Add freesurfer and brainvoyager options to LN2_RIMIFY
Opened this issue · 2 comments
There are requests to easily convert such segmentation files (e.g. whole brain) to LayNii rim format and use e.g. LN2_LAYERS.
Therefore, I want to add two convenience flags to LN2_RIMIFY:
-
freesurfer(aseg) -
brainvoyager(100 & 150, 240 & 243)
I agree, this would be very useful for many people.
I think the relabeling of segmentation valued from freesurfer might be relatively straight forward. The harder part might be to have a documentation about how to convert freesurfer surfaces in freesurfer-space to the EPI space of functional slab protocols. I am not sure if you also envision the latter part?
- There is the issue of making sure that the rim file contains a contentious GM/CSF border (kissing gyri).
- And there is the issue of header logistics (even when structure is aligned to the functional EPI slab).
- An early version of this pipeline is described here: https://layerfmri.com/2017/11/26/getting-layers-in-epi-space/,
@kenshukoiso has ported this to the newer LayNii programs: https://github.com/kenshukoiso/Whole_Brain_Project/blob/main/script/s04_AutoSeg2layering_wo_MC.sh . But I think there is room for optimization and modernization.
The harder part might be to have a documentation about how to convert freesurfer surfaces in freesurfer-space to the EPI space of functional slab protocols. I am not sure if you also envision the latter part?
I was planning to implement the easy part (relabeling of each voxel). So I am not planning to look into converting the surfaces. At least not within the scope of LN2_RIMIFY right now.