[Freesurfer] Surface-based Interhemispheric Registration generate average surface from average subject

Hi FSexperts, I would like to compute a symmetrical template out of the anatomical images in a group of subjects. I followed the description in: https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi Afterwards I recognized that no surfaces were generated. Since the computation takes quiet a while

Re: [Freesurfer] visualize subcortical areas in tksurfer?

HI Daniel no, that won't work. Vol2surf samples a volume to an existig surface and none of the subcortical structures will be anywere near the cortical surface. You would need to run mri_tessellate on each subcortical label that you want to generate a surface for, but I'm still not sure what y

[Freesurfer] manually drawn ROI mean thickness extraction

Dear all freesurfers, I have manually drawn a region of interest and saved it as a label file in the /label folder and I now want to extract mean thickness of this ROI. How can I do it? Thanks a lot Claudia -- Dott.ssa Claudia Dacquino, Specialista in Neuropsicologia Laboratorio di Neuropsichia

[Freesurfer] Subcortical Projection

Hi Freesurfer Experts, I'd like to project a subset of the subcortical structures from the aparc.a2009s+aseg annotation onto the closest medial surface vertices and write them into an annotation file. Is this possible? If so, what would be the easiest way to accomplish it? Thanks. - Archana _

Re: [Freesurfer] Subcortical Projection

I'm not sure why you would want to do that and there's no freesurfer tools I know of that will help you do that. What I can think of doing which requires a bit of programming is, identifying the set of surface vertices with a minimum distance to any voxel in the subcortical structure of interest, a

Re: [Freesurfer] manually drawn ROI mean thickness extraction

Hi Claudia I think mris_anatomical_stats can take a label file, which would do the trick cheers Bruce On Fri, 20 Feb 2015, Claudia Dacquino wrote: Dear all freesurfers, I have manually drawn a region of interest and saved it as a label file in the /label folder and I now want to extract mean

Re: [Freesurfer] ERROR: mritotal failed, see transforms/talairach.log

Hello Kathleen, The mritotal program is only run after our primary talairach alignment utility fails. Make sure your 'orig.mgz' looks 'good', that it, like the orig.mgz does in the sample subject 'bert': full head view with good orientation, and decent gm/wm contrast. If it is ok, then a workaro

Re: [Freesurfer] segmentation fault mri_convert Ubuntu 14.04

Luigi, I will be able to assist you in getting this to work but I am away at the moment and won't be back till mid next week. If no one else provides you with a solution I will be able to help you at that time. -Zeke > On Feb 19, 2015, at 12:14 AM, Luigi Antelmi wrote: > > Dear all, > I'm

[Freesurfer] Creating subject-wise functional ROIs on the cortical surface

Hello Freesurfers, I've run into issues trying to create functionally-defined ROIs on the cortical surface in FreeSurfer 5.3. I processed my functional localizer data in FsFast, which produced nice activation maps on the cortical surface. I would like to create ROIs from those maps (i.e., freesur