V2.2.7

[mathrip]

Minor changes

🔧 Enable parallelisation of inferences

Changes made over the code to enable robust parallelisation of the inferences. Contribution from Cornelius Kronlage

• Fixes that allow parallelising MELD-graph inference (no hardcoded temp file paths, wrapper around open_hdf5_file that just retries it the file can't be opened in parallel)
• Add --threads argument for calling freesurfer with multiple threads (also useful for parallelizing)
• --skip-feature-plotting speeds up inference for big cohorts when these plots are not needed
• Move the MELD-graph prediction outputs in surface space etc. to the predictions_reports/ folder, e.g.:

output/predictions_reports/sub-27/predictions
├── prediction.nii.gz
├── lh.prediction.nii.gz
├── rh.prediction.nii.gz
├── fsaverage_sym
│   ├── lh.prediction.mgh
│   └── rh.prediction.mgh
├── surf_native
│   ├── lh.prediction.mgh
│   └── rh.prediction.mgh
├── vol_freesurfer
│   ├── lh.prediction.mgz
│   └── rh.prediction.mgz
└── vol_native
    ├── lh.prediction.mgz
    └── rh.prediction.mgz

Which makes them easier to find and also avoids conflicts when running multiple predictions (with different harmo parameters) using the same freesurfer outputs.

• Write the freesurfer expert-options fix for FLAIRpial segmentation to a per-subject file (instead of relying on the output/freesurfer_outputs directory to contain it)
• Update docs to explain the changes and give an example of how inference can be parallelised for large cohorts

🧠 Fix QC plotting
This fixes the FLAIR and T1 scans used to visualised Freesurfer surfaces and MELD prediction when using the script new_pt_qc_script.py. The scans are now chosen to be in the same space than Freesurfer outputs to avoid potential misalignment of FLAIR. Fixes issue #113

🧹 Other minor code cleanup : fixes issues #112 #115