The subjects.csv is the file which is use by the generate_template.py to read specific files that are used for the template creation. The issue right now was that the subjects.csv file was created in the <DATASET>/derivatives/sct_straighten_spinalcord/<LAST_SUBJECT>.
Along with this, there was a minor bug in the pathname that was appended in the subject.csv leading to the need of manual correction of the pathname.
There was no clear instruction in the README as to change the pathname of subjects.csv in the generate_template.py script.
What does the PR solve:
The PR solves the above issues.
The subjects.csv file with the correct pathnames are now created inside the <DATASET>/derivatives/template making it easier to find.
Also provides with the clear instructions to change pathname in the generate_template.py
Fixes #83
Context:
subjects.csvis the file which is use by thegenerate_template.pyto read specific files that are used for the template creation. The issue right now was that thesubjects.csvfile was created in the<DATASET>/derivatives/sct_straighten_spinalcord/<LAST_SUBJECT>.subject.csvleading to the need of manual correction of the pathname.subjects.csvin thegenerate_template.pyscript.What does the PR solve:
The PR solves the above issues.
subjects.csvfile with the correct pathnames are now created inside the<DATASET>/derivatives/templatemaking it easier to find.Also provides with the clear instructions to change pathname in the
generate_template.pyIt has been tested on the Dog data ✅