You use bbregister to compute the registration. You will need a template for your atlas (eg, an average anatomy).
doug
On 5/27/11 7:09 PM, kwa1@rice.edu wrote:
Do I feed the registration matrix into another FS command or does bbregister use the reg matrix to transform the atlas mask into FS anatomical space? I will try the bbregister with 12 DOF as you recommend too.
Thank you, Kareem
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html