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* <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Date: 2011/3/23 > Subject: Re: [Freesurfer] [Fressurfer] fMRI and anatomical T1 > To: leonardo kay <leonardo....@gmail.com <mailto:leonardo....@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 > gr...@nmr.mgh.harvard.edu <mailto:gr...@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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
