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When re-runing with the same atlases, load segmentations #153

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merged 3 commits into from
May 31, 2024
Merged

When re-runing with the same atlases, load segmentations #153

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6af3eea
[full_test] fix rerun
htwangtw May 31, 2024
541e0fd
Merge branch 'main' into test/hotfix-file-type
htwangtw May 31, 2024
f413d03
[full_test] fix output of mask/seg checking
htwangtw May 31, 2024
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9 changes: 5 additions & 4 deletions giga_connectome/mask.py
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Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,9 @@ def generate_gm_mask_atlas(
subject_mask_nii, subject_mask_dir / target_subject_mask_file_name
)
else:
subject_mask_nii = load_img(target_subject_mask)
subject_mask_nii = load_img(
subject_mask_dir / target_subject_mask_file_name
)

if not target_subject_seg or not target_subject_mask:
# resample if the grey matter mask was not generated
Expand All @@ -85,11 +87,10 @@ def generate_gm_mask_atlas(
)
else:
subject_seg_niis = [
load_img(subject_mask_dir / i)
for i in target_subject_seg_file_names
subject_mask_dir / i for i in target_subject_seg_file_names
]

return subject_mask_nii, subject_seg_niis
return subject_mask_dir / target_subject_mask_file_name, subject_seg_niis


def generate_subject_gm_mask(
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