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Cropped template after registration and inverse warping not working #2531

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jcohenadad opened this issue Nov 21, 2019 · 3 comments · Fixed by #2532
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Cropped template after registration and inverse warping not working #2531

jcohenadad opened this issue Nov 21, 2019 · 3 comments · Fixed by #2532
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@jcohenadad
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bug category: fixes an error in the code priority:HIGH sct_register_to_template context:

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@jcohenadad
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Weirdly, when running standard registration to the template, the template2anat file is cropped (see below), and the anat2template is empty.

Screen Shot 2019-11-21 at 2 14 32 PM

to reproduce:

sct_download_data -d sct_example_data
cd sct_example_data/t2
sct_propseg -i t2.nii.gz -c t2
sct_label_utils -i t2.nii.gz -create-viewer 3,9 -o labels.nii.gz
sct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -l labels.nii.gz -v 2 -r 0
@jcohenadad jcohenadad self-assigned this Nov 21, 2019
@jcohenadad jcohenadad added bug category: fixes an error in the code priority:HIGH sct_register_to_template context: labels Nov 21, 2019
@jcohenadad
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The problem was introduced at 4.1.0

@jcohenadad
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I tried reversing this PR #2444 but it didn't help

@jcohenadad
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The problem is related to the cropping of the image at the end of the process, here:
https:/neuropoly/spinalcordtoolbox/blob/master/scripts/sct_register_to_template.py#L711

To fix it, i changed the crop flag to 0 instead of 1:

sct.run(['sct_apply_transfo', '-i', 'template.nii', '-o', 'template2anat.nii.gz', '-d', 'data.nii', '-w', 'warp_template2anat.nii.gz', '-crop', '0'], verbose)
sct.run(['sct_apply_transfo', '-i', 'data.nii', '-o', 'anat2template.nii.gz', '-d', 'template.nii', '-w', 'warp_anat2template.nii.gz', '-crop', '0'], verbose)

jcohenadad added a commit that referenced this issue Nov 21, 2019
@jcohenadad
sct_register_to_template: Fixed cropped registered image
c8c9148 
Fixes #2531
@jcohenadad jcohenadad mentioned this issue Nov 21, 2019
Merged
jcohenadad added a commit that referenced this issue Nov 26, 2019
@jcohenadad
sct_register_to_template: Fixed cropped registered image (#2532)
eb1be05 
Fixes #2531
jcohenadad added a commit that referenced this issue Dec 17, 2019
@jcohenadad
sct_register_to_template: Fixed cropped registered image
41dce5c 
Fixes #2531


Former-commit-id: 6cd25b4ea5d6b851019a48cc16b582bce2f0148f [formerly c8c9148]
Former-commit-id: aee8fe86103510b2c4b48ba05596aba7230bdc8a
jcohenadad added a commit that referenced this issue Dec 18, 2019
@jcohenadad
sct_register_to_template: Fixed cropped registered image (#2532)
9bd3054 
Fixes #2531

Former-commit-id: eb1be05
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Fixed cropping of registered image spinalcordtoolbox/spinalcordtoolbox
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