➕ Reorient resources to set orientation in config

[shnizzedy]

Fixes

Related to #2140 by @birajstha
Related to #2161 by @shnizzedy
Fixes #2138 by @sgiavasis for v1.8.7.post1

Description

Merges

the changes

Description

This PR fixes the different orientation in CPAC output dir that were caused by the different orientation of templates being ingressed.

• Added reorientation to the templates that are being ingressed and /or resampled (for different resolution) in CPAC.
• Added desired_orientation as config key in blank-config and set it default to RPI
  With this PR the desired orientation of the outputs can be selected by modifying this key in the config.

Technical details

First of all,
The reorientation of templates are done as below

• resolve_resolution function is modified to take in orientation as extra input.
• Orientation inputs are taken from the config and are added in the following spots

1. resolve_resolution
2. freesurfer_fs_brain_connector
3. anatomical_init_T1
4. anatomical_init_T2
5. func_reorient

Tests

For testing you can run this branch of CPAC on one test subject / session with your config (set as desired_orientation) and check the orientations of the images in the output directory both anat and func

1. cd into the anat or func directory.
2. run for file in *.nii.gz; do orientation=$(3dinfo -orient "$file" 2>/dev/null); echo "$file: $orientation"; done

You should see the filename with orientations as below
anat :

func :

Screenshots

Problem: Different orientations in the CPAC output dir

1. anat dir:
   

2. func dir:
   

After fix:

1. anat dir:
   

2. func dir:
   

from #2140 onto 6b3c934.

Checklist

• My pull request has a descriptive title (not a vague title like Update index.md).
• My pull request targets the hotfix/1.8.7-1 branch of the repository.
• My commit messages follow best practices.
• My code follows the established code style of the repository.
• I added tests for the changes I made (if applicable).
• I updated the changelog.
• I added or updated documentation (if applicable).
• I tried running the project locally and verified that there are no visible errors.

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[shnizzedy]

I'm not sure if 043a004 and c725a9d are relevant here. They're included in #2161 but not in #2140