[Freesurfer] Correcting MRI distortions: NITRC and grad_unwarp problems.

2010-07-28 Thread Matt Russell
Hello All, I’m working with some data that I would like to compare inter-site, and would like to correct the gradient distortion from the different scanners (Siemens Allegra and Trio). That being said, I have looked online at the documentation to do this and have not been able to

[Freesurfer] mri/orig File naming requirements

2010-10-09 Thread Matt Russell
Hello All, I'm currently working an automation program to setup a FreeSurfer file system for processing. I was wondering if I put a quality check pipeline in the code, deleting files that fail an inspection, would I have problems if the file name order ceased to be 001.mgz, 002.mgz, 003.mgz and w

[Freesurfer] Running multiple GLM analyses together

2010-11-15 Thread Matt Russell
Hello, I'm currently trying to run an analysis on data that has 1 group and 5 covariates. As each of these covariates of interest independently, I would like to calculate a GLM for each of them using FreeSurfer. Is it possible to run all 5 of these in one glm_fit call? If so, how would I s

Re: [Freesurfer] Intensity Problem

2011-03-08 Thread Matt Russell
y away > from the affected regions. It's hard to tell from one slice. > Cheers > Bruce > > > > On Mar 3, 2011, at 9:47 PM, Matt Russell wrote: > > > Dear FreeSurfer Experts, > > > > I'm currently working with a data set that seems to have a systematic