[Freesurfer] mri_glmfit-sim on longitudinal data

Hi, I have read the Freesurfer Tutorial, but there is still something I do not understand. I want to run the mri_glmfit-sim command on our data. I have one sample (10 subjects), which were examined at 2 different timepoints. I tried to use this command: mri_glmfit-sim --glmdir Plast_injury

[Freesurfer] select_talairach_point

Hi, I would like to go over a list of talairach coordinates (which describe my electrode locations) and send these vertices as labels. I'm using select_talairach_point function, but the problem is that it only keeps the latest selection. So I end up with just one vertex. I'm using this TCL script t

Re: [Freesurfer] select_talairach_point

After seeing this post http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12855.html , I added a line to the script mark_vertex $select on but still the previous selections are not kept, selection of each point overwrites the previous ones. I'm guessing the cure is easy, any idea

Re: [Freesurfer] mri_glmfit-sim on longitudinal data

Nicki, can you send the log file that the simulation creates? doug Nicki Langer wrote: > Hi, > > I have read the Freesurfer Tutorial, but there is still something I do > not understand. > > I want to run the mri_glmfit-sim command on our data. I have one > sample (10 subjects), which were exami

[Freesurfer] Lobe mapping, based on the Desikan-Killiany Atlas

Dear Freesurfers, I would like to do Lobe mapping, based on the Desikan-Killiany atlas, see http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation. I was wondering if there is a reason why the banksts is not included in the list under temporal lobe. My first guess is because this is a su

Re: [Freesurfer] Questions about event related processing and selxavg-sess and selxavg3-sess

Ok, so looking at the FIR analysis, when I advance it to time point 5, I see my activation (yay!) but does this mean my timewindow, etc is set up wrong, or is this just something you have to do when you do a FIR analysis? Katie On Wed, Nov 3, 2010 at 7:05 PM, Douglas N Greve wrote: > The FIR doe

Re: [Freesurfer] Questions about event related processing and selxavg-sess and selxavg3-sess

It sounds like it is set up correctly. If you want a single map of the activation, you'll have to set up a proper contrast to do it. In mkcontrast-sess you can simply use -sumdelays; this will create a map based on the summation of the delays in the FIR. You can also choose a time point in the

Re: [Freesurfer] Voxel-wise T-test

gammavar is the "standard" variance (ie, the square of the standard error). The residual variance is in rvar. Mark Hollenbeck wrote: > Hi Doug, > > Thanks again for all your help! — Could you explain gammavar.mgh? Would this > be considered the stdev of the results found in gamma.mgh? > > Thanks

Re: [Freesurfer] Lobe mapping, based on the Desikan-Killiany Atlas

Hi Ruthger, The temporal lobe list/label should include the banks of the superior temporal sulcus (bankssts). Not sure why it's not in there but we will include it. Thanks for pointing this out! Best, Rahul > Dear Freesurfers, > > I would like to do Lobe mapping, based on the Desikan-Killiany a

[Freesurfer] How to get the Talairach coordinate of labels

Hi, Freesurfers, As the *.label file provide the vertex number and R,A,S positions. How could I get the corresponding position in Talairach coordinates for each vertex? That is, how could I convert the label in a subject's space into that in talairach space, considering the label is generated from

Re: [Freesurfer] FS 5.1

Hi, as mentioned before, target for 5.1 is still end of November. Best, Martin On Thu, 2010-11-04 at 19:40 -0400, Bruce Fischl wrote: > Martin is the one to ask > Bruce > On Thu, 4 Nov 2010, Alan Francis wrote: > > > Hi Bruce, Doug: > > > > I am planning to process scans in a longitudinal study