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Code Issues 14 Pull requests 2 Packages Activity Actions

[BUG]: Merge parcellations fail with extra dimensions #331

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synchon merged 3 commits from fix/extra-parc-dim-in-merge into main 2024-05-06 10:28:28 +00:00
Conversation 5 Commits 3 Files changed 2 +4 -1
2 changed files with 4 additions and 1 deletions
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1
docs/changes/newsfragments/331.bugfix Normal file
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@ -0,0 +1 @@
Remove extra dimension from parcellations warped via ANTs when merging parcellations by `Synchon Mandal`_

4
junifer/data/parcellations.py
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@ -326,7 +326,9 @@ def get_parcellation(
# Call antsApplyTransforms
run_ext_cmd(name="antsApplyTransforms", cmd=apply_transforms_cmd)
img = nib.load(warped_parcellation_path)
raw_img = nib.load(warped_parcellation_path)
# Remove extra dimension added by ANTs
img = image.math_img("np.squeeze(img)", img=raw_img)
# Resample parcellation to target image
img_to_merge = image.resample_to_img(