add composed itk warps from T1w to unfold (incl corobl to unfold)

hippunfold/config/snakebids.yml

@@ -167,6 +167,7 @@ singularity:
   prepdwi: 'docker://khanlab/prepdwi:latest'  
   autotop: 'docker://khanlab/autotop_deps:v0.2'
   fsl: '/project/6050199/akhanf/singularity/bids-apps/fsl_6.0.3_cuda9.1.sif'  #fsl with cuda container not on docker hub yet.. only used for dwi workflow anyhow..
+  ants: 'docker://kaczmarj/ants:2.3.4'
 
 
 template: CITI168

hippunfold/pipeline_description.json

@@ -5,7 +5,7 @@
     "GeneratedBy": [
         {
             "Name": "hippunfold",
-            "Version": "0.1.0",
+            "Version": "0.3.0",
             "CodeURL": "https://github.com/khanlab/hippunfold",
             "Author": "Jordan DeKraker & Ali Khan",
             "AuthorEmail": "ali.khan@uwo.ca"

hippunfold/resources/desc-flipLR_type-itk_xfm.txt

@@ -0,0 +1,5 @@
+#Insight Transform File V1.0
+#Transform 0
+Transform: MatrixOffsetTransformBase_double_3_3
+Parameters: -1 0 0 0 1 0 0 0 1 0 0 0
+FixedParameters: 0 0 0

hippunfold/workflow/Snakefile

@@ -62,9 +62,10 @@ def get_final_subfields():
     for modality in config['modality']:
         mod_index = get_modality_key(modality)
         subfields = subfields + \
-            expand(bids(root='results',datatype='seg_{modality}',desc='subfields',suffix='dseg.nii.gz', space='cropT1w',hemi='{hemi}', **config['subj_wildcards']),
+            expand(bids(root='results',datatype='seg_{modality}',desc='subfields',suffix='dseg.nii.gz', space='{space}',hemi='{hemi}', **config['subj_wildcards']),
                 modality=modality,
                 hemi=['L','R'],
+                space=['cropT1w','unfold'],
                 subject=config['input_lists'][mod_index]['subject'],
                 session=config['sessions'])
 
@@ -97,7 +98,6 @@ def get_final_anat():
 
     return anat
 
-
 def get_final_qc():
     qc = []
     qc = qc + expand(bids(root='work',datatype='qc',**config['subj_wildcards'],suffix='regqc.png',

hippunfold/workflow/rules/autotop.smk

@@ -50,6 +50,8 @@ rule run_autotop:
         warp_unfold2native_extrap = bids(root='work',**config['subj_wildcards'],suffix='autotop/Warp_unfold2native_extrapolateNearest.nii',desc='cropped',space='corobl',hemi='{hemi,Lflip|R}',modality='{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,Lflip|R}',modality='{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='{modality}', **config['subj_wildcards']),dir=['AP','PD','IO'],allow_missing=True)
     threads: 8
@@ -88,8 +90,10 @@ 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='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}'),
+        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)
     threads: 8
     resources:
@@ -120,6 +124,9 @@ rule map_to_full_grid:
         script = os.path.join(config['snakemake_dir'],'workflow','scripts','mapUnfoldToFullGrid.sh')
     output:
         warp_unfoldtemplate2unfold = bids(root='work',**config['subj_wildcards'],suffix='autotop/Warp_unfoldtemplate2unfold.nii',desc='cropped',space='corobl',hemi='{hemi,Lflip|R}',modality='{modality}'),
+        warp_unfold2unfoldtemplate = bids(root='work',**config['subj_wildcards'],suffix='autotop/Warp_unfold2unfoldtemplate.nii',desc='cropped',space='corobl',hemi='{hemi,Lflip|R}',modality='{modality}'),
+        warpitk_unfoldtemplate2unfold = bids(root='work',**config['subj_wildcards'],suffix='autotop/WarpITK_unfold2unfoldtemplate_0InverseWarp.nii.gz',desc='cropped',space='corobl',hemi='{hemi,Lflip|R}',modality='{modality}'),
+        warpitk_unfold2unfoldtemplate = bids(root='work',**config['subj_wildcards'],suffix='autotop/WarpITK_unfold2unfoldtemplate_0Warp.nii.gz',desc='cropped',space='corobl',hemi='{hemi,Lflip|R}',modality='{modality}'),
     container: config['singularity']['autotop']
     group: 'subj'
     threads: 8
@@ -142,5 +149,45 @@ rule unflip_autotop_nii:
     shell: 'c3d {input} -flip x {output}'
 
 
+rule compose_warps_corobl2unfold_rhemi:
+    """ Compose corobl to unfold (unfold-template), for right hemi (ie no flip)"""
+    input:
+        native2unfold = bids(root='work',**config['subj_wildcards'],suffix='autotop/WarpITK_native2unfold.nii',desc='cropped',space='corobl',hemi='R',modality='{modality}'),
+        unfold2unfoldtemplate = bids(root='work',**config['subj_wildcards'],suffix='autotop/WarpITK_unfold2unfoldtemplate_0Warp.nii.gz',desc='cropped',space='corobl',hemi='R',modality='{modality}'),
+        ref = os.path.join(config['snakemake_dir'],'hippocampal_autotop','misc','unfold_ref_256x128x16.nii.gz'),
+    output:
+        corobl2unfold = bids(root='work',datatype='seg_{modality}',**config['subj_wildcards'],suffix='xfm.nii.gz',hemi='R',from_='corobl',to='unfold',mode='image')
+    container: config['singularity']['ants']
+    group: 'subj'
+    shell: 'ComposeMultiTransform 3 {output.corobl2unfold} -R {input.ref} {input.unfold2unfoldtemplate} {input.native2unfold}'
+
+
+rule compose_warps_corobl2unfold_lhemi:
+    """ Compose corobl to unfold (unfold-template), for left hemi (ie with flip)"""
+    input:
+        native2unfold = bids(root='work',**config['subj_wildcards'],suffix='autotop/WarpITK_native2unfold.nii',desc='cropped',space='corobl',hemi='Lflip',modality='{modality}'),
+        unfold2unfoldtemplate = bids(root='work',**config['subj_wildcards'],suffix='autotop/WarpITK_unfold2unfoldtemplate_0Warp.nii.gz',desc='cropped',space='corobl',hemi='Lflip',modality='{modality}'),
+        ref = os.path.join(config['snakemake_dir'],'hippocampal_autotop','misc','unfold_ref_256x128x16.nii.gz'),
+        flipLR_xfm = os.path.join(config['snakemake_dir'],'resources','desc-flipLR_type-itk_xfm.txt')
+    output:
+        corobl2unfold = bids(root='work',datatype='seg_{modality}',**config['subj_wildcards'],suffix='xfm.nii.gz',hemi='L',from_='corobl',to='unfold',mode='image')
+    container: config['singularity']['ants']
+    group: 'subj'
+    shell: 'ComposeMultiTransform 3 {output.corobl2unfold} -R {input.ref} {input.unfold2unfoldtemplate} {input.native2unfold} {input.flipLR_xfm}'
+
+
+
+rule compose_warps_t1_to_unfold:
+    """ Compose warps from T1w to unfold """
+    input:
+        corobl2unfold = bids(root='work',datatype='seg_{modality}',**config['subj_wildcards'],suffix='xfm.nii.gz',hemi='{hemi}',from_='corobl',to='unfold',mode='image'),
+        ref = os.path.join(config['snakemake_dir'],'hippocampal_autotop','misc','unfold_ref_256x128x16.nii.gz'),
+        t1w2corobl = bids(root='work',datatype='anat',**config['subj_wildcards'],suffix='xfm.txt',from_='T1w',to='corobl',desc='affine',type_='itk'),
+    output: 
+        bids(root='results',datatype='seg_{modality}',**config['subj_wildcards'],suffix='xfm.nii.gz',hemi='{hemi}',from_='T1w',to='unfold',mode='image')
+    container: config['singularity']['ants']
+    group: 'subj'
+    shell: 'ComposeMultiTransform 3 {output} -R {input.ref} {input.corobl2unfold} {input.t1w2corobl}'
 
 
+

hippunfold/workflow/rules/nnunet.smk

@@ -13,10 +13,8 @@ def get_nnunet_input (wildcards):
 def get_model_tar (wildcards):
 
     if 'HIPPUNFOLD_CACHE_DIR' in os.environ.keys():
-        print(f"HIPPUNFOLD_CACHE_DIR defined, using: {os.environ['HIPPUNFOLD_CACHE_DIR']}")
         download_dir = os.environ['HIPPUNFOLD_CACHE_DIR']
     else:
-        print(f'HIPPUNFOLD_CACHE_DIR not defined, using default location')
         #create local download dir if it doesn't exist
         dirs = AppDirs('hippunfold','khanlab')
         download_dir = dirs.user_cache_dir

hippunfold/workflow/rules/subfields.smk

@@ -135,3 +135,18 @@ rule concat_subj_vols_tsv:
         import pandas as pd
         pd.concat([pd.read_table(in_tsv) for in_tsv in input ]).to_csv(output.tsv,sep='\t',index=False)
 
+
+rule resample_subfields_to_unfold:
+    """Resampling to unfold space"""
+    input:
+        nii = bids(root='work',datatype='seg_{modality}',desc='subfields',suffix='dseg.nii.gz', space='corobl',hemi='{hemi}', **config['subj_wildcards']),
+        xfm = bids(root='work',datatype='seg_{modality}',**config['subj_wildcards'],suffix='xfm.nii.gz',hemi='{hemi}',from_='corobl',to='unfold',mode='image')
+    output:
+        nii = bids(root='results',datatype='seg_{modality}',suffix='dseg.nii.gz', desc='subfields',space='unfold',hemi='{hemi}', **config['subj_wildcards'])
+    container: config['singularity']['autotop']
+    group: 'subj'
+    shell:
+        'ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS={threads} '
+        'antsApplyTransforms -d 3 --interpolation MultiLabel -i {input.nii} -o {output.nii} -r {input.xfm}  -t {input.xfm}' 
+
+

setup.py

@@ -42,6 +42,7 @@
         "nibabel",
         "numpy",
         "scipy",
+        "nilearn",
         "seaborn"
     ],
     python_requires='>=3.7'