Write a script to fetch sequence parameters

[valosekj]

Write a simple bash script (which can be run by sct_run_batch across all subjects) to fetch the resolution of all images. This will allow us to check if sequence parameters are the same across/within centres.

pixdim can be found, for example, by:

sct_image -i <filename> -header fslhd | grep pixdim1 | awk '{print $2}'

Alternatively, we can consider writing some more sophisticated script, like params_checker.py

[jcohenadad]

This is a great idea, but instead of developing a new script, I suggest re-using (or updating) what has already been developed for the spine-generic project. See notably:

• https://github.com/spine-generic/spine-generic/blob/master/spinegeneric/cli/check_data_consistency.py
• https://github.com/spine-generic/spine-generic/blob/master/spinegeneric/cli/params_checker.py
• more specific: https://github.com/spine-generic/data-multi-subject/tree/master/code
• automation of data checking using Github action: https://github.com/spine-generic/data-multi-subject/blob/master/.github/workflows/validator.yml
  • example of Github action after dataset was updated: https://github.com/spine-generic/data-multi-subject/actions/runs/3526009533/jobs/5913419703

[valosekj]

model_seg_sci/utils/fetch_sequence_parameters.py might be relevant