Yes, there's no other way for FS to know where data should go -- it has no idea how you derived the input. You can try using bbregister with 12 DOF to register the atlas template to the FS anatomical. This will give you a registration matrix. Check it visually to make sure that it is reasonably accurate.
doug
kwa1@rice.edu wrote:
Hmm, well I derived the volume from an FSL atlas which I exported, binarized, then fed into the commands I listed initially. Do I need to register the temporal pole volume to some FS space? And how would I so?
Best, Kareem
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
Then it means that the registration is incorrect. How did you create the reg?
kwa1@rice.edu wrote:
No it doesn't look right. It is supposed to map on to the temporal pole but doesn't do so. I don't think it's in the right space. Is there a command we are perhaps missing to bring it to native FS space?
Best, Kareem
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
It looks like your commands are correct. When you load mask.surf.nii.gz onto the surface, does it look ok?
doug
kwa1@rice.edu wrote:
Hello,
I've derived a .nii.gz atlas-based volume for a specific part of the cortical surface. I've binarized the volume and now I want to convert the file to a .label file that I can use to identify particular vertices in native FS space for that same subject.
This is what I have tried so far:
mri_vol2surf --src mask.nii.gz --srcreg /tmp/reg.dat --surf pial --projfrac 0.5 --hemi lh --out mask.surf.nii.gz
mri_cor2label --i mask.surf.nii.gz --id 1 --l mask.label --surf SUBJ1 lh pial
However when I overlayed the .label onto SUBJ1 the vertices did not match up and was completely off the region of interest on the cortical surface.
Does anyone know how to fix this or how to proceed with conversion differently?
Thank you very much, Kareem
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