Dear HCP Experts,
I apologize for the repeated posting but am really hoping for some
assistance/feedback regarding this issue. I understand a lot has been
mentioned about similar type analyses but unfortunately I am unable to pin
down the exact specifics for the type of analysis I hope to do.
After going through several posts, I understand the advice is to seed
directly from the surfaces
(i.e.
${StudyFolder}/${Subject}/T1w/fsaverage_LR32k/${Subject}.${Hemisphere}.white.32k_fs_LR.surf.gii)
and use the pial surface as stop mask for whole brain tractography. My
confusion stems from not understanding if this is equivalent to seeding
from Freesurfer label-based ROIs and then allowing me to then project the
results onto a connectivity matrix with Freesurfer labels. Is this the case
or do I have to do some prior step(s) to the data? I understand there are
also files labeled "${Subject}.${Hemisphere}.aparc.32k_fs_LR.label.gii" --
are these files relevant for what I would like to accomplish? In addition,
is it necessary to specify --meshspace=freesurfer as per the FSL
documentation?
Also, if I would like to combine the left and right hemisphere files to use
a single seed file, would it be best to use mris_convert --combinesurfs
command or to use what was suggested by Stam some years ago, i.e.
Left Surface:
surf2surf -i
$Subject/MNINonLinear/fsaverage_LR32k/${Subject}.L.white.32k_fs_LR.surf.gii -o
white.L.asc --outputtype=ASCII
--values=$Subject/MNINonLinear/fsaverage_LR32k//${Subject}.L.atlasroi.32k_fs_LR.shape.gii
Right Surface:
surf2surf -i
$Subject/MNINonLinear/fsaverage_LR32k/${Subject}.R.white.32k_fs_LR.surf.gii -o
white.R.asc --outputtype=ASCII
--values=$Subject/MNINonLinear/fsaverage_LR32k//${Subject}.R.atlasroi.32k_fs_LR.shape.gii
Thereafter combining both white.L.asc and white.R.asc into a text file to
input into the seed argument?
I would also really appreciate kind advice regarding:
- If it is advisable to do this in MNI space or subject's native space?
- If in the MNI space, if the seed ref should be
"/MNINonLinear/T1w_restore.nii.gz", and if in subject native space, what
should be used?
- What waypoint / target masks would be necessary?
- I am assuming matrix 1 would be the best?
Thanks very much in advance.
Michiko.
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