✨ Introduce mri_robust_template as option for longitudinal template generation

[shnizzedy]

Fixes

Related to #2164 by @shnizzedy & @Shinwon Park

Description

• Adds using option to longitudinal_template_generation with a choice of mri_robust_template (default) or C-PAC legacy

  C-PAC/CPAC/resources/configs/pipeline_config_default.yml

  Line 243 in e6d33f5

  longitudinal_template_generation:

  C-PAC/CPAC/resources/configs/pipeline_config_default.yml

  Lines 253 to 255 in e6d33f5

  	# Implementation to use
  	# Options: mri_robust_template, C-PAC legacy
  	using: mri_robust_template

• Updates intergraph connections for the $2n+1$ graphs used to run longitudinal template generation

  flowchart LR
  anat_longitudinal_pre-preproc("<code>anat_longitudinal_pre-preproc</code><br>(one per subject session)") --> template_node_brain("<code>template_node_brain</code><br>(one per subject)")
  template_node_brain --> ses_wf("<code>ses_wf</code><br>(one per subject session)")
  

  Loading
• Updates output logic to have a structure like

  └── pipeline_cpac-default-pipeline
      └── sub-01
          ├── anat
          │   ├── sub-01_from-longitudinal_to-MNI152NLin2009cAsym_mode-image_desc-linear_xfm.json
          │   ├── sub-01_from-longitudinal_to-MNI152NLin2009cAsym_mode-image_desc-linear_xfm.mat
          │   ├── sub-01_space-longitudinal_desc-brain_T1w.json
          │   ├── sub-01_space-longitudinal_desc-brain_T1w.nii.gz
          │   ├── sub-01_space-longitudinal_desc-head_T1w.json
          │   └── sub-01_space-longitudinal_desc-head_T1w.nii.gz
          ├── ses-1
          │   └── anat
          │       ├── sub-01_ses-1_desc-brain_mask.json
          │       ├── sub-01_ses-1_desc-brain_mask.nii.gz
          │       ├── sub-01_ses-1_desc-head_T1w.json
          │       ├── sub-01_ses-1_desc-head_T1w.nii.gz
          │       ├── sub-01_ses-1_desc-preproc_T1w.json
          │       ├── sub-01_ses-1_desc-preproc_T1w.nii.gz
          │       ├── sub-01_ses-1_from-T1w_to-longitudinal_mode-image_desc-linear_xfm.json
          │       ├── sub-01_ses-1_from-T1w_to-longitudinal_mode-image_desc-linear_xfm.mat
          │       ├── sub-01_ses-1_from-T1w_to-MNI152NLin2009cAsym_mode-image_desc-li ear_xfm.json
          │       ├── sub-01_ses-1_from-T1w_to-MNI152NLin2009cAsym_mode-image_desc-linear_xfm.mat
          │       ├── sub-01_ses-1_space-longitudinal_desc-brain_T1w.json
          │       └── sub-01_ses-1_space-longitudinal_desc-brain_T1w.nii.gz
          └── ses-2
              └── anat
                  ├── sub-01_ses-2_desc-brain_mask.json
                  ├── sub-01_ses-2_desc-brain_mask.nii.gz
                  ├── sub-01_ses-2_desc-head_T1w.json
                  ├── sub-01_ses-2_desc-head_T1w.nii.gz
                  ├── sub-01_ses-2_desc-preproc_T1w.json
                  ├── sub-01_ses-2_desc-preproc_T1w.nii.gz
                  ├── sub-01_ses-2_from-T1w_to-longitudinal_mode-image_desc-linear_xfm.json
                  ├── sub-01_ses-2_from-T1w_to-longitudinal_mode-image_desc-linear_xfm.mat
                  ├── sub-01_ses-2_from-T1w_to-MNI152NLin2009cAsym_mode-image_desc-linear_xfm.json
                  ├── sub-01_ses-2_from-T1w_to-MNI152NLin2009cAsym_mode-image_desc-linear_xfm.mat
                  ├── sub-01_ses-2_space-longitudinal_desc-brain_T1w.json
                  └── sub-01_ses-2_space-longitudinal_desc-brain_T1w.nii.gz
  

  • There's probably some missing outputs in this example, but the idea is just that there's an anat directory that's a sibling to all the session directories, and that that anat directory has all the subject-but-not-session-specific outputs in it.
  • Do we want all of from-T1w_to-longitudinal and from-longitudinal_to-{template} and from-T1w_to-{template} or do we want to leave any out to be recalculated as needed?

Technical details

• This PR merges into a branch that just restructures the longitudinal code from develop so those non-logic changes aren't part of this PR.
• This PR leaves `"C-PAC legacy" broken.

Still to do

• do we want to remove or rename "C-PAC legacy"?
• test both participant and test_config analysis levels
• fix filenaming that's leading to names like sub-01_ses-1_from-longitudinal_to-*_mode-image_xfm
• check outputs and make sure
  • they have the longitudinal template in their provenance where applicable
  • they seem reasonable

Tests

Screenshots

Checklist

• My pull request has a descriptive title (not a vague title like Update index.md).
• My pull request targets the prep_for/mri_robust_template 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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