Re: [Freesurfer] Monte Carlo Simulation w/ custom design matrix

How did I miss that??? Thanks! - Jerry On Thu, Apr 17, 2008 at 3:01 PM, Doug Greve <[EMAIL PROTECTED]> wrote: > there should be a fwhm.dat file in the output. > > doug > > > Jerry Yeou-Wei Chen wrote: > > Hello, > > I have a question regarding performing Monte Carlo simulations when a > custom d

Re: [Freesurfer] Monte Carlo Simulation w/ custom design matrix

Jerry, can you post your command lines and log file? there should be fwhm.dat along with the y.fsgd. > How did I miss that??? > Thanks! > - Jerry > > On Thu, Apr 17, 2008 at 3:01 PM, Doug Greve <[EMAIL PROTECTED]> > wrote: > >> there should be a fwhm.dat file in the output. >> >> doug >> >> >> J

Re: [Freesurfer] Monte Carlo Simulation w/ custom design matrix

Actually, I do have the fwhm.dat file... I was just commenting on how obvious that should have been to me! Thanks, though! - Jerry On Fri, Apr 18, 2008 at 10:56 AM, Pratap Kunwar <[EMAIL PROTECTED]> wrote: > Jerry, > > can you post your command lines and log file? there should be fwhm.dat > along

Re: [Freesurfer] subcortical segmentation

Hi Abel, yes, they will change the volume. You can manually correct them in the aseg.mgz if you want. cheers, Bruce On Fri, 18 Apr 2008, abel cruz vadell wrote: Hello I’m doing a thalamus volumetric analysis between two populations and checking the thalamus segmentation I found some pixels

[Freesurfer] "Talairach failure detection" in longitudinal processing

Nick, I thought I would send your very precise fix to the list in case anyone else just might run into the a similar issue. I'd also like to thank you and Bruce profusely for all your great help! The longitudinal subject ran through successfully last night. Sky At 04:01 PM 4/17/2008, Nick Schman

[Freesurfer] LGI: EXITS with ERRORS

I recently downloaded and installed fs4v03 (CentOS 4x86_64) on my new 64bit linux box running RHEL 5 (Tikanga). I didn't see any special notes on the download page for RHEL 5 (only RHEL 4 is noted). While test-driving my first dataset through the fsv403 pipeline, I encountered some difficulties

Re: [Freesurfer] LGI: EXITS with ERRORS

Jenifer, The new -localGI feature makes use of the pial surfaces that the freesurfer processing stream produces, so it is necessary for those to exist first. You can accomplish either with: recon-all -s -all and inspect the surfaces, and then: recon-all -s -localGI or in one step with:

[Freesurfer] LocalGI:exit with errors

Hi, I download the Freesurfer 4.0.3 and installed it on linux,I tested it on the subject bert which is included in /freesurfer/subjects, I run "recon-all -s bert -localGI" but it exited with errors as follows: lGI for vertex number 20101 of the outer mesh is 3.0478 lGI for vertex number 20201 of