Merge pull request #51 from khanlab/patch-segT2w

Patch seg t2w
khanlab · Apr 20, 2021 · 9703eb8 · 9703eb8
2 parents 947f19e + 75e0abe
commit 9703eb8
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Showing 4 changed files with 19 additions and 2 deletions.
diff --git a/hippunfold/tests/hippunfold_test.py b/hippunfold/tests/hippunfold_test.py
@@ -24,4 +24,8 @@ def test_dry_runs(script_runner):
         ret = script_runner.run('hippunfold', 'test_data/bids_singleT2w_longitudinal',output_dir,'participant','-np')
         assert ret.success
 
+    with tempfile.TemporaryDirectory() as output_dir:
+        ret = script_runner.run('hippunfold', 'test_data/bids_segT2w',output_dir,'participant','-np','--modality','segT2w')
+        assert ret.success
+
 
diff --git a/hippunfold/workflow/rules/autotop.smk b/hippunfold/workflow/rules/autotop.smk
@@ -92,6 +92,8 @@ rule run_autotop_inputseg:
         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}'),
+        warpitk_unfold2native = bids(root='work',**config['subj_wildcards'],suffix='autotop/WarpITK_unfold2native.nii',desc='cropped',space='corobl',hemi='{hemi,Lflip|R}',modality='seg{modality}'),
+        warpitk_native2unfold= bids(root='work',**config['subj_wildcards'],suffix='autotop/WarpITK_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

diff --git a/hippunfold/workflow/rules/subfields.smk b/hippunfold/workflow/rules/subfields.smk
@@ -110,9 +110,20 @@ rule plot_subj_subfields:
     script: '../scripts/plot_subj_subfields.py'
 
 
+
+def get_bg_img_for_subfield_qc(wildcards):
+
+    if wildcards.modality[:3] == 'seg':
+        bg_modality = wildcards.modality[3:] 
+    else:
+        bg_modality = wildcards.modality
+
+    return  bids(root='results',datatype='seg_{modality}',desc='preproc',suffix=f'{bg_modality}.nii.gz', space='cropT1w',hemi='{hemi}', **config['subj_wildcards'])
+
 rule qc_subfield:
     input:
-        img = bids(root='results',datatype='seg_{modality}',desc='preproc',suffix='{modality}.nii.gz', space='cropT1w',hemi='{hemi}', **config['subj_wildcards']),
+        img = get_bg_img_for_subfield_qc,
+        #bids(root='results',datatype='seg_{modality}',desc='preproc',suffix='{modality}.nii.gz', space='cropT1w',hemi='{hemi}', **config['subj_wildcards']),
         seg = bids(root='results',datatype='seg_{modality}',suffix='dseg.nii.gz', desc='subfields',space='cropT1w',hemi='{hemi}', **config['subj_wildcards'])
     output:
         png = report(bids(root='work',datatype='qc',suffix='dseg.png', desc='subfields',from_='{modality}',space='cropT1w',hemi='{hemi}', **config['subj_wildcards']),

diff --git a/setup.py b/setup.py
@@ -34,7 +34,7 @@
         'hippunfold_download_models=hippunfold.download_models:main'
     ]},
     install_requires=[
-        "snakebids>=0.2.0",
+        "snakebids==0.2.1",
         "snakemake>=5.28.0",
         "nnunet @ git+https://github.com/ylugithub/nnUNet.git@v1.6.6",
         "appdirs",