Update the format of `preprocess_segment.sh` outputs

[NadiaBlostein]

Context

From the following: https://github.com/neuropoly/template/pull/53#discussion_r1261649236

Solution

• we run the process on the output path
• we do the qc and label the files that need correction by downloading a YML file (see SCT doc)
• we manually correct when needed using https://github.com/spinalcordtoolbox/manual-correction (@valosekj @sandrinebedard can help)
• we copy the corrected files (or non-corrected that are fine) on the input dataset
• we git-annex the data so the labels are up to date

[NadiaBlostein]

commit dcb7fe1d79746314f986f0f569b54074d24b4e2a