Hey FSL Surface experts,
Q1: I'm interested in using surface-based registration to spatially normalize my seeds_to_target.nii.gz classy output from probtrackx2. I'm not using any HCP data/tools so I assume I should be able to accomplish this using strictly FSL/Freesurfer commands. My understanding is that I could project my data onto the individual lh.white.asc surface using "surf_proj" (followed by surf2surf to convert ".gii" to ".func.gii"?) but I've had no success in visualizing the results in any viewers (fsleyes/freeview) as a sanity check to see if the results are plausible. Using surf2volume on the output looks right but i'd like to visualize the data as a surface. Are there any recommendations for viewing projected probtrackx2 data (.func.gii) overlaid onto the individual surface (.surf.gii)? I've noticed a few threads with a similar question but didn't see a definitive answer...
Commands (using fdt_paths.nii.gz as an example):
surf_proj --data=fdt_paths.nii.gz --surf=lh.white.asc --meshspace=freesurfer --meshref=brain.nii.gz --xfm=fa2fs.mat --out=fdt_paths_alt --surfout
surf2surf -i fdt_paths_alt.gii -o fdt_paths_alt.func.gii --volin=brain.nii.gz --convin=freesurfer --values=fdt_paths_alt.gii
Q2: I used seeds and targets that were constrained to the white matter surface and so using FLIRT/FNIRT to spatially normalize the resulting seeds_to_targets data is problematic. Ultimately, i'd like to replicate aspects of the methods from this paper,"Asymmetric projections of the arcuate fasciculus to the temporal cortex underlie lateralized language function in the human brain", but rather than spatially normalizing fdt_paths I would normalize results from "find_the_biggest" to "fsaverage_sym" space. Assuming the data are projected correctly onto an individual surface with surf_proj, is then the spatial normalization accomplished using freesurfer's "mri_surf2surf"? Any ideas?
Q2 is more of a freesurfer question so it's a shot in the dark but if Q1 could be addressed that would still be helpful.
Thanks in advance!
-vatché
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