modality}}', **config['subj_wildcards']),surfname=['inner','outer','midthickness'],allow_missing=True)
+        postproc = bids(root='work',**config['subj_wildcards'],suffix='autotop/labelmap-postProcess.nii.gz',desc='cropped',space='corobl',hemi='{hemi,Lflip|R}',modality='seg{modality}'),
+        warp_unfold2native_extrap = bids(root='work',**config['subj_wildcards'],suffix='autotop/Warp_unfold2native_extrapolateNearest.nii',desc='cropped',space='corobl',hemi='{hemi,Lflip|R}',modality='seg{modality}'),
+        warp_unfold2native = bids(root='work',**config['subj_wildcards'],suffix='autotop/Warp_unfold2native.nii',desc='cropped',space='corobl',hemi='{hemi,Lflip|R}',modality='seg{modality}'),
+        warp_native2unfold= bids(root='work',**config['subj_wildcards'],suffix='autotop/Warp_native2unfold.nii',desc='cropped',space='corobl',hemi='{hemi,Lflip|R}',modality='seg{modality}'),
+        gii = expand(bids(root='work',suffix='autotop/{surfname}.unfoldedtemplate.surf.gii',desc='cropped', space='corobl',hemi='{hemi,Lflip|R}',modality='seg{modality}', **config['subj_wildcards']),surfname=['inner','outer','midthickness'],allow_missing=True),
+        coords = expand(bids(root='work',suffix='autotop/coords-{dir}.nii.gz',desc='cropped', space='corobl',hemi='{hemi,Lflip|R}',modality='seg{modality}', **config['subj_wildcards']),dir=['AP','PD','IO'],allow_missing=True)
     threads: 8
     resources:
         time = 180 #3 hrs (so grouped job is set at 3hrs, since snakemake grouped resources not summed, but takes the max)

hippunfold/workflow/rules/subfields.smk

@@ -1,3 +1,4 @@
+
 rule label_subfields_from_vol_coords_corobl:
     """ Label subfields using the volumetric coords and bigbrain labels"""
     input:  
@@ -25,7 +26,7 @@ rule combine_tissue_subfield_labels_corobl:
         then, we just need to add those in, using max(old,new) to override old with new in case of conflict
     """
     input:
-        tissue = bids(root='work',datatype='seg_{modality}',suffix='dseg.nii.gz',desc='nnunet',space='corobl',hemi='{hemi}',**config['subj_wildcards']),
+        tissue = bids(root='work',**config['subj_wildcards'],suffix='autotop/labelmap-postProcess.nii.gz',desc='cropped',space='corobl',hemi='{hemi}',modality='{modality}'),
         subfields = bids(root='work',datatype='seg_{modality}',desc='subfieldsnotissue',suffix='dseg.nii.gz', space='corobl',hemi='{hemi}', **config['subj_wildcards'])
     params:
         remap_dg = '-threshold 8 8 6 0 -popas dg',