You need to include a registration file with your tksurfer command, something like: tksurfer subjectid rh inflated -reg featdir/reg/freesurfer/register.dat -overlay featdir/rendered_thresh_zstat1.nii.gz
Did you check the registration with tkregister2? If not, do so first. You can also load it on the volume witth:
tkmedit subjectid orig -reg featdir/reg/freesurfer/register.dat -overlay featdir/rendered_thresh_zstat1.nii.gz
doug
leonardo kay wrote:
Thanks Doug.
After doing reg-feat2anat , I checked the registration and overlaid zstat file:
tksurfer subjectid rh inflated -overlay featdir/rendered_thresh_zstat1.nii.gz
I have attached an image of tksurfer interface . I'm not quite sure about what blue and red clusters mean. They are suposed to be activations, but I'm not watching the same in FSL-view. Could you give me a hand please? Am I using the right stat file?
Thanks in advance best regards.
---------- Forwarded message ---------- From: *Douglas N Greve* <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> Date: 2011/3/23 Subject: Re: [Freesurfer] [Fressurfer] fMRI and anatomical T1 To: leonardo kay <leonardo.kay@gmail.com mailto:leonardo.kay@gmail.com> Cc: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu
There is a tutorial on this on our wiki. Basically, you need to run reg-feat2anat to get a registration file, then run tksurfer passing it the registration file and the stat volume as the overlay.
doug
leonardo kay wrote:
Hi all Can anyone help me overlaying fMRI activations from fsl on a anatomical T1 volume in freesurfer. Is there any previous format conversion to do before? Thanks in advance best regards, -- Leo Kay. ------------------------------------------------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
-- Leo Kay.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer