[Freesurfer] Extract values in ROI to ascii file

Dear Freesurfers, I am using mris_convert to obtain per vertex thickness values in an ascii file. What I would like to do is to limit the requested area to a certain region of interest using a label file. Is this possible? (analogous to mris_anatomical_stats where a label flag can be given?).

Re: [Freesurfer] Extract values in ROI to ascii file

Hi Ruthger sorry, I don't think we have anything to do exactly what you want. It would be easy enough to do in matlab though cheers Bruce On Fri, 27 Feb 2015, Righart, Ruthger wrote: Dear Freesurfers, I am using mris_convert to obtain per vertex thickness values in an ascii file. What I

[Freesurfer] freeview registration

Hi All, After using freeview to manually adjust the registration between a functional and T1.mgz generated by bbregister, I saved the registration file in freeview as lta format, which seems the only option. However, the registration file has same file name for source and target volume. So,

[Freesurfer] regional surface area differences

Hi Freesurfer group, I wanted to use mris_preproc to calculate regional differences in surface area between two groups. Ideally I would like to use something that is vertex-wise and preserves regional area, but I've had trouble with spherical demons (using the Winkler methodology). So I am going

[Freesurfer] Expediting the pial surface calculation

Hi, We are wondering if there is a faster way to generate lh.pial and rh.pial than running the 24 hour long recon-all function. We took a look at http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllFilesVsSteps and it seems that the inputs for lh.pial and rh.pial are needed from the recon-all

Re: [Freesurfer] Tracula: missing or incomplete tracts

Hi Anastasia, Sorry for the delay -- I missed your response. I did look at the anatomical segmentations and thought they looked OK. I've uploaded the tracula and corresponding freesurfer data for two subjects: one with complete tracts and one with missing/incomplete tracts. I also uploaded my

[Freesurfer] Projection of CBF maps on fsaverage and smooth

Dear Freesurfer's experts, I computed some perfusion maps from ASL data. These perfusion maps were registered on anatomical T1 and I would like to make a group analysis on surfaces. Please find below my actual commands in order to project these volumic maps on fsaverage then smooth the data