Re: [Freesurfer] (no subject)

it should not take mri_glmfit that long to run. Or did that run ok and your off to -sim? If so, check the glmdir/fwhm.dat file to see if the FWHM is ok (should be a little larger than the amount your smoothed). doug On 11/02/2012 04:17 PM, Ryan wrote: > Doug, >The analysis has been running f

Re: [Freesurfer] (no subject)

Doug, The analysis has been running for about 45 minutes, but I'll e-mail you if there are any more errors. Thank you. On Fri, Nov 2, 2012 at 12:41 PM, Douglas N Greve wrote: > If this is a surface based analysis, then you'll need to add --surface > fsaverage rh > doug > > > On 11/02/2012 11:

[Freesurfer] checking talairach.lta

Hi folks, In previous threads, the command provided to check the talairach.lta is... tkregister2 --mov $FREESURFER_HOME/average/RB_all_2008-03-26.gca \ --targ ../brainmask.mgz --lta-inv talairach.lta --reg talairach.lta.reg.dat \ --surfs --s $subject When I try to run this command, I run into t

Re: [Freesurfer] source of recon-all errors?

Can you send the log file? doug On 11/01/2012 08:04 PM, Angie Morales wrote: > Thanks for the reply. Unfortunately, disk space does not seem to be > the problem. > > On Thu, Nov 1, 2012 at 1:43 PM, Angie Morales > wrote: > > I'm using Freesurfer version 5.1.0 and

Re: [Freesurfer] (no subject)

If this is a surface based analysis, then you'll need to add --surface fsaverage rh doug On 11/02/2012 11:34 AM, Ryan wrote: > Doug, >I ran: mri-glmfit --glmdir rh.rmanova --y rh.thickness.sm25.mgh > --fsgd fsgd doss --C training-effect.mtx > > > On Thu, Nov 1, 2012 at 7:13 PM, Douglas N Gre

Re: [Freesurfer] (no subject)

Doug, I ran: mri-glmfit --glmdir rh.rmanova --y rh.thickness.sm25.mgh --fsgd fsgd doss --C training-effect.mtx On Thu, Nov 1, 2012 at 7:13 PM, Douglas N Greve wrote: > > > On 11/01/2012 06:35 PM, Ryan wrote: > >> Doug, >>Picture 4 shows the difference between the medial surface for this >

Re: [Freesurfer] overlapping surfaces after running recon-all

Hi Deirdre I think the -noaseg is causing your problems. Can you point us at the tutorial that says to include that flag? cheers Bruce On Thu, 1 Nov 2012, Deirdre O Shea wrote: > Hello FreeSurfer experts, > > I am having a lot of trouble with the surfaces on some of my subjects. The > main pr

[Freesurfer] whole brain volume from ADNI UCSFFSL table

I knew this question has been asked before and it was suggested to use SupraTentorial as the whole brain volume. I am working with ADNI data and cannot find this measurement from UCSFFSL table. As my understanding, UCSFFSL table was generated by Freesurfer 4.4. I was wondering which structures

Re: [Freesurfer] recon-all: too many levels of symbolic links

Hi Linda it sounds like you put your own subjects into the directory $FREESURFER_HOME/subjects, which is where we store our average data and symlink within your SUBJECTS_DIR. Try putting them somewhere else cheers Bruce On Fri, 2 Nov 2012, Linda Zhang wrote: Dear all, I've been running re

[Freesurfer] recon-all: too many levels of symbolic links

Dear all, I've been running recon-all on my dataset, but all of them are exiting with the same error. The command line is: recon-all -subjid ncpoCCW -autorecon2 -autorecon3 The error reads: #@# Ex-vivo Entorhinal Cortex Label lh Sat Aug 25 11:54:33 HKT 2012 INFO: lh.EC_average subject does not e