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neuropoly / data-management

Repo that deals with datalad aspects for internal use
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Fix canproco SC segmentations #307

Closed NathanMolinier closed 5 months ago

NathanMolinier commented 5 months ago

Description

I created this issue to mention that I pushed a new branch nm/fix_calgary_and_resample on the canproco dataset. This commit is fixing header issues (see https://github.com/neuropoly/data-management/issues/305) with the subjects from Calgary. Also, to limit future mistakes, the SC segmentations were resampled to be in the same space as the images.

Related issue

https://github.com/neuropoly/data-management/issues/305

NathanMolinier commented 5 months ago

We need to update the dtype to uint8 https://github.com/neuropoly/data-management/issues/305#issuecomment-2045889662

NathanMolinier commented 5 months ago

I just used this command to convert all SC segmentation from Calgary to dtype uint8:

for sub in sub-cal*;do for file in $(find -type f -name "$sub"*_seg-manual*.nii.gz);do git annex get "$file"; sct_image -i "$file" -type uint8;done;done

The branch nm/fix_calgary_and_resample is now ready to merge

mguaypaq commented 5 months ago

I turned this into a PR on the canproco dataset and merged it :+1: