Nativeprosampling

[jordandekraker]

Still a WIP

All 01_*.sh scripts are now sampling in space-nativepro. I made a new directory with all space-nativepro data (volumes, surfaces, surface metrics, and subcortical csvs) which can make for easy loading into a Freeview (or other viewer) scene.

TODO:

• [x] update 02.sh (and .py?) files to make reports using the new output filenames
• [ ] currently all modalities are sampled to nativepro resolution. To save space, they could keep their original resolution but the a new method will need to be used for subcortical ROI sampling
• [x] reporting. I barely touched the Nsteps variable so this should probably be made more consistent

[jordandekraker]

After discussion with @royj23

Name changes TODO:

• [x] csv files space-nativepro, desc subcortical
• [x] no unsmoothed func.gii
• [ ] look into FSL aseg instead of FS
• [ ] possible remove c3d
• [x] sub_ses to sub/ses
• [x] always rerun flair and qt1 registration (old ones may be different reg types)
• [x] sctx to morph and post_dwi to proc_dwi

Roadmap:

• Jessica will push her changes to the reports and csv files into a new branch and we will resolve conflicts together AFTER i merge this to main
• Transforms that SHOULD exist in micapipe will be written there, but everything else will be written in z-brains
• Eventually we will need to rename according to micapipe_v0.2.0 output filenames, but we will need to keep alll the current version anyway

[jordandekraker]

This is now mostly handled within micapipe