[Freesurfer] Petsc Error in Freesurfer v6.0

Hello Freesurfer Developers, I've just installed Freesurfer v6.0 and attempted to run the commands printed below in order to test the installation: freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \

Re: [Freesurfer] intensity normalization and GM exclusion

​ ta7029.zip ​Hi Bruce, Thank you for your prompt response. I added an expert.opts file with the line "mris_make_surfaces -max_gray_at_csf_border 60 -max_csf 35" and ran recon-all -s ta7029 -autorecon2 -

Re: [Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams

Thanks for taking another look at our data. I have uploaded another subject in the archive dsemanek2.zip . For this subject I have: 1) run the cross processing stream on both timepoints 2) created the base 3) edited the wm.mgz on the base 4) rerun –base –autorecon2-wm –autorecon3 5) run the long

Re: [Freesurfer] Thickness asymmetry and LH/RH corresponding vertices in fsaverage

Yes, I think so. One hemi will be systematically different than the other, and this can easily be picked up in the stats On 03/23/2017 10:07 AM, Dorian P. wrote: > Thank you Douglas. > > I understand the rigor needed in the analysis and I agree. One more > question for my curiosity. > > My thic

Re: [Freesurfer] Qdec 1.5

need more info On 03/22/2017 09:37 PM, Duy Nguyen wrote: > Dear Douglas > > Thank you for your response. I cannot run asegstats2table and > aparcstats2table command outside of qdec. > > Best regards, > Duy Nguyen > > *--v-- Peace --v--* > *Duy Nguyễn * > *Biomedical Engineering Department- IU H

[Freesurfer] Petsc Error in Freesurfer v6.0

This problem has been resolved by installing Freesurfer v6.0 on a Ubuntu 16.04 64-bit guest OS with "fixed disk space" instead of "Dynamically allocated". Michael The opinions, conclusions and other information expressed in the above message, or contained within attachments to the above messa

[Freesurfer] Smooth overlay in command line

Is it possible to set the smooth overlay option (i.e. no of iterations) from command line instead of freeview? I am taking some screenshots that would look nicer with a smoothed overlay. Dorian ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu h

Re: [Freesurfer] question about "mean curvatura"

Hello Bruce, Could you send me some papers using "meancurv" as the brain structure index to understand this concept? Thank you. Hui Li At 2017-03-22 21:58:12, "Bruce Fischl" wrote: >Hi Hui > >meancurv is the spatially smoothed mean curvature of the surface at each >point (that is,

Re: [Freesurfer] question about "mean curvatura"

Not sure what papers have used it (although we do in our spherical registration). The concept is: https://en.m.wikipedia.org/wiki/Mean_curvature > On Mar 23, 2017, at 8:22 PM, 李慧 wrote: > > Hello Bruce, > > Could you send me some papers using "meancurv" as the brain structure index > to unde

Re: [Freesurfer] Smooth overlay in command line {Disarmed}

You can use mri_surf2surf with the -nsmooth flag but just remember to set the target and source subject as the same subject, [check out the info in --help :) ] Cheers, *Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Resonance Center, The University of Nottingham. Honorary Resea

Re: [Freesurfer] question about "mean curvatura"

Thank you. Hui At 2017-03-24 08:44:41, "Bruce Fischl" wrote: Not sure what papers have used it (although we do in our spherical registration). The concept is: https://en.m.wikipedia.org/wiki/Mean_curvature On Mar 23, 2017, at 8:22 PM, 李慧 wrote: Hello Bruce, Could you send me some