I did a quick test using the gray matter volume. I registered that to fsaverage using a 9dof transform
fslregister --mov Tissue_Gray_Matter.nii --s fsaverage --reg reg.dof9.Tissue_Gray_Matter.dat --dof 9
The results are not terrible (good by talairach standards), so you could use this. Then just
mri_label2vol --seg labelX.nii --reg reg.dof9.Tissue_Gray_Matter.dat --invertmtx --template $SUBJECTS_DIR/fsaverage/mri/orig.mgz --o $SUBJECTS_DIR/fsaverage/mri/labelX.mgz
Note that it will be hopeless to try to put these on the surface.
doug
On 09/26/2013 05:55 PM, Maryam Vaziri Pashkam wrote:
I am not sure. In the online tool it is possible to load the labels on a volume.
http://www.talairach.org/applet/
There is nothing on their website but I have been in contact with someone who might know. I just emailed them to ask.
Actually what I want is labels for brodmann areas 20, 38, 46 and 9. Is there any way to get those for freesurfer?
Maryam
On Thu, Sep 26, 2013 at 5:45 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Maryam, it is not easy to do. Do they also supply an anatomical volume that you can view the labels on? doug On 09/26/2013 05:40 PM, Maryam Vaziri Pashkam wrote: Hi Doug, I have a bunch of label files donlowded from talairach Daemon website that I would like to upload to freesurfer and I am having trouble with it: http://www.talairach.org/nii/gzip/ I could read the files to matlab using MRI_read and they are volume masks of zeros and ones with the size: 172x141x110 Now I would like to import these into freesurfer and visualize them on the fsaverage suface or volume. The volume size in the mri folder of fsaverage is 256*256*256 and even though there is a transform function I am not sure how to match two volumes with very different sizes. Is this even possible? Thanks, Maryam -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.