Re: [Freesurfer] volume won't load in tkregister (fwd)

There does not appear to be a talairach.xfm file there. Did you just delete/move it? It looks like this data was collected way off from the magnet isocenter, and this may be causing it to be offset too far in the tkregister FoV. I've seen this type of thing before, but never quite so extreme.

[Freesurfer] volume won't load in tkregister (fwd)

Hi, I'm on thigpen and I ran source /usr/local/freesurfer/nmr-std-env setenv SUBJECTS_DIR /space/thigpen/8/users/akram/ADNI_processing tkregister2 --mgz --s 023_S_0030 --fstal but no volume will load. Any suggestions? Thanks! Akram. -- ---

Re: [Freesurfer] segmentation fault during mri_glmfit

I can't figure out what's happening, so I'll probably need the data. Can you tar up the input data, the fsgd, and the contrast matrices and drop them for me at: www.nmr.mgh.harvard.edu/facility/filedrop? Bum Seok Jeong wrote: Dear freesurfer users I got an error message during mri_glmfit.

Re: [Freesurfer] FSGD and design matrix

There are two ways to do a paired-t. The easiest, I think, is to use the --paired-t option to mris_preproc. The other option is to set it up in the fsgd file, but that's more complicated and less flexible. What do you mean by "group"? A class in the fsgd gets it's on mean regressor and possib

[Freesurfer] FSGD and design matrix

All- I am looking to run freesurfer group analysis on a longitudinal study, examining the changes between baseline and follow-up. I would like to set up a paired t-test, yet I am still in need of some assistance creating my FSGD file and my design matrix. I have read the GroupAnalysis wiki pa

[Freesurfer] error message during CA normalize (3T image)

I'm trying to analyze 3T spgr image with freesurfer. I faced error message during autorecon2 step. And typed 'recon-all -autorecon2 -conorm -subjid case to figure out which process it occured in. This is error message after putting '-conorm' tag.

Re: [Freesurfer] error message during CA normalize (3T image)

check the brainmask.mgz to see if it looks reasonable On Thu, 30 Nov 2006, Bum Seok Jeong wrote: I'm trying to analyze 3T spgr image with freesurfer. I faced error message during autorecon2 step. And typed 'recon-all -autorecon2 -conorm -subjid case to figure out which process it occured

[Freesurfer] segmentation fault during mri_glmfit

Dear freesurfer users I got an error message during mri_glmfit. (please see below my error message) I was able to find 'mri_glmfit.log' file in './glm/lh.dx_age.glmdir' directory Thank you for advance --- These are my constrasts. : to construct

Re: [Freesurfer] ASL perfusion maps

Hello all I am still having some trouble getting started on preprocessing of my ASL data. Steve Smith has suggested that I do sub-TR timing-adjustment before a subtraction analysis in FEAT. I wonder if anyone in the Martinos center has expertise with this kind of analysis. If possible, I'd lik