[Freesurfer] mri_glmfit reference

Hi, following these refs I've found on the list and the mri_glmfit help, I assume the cluster-wise probability of the permutation simulation is based on cluster mass inference, is that right? Thanks, Georg Statistical Science 2004, Vol. 19, No. 4, 676-685 Institute of Mathematical Statistics,

Re: [Freesurfer] ICV Error fs 4.3.1

Did you check the transform to make sure it is accurate? tkregister2 --s subject --fstal --surf It could be that the scaling is not good. I've seen this before (no solution yet). doug Jeff Sadino wrote: > Thanks Doug. That is very good news to hear! > > Maybe I spoke too soon about fixing the

Re: [Freesurfer] ICV Error fs 4.3.1

Thanks Doug. That is very good news to hear! Maybe I spoke too soon about fixing the problem. I looked at 4 more subjects, and even though the icv value is unique, its magnitude seems wrong. Often times, it is smaller than the BrainSegVol, which doesn't make much sense and it is also low overal

Re: [Freesurfer] ICV Error fs 4.3.1

You just need to re-run segstats doug Jeff Sadino wrote: > Doug - > Thank you for your suggestion. I looked, and the > talairach_with_skull.lta file was unique to each subject. However, > the talairach.xfm file was actually a shortcut to > /apps/freesurfer3/subjects/fsaverage/mri/transforms/

Re: [Freesurfer] ICV Error fs 4.3.1

Doug - Thank you for your suggestion. I looked, and the talairach_with_skull.lta file was unique to each subject. However, the talairach.xfm file was actually a shortcut to /apps/freesurfer3/subjects/fsaverage/mri/transforms/talairach.xfm. This is because of some in-house legacy code that we use

Re: [Freesurfer] can't change common-space subject in qdec

which version of freesurfer are you using? it should be possible to edit the common-space subject in qdec included with v4.5. n. On Thu, 2010-02-25 at 14:53 -0500, Danielian, Laura (NIH/NINDS) [E] wrote: > Hi, > > I've created an average brain and would like to use that as the > "common-space s

[Freesurfer] can't change common-space subject in qdec

Hi, I've created an average brain and would like to use that as the "common-space subject" in my qdec analysis. However, the program does not seem to allow editing of that box - I can't seem to delete or type over the default fsaverage. Is there a trick to changing this information or another wa

Re: [Freesurfer] modification made to longitudinal results

Hi Guang, Depending on what you do you can choose different routes. Note, for both of these you first need to run the new timepoint cross sectionally (step 1 in the description http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing ): recon-all -all -s newtpid -i path/to/dicom Here are t

[Freesurfer] modification made to longitudinal results

Hi, there, I need add some control points to the longitudinal results. After adding control points, I need rerun it. which command should I use? recon-all -s subj.long.baseid or recon-all -long subj baseid Thanks! Guang ___

Re: [Freesurfer] LGN label or ROI....

no, sorry, not yet. On Wed, 24 Feb 2010, Ritobrato Datta wrote: > Hi All, > > Is there a method for obtaining an ROI for the lateral geniculate nucleus in > freesurfer ? > > Thanks, > > Ri > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.