[Freesurfer] small difference in recon-all for Ubuntu 11.10 and Centos 5.7

Hi I used recon-all on two different system one with Ubuntu 11.10 and a cluster with Centos 5.7. When I compare the recon-all of these two recon-all run I see that there is a small difference. Is this difference caused by difference in math libraries, and difference in the way floating point i

Re: [Freesurfer] trakula segmentation fault

Hi Anastasia, Here is the data: https://transfert.inria.fr/fichiers/4531ddb4948dff7223febc5a5b4f7e7d/testData.tar.gzLet me know if you have any trouble. I changed to the other track-all, and the error is the same. Please let me know if I'm doing anything wrong! Thank you! Viviana Siless -- Parieta

Re: [Freesurfer] small difference in recon-all for Ubuntu 11.10 and Centos 5.7

On Fri, Apr 6, 2012 at 4:05 AM, Knut J Bjuland wrote: > I used recon-all on two different system one with Ubuntu 11.10 and a > cluster with Centos 5.7. When I compare the recon-all of these two > recon-all run I see that there is a small difference. Is this difference > caused by difference in ma

Re: [Freesurfer] mri_label2vol cannot allocate memory

Hello--was wondering if you guys have any ideas. I am a bit stumped. Thanks for the help! Anthony On 4/4/12 4:50 PM, Anthony Dick wrote: > No, but the conversion from the original .nii works... > > [miles:[PATH]] adick% mri_convert chuman_1.mgz junk.mgh > mri_convert chuman_1.mgz junk.mgh > $Id:

Re: [Freesurfer] mri_label2vol cannot allocate memory

can you upload chuman_1.nii to our file drop? On 04/06/2012 11:30 AM, Anthony Dick wrote: > Hello--was wondering if you guys have any ideas. I am a bit stumped. > Thanks for the help! > > Anthony > > On 4/4/12 4:50 PM, Anthony Dick wrote: >> No, but the conversion from the original .nii works...

[Freesurfer] mkanalysis-sess gui

Does the GUI front-end for mkanalysis-sess still work in version 5? If I try `mkanalysis-sess -gui`, it starts asking for additional parameters (e.g., -fsd flag). If I specify all of the additional parameters, it just creates the analysis without launching a GUI. Am I missing something? Thanks,

Re: [Freesurfer] mkanalysis-sess gui

no, sorry, the GUI ended up being too difficult to maintain. doug On 04/06/2012 12:27 PM, Greg Burgess wrote: > Does the GUI front-end for mkanalysis-sess still work in version 5? If I try > `mkanalysis-sess -gui`, it starts asking for additional parameters (e.g., > -fsd flag). If I specify all

Re: [Freesurfer] mri_label2vol cannot allocate memory

if you email me the .mgz I'll fix it. On Fri, 6 Apr 2012, Anthony Dick wrote: > Hello--was wondering if you guys have any ideas. I am a bit stumped. > Thanks for the help! > > Anthony > > On 4/4/12 4:50 PM, Anthony Dick wrote: >> No, but the conversion from the original .nii works... >> >> [mile

[Freesurfer] grid overlay?

Hello, I have been trying to figure out if it is possible to overlay a grid on a surface (such as the regular non-inflated pial surface). I would like the grid to ignore the cortical convolutions and follow just the overall curvature of the cortex. I am trying to represent a grid of electrodes o

Re: [Freesurfer] grid overlay?

Hi Phiroz, I'm not sure I understand, but I think what you could do is create a volume representation of the grid, then sample it onto the surface with mri_vol2surf cheers Bruce On Fri, 6 Apr 2012, Phiroz Tarapore wrote: > Hello, > > I have been trying to figure out if it is possible to overl

Re: [Freesurfer] grid overlay?

If you don't want it to go into the folds of the sulci, you may want to use the brain surface from mri_watershed (note you will have to re-run with --save). This option is probably the simplest and most straightforward. If you are unhappy with those results there are many other options, which c

Re: [Freesurfer] grid overlay?

sorry, it should have said -surf -useSRAS options Bruce Fischl wrote: > Hi Phiroz, > > I'm not sure I understand, but I think what you could do is create a > volume representation of the grid, then sample it onto the surface with > mri_vol2surf > > cheers > Bruce > > On Fri, 6 Apr 2012, Phiro