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image must be passed to autotop
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even when running on a manual segmentation
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@jordandekraker
jordandekraker authored Feb 19, 2021
1 parent 775f084 commit a2a4ce0
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4 changes: 4 additions & 0 deletions hippunfold/workflow/rules/autotop.smk
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Expand Up @@ -24,8 +24,12 @@ def get_autotop_cmd (wildcards, input, output):
def get_autotop_input (wildcards):
if wildcards.modality == 'T2w':
nii = bids(root='work',datatype='anat',**config['subj_wildcards'],suffix='T2w.nii.gz',desc='cropped',space='corobl',hemi='{hemi}'),
if wildcards.modality == 'segT2w':
nii = bids(root='work',datatype='anat',**config['subj_wildcards'],suffix='T2w.nii.gz',desc='cropped',space='corobl',hemi='{hemi}'),
elif wildcards.modality == 'T1w':
nii = bids(root='work',datatype='anat',**config['subj_wildcards'],suffix='T1w.nii.gz',desc='cropped',space='corobl',hemi='{hemi}'),
elif wildcards.modality == 'segT1w':
nii = bids(root='work',datatype='anat',**config['subj_wildcards'],suffix='T1w.nii.gz',desc='cropped',space='corobl',hemi='{hemi}'),
elif wildcards.modality == 'b500':
nii = bids(root='work/preproc_dwi',suffix='b500.nii.gz',desc='cropped',datatype='dwi',**config['subj_wildcards'],space='corobl',hemi='{hemi}'),
elif wildcards.modality == 'b1000':
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@jordandekraker
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AutoTop requires an input image even when running only on a segmentation. This doesn't seem to be passing any input images to it, and I'm not too sure how else to go about passing one. I could modify AutoTop code to accommodate no input image (since its not actually used), but that would require a new MCR compile so I thought it would be easier to just pass a corobl T1w or T2w image here.

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