[Freesurfer] Separating Regions of the Brain from Choi and Yeo Loose and Tight Atlases

close to the original liberal mask as possible. -- *Thomas DeRamus* UAB Department of Psychology, Behavioral Neuroscience Graduate Research Trainee Civitan International Research Center 1719 6th Ave S, Suite 235J, Birmingham, AL 35233 *Phone*: 205-934-0971 *Email:* tpdera

Re: [Freesurfer] trac-all -path error "Segmentation Fault (Core Dumped)"

mr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Complia

Re: [Freesurfer] --pca flag on mri_glmfit

look at them > and decide they are too big. The u.mtx are the "temporal" components. > > doug > > On 12/04/2014 11:10 AM, Thomas DeRamus wrote: > > Dear Freesurfer experts, > > > > Potentially super-noob question here, but I'm curious about the --pca

[Freesurfer] --pca flag on mri_glmfit

if so, what do these components reflect?). And most importantly, is this meant primarily for functional data or can it be applied to mophometric data? If it can be used for the latter, what is being fed into the PCA/SVD to determine spatial components? -- *Thomas DeRamus* UAB Department of Psych

Re: [Freesurfer] Running mri_glmfit-sim with pre-computed Monte-Carlo

How do I change the path so that it's reading from the label I made (Socialbrain) in lieu of the cortex? On Mon, Oct 20, 2014 at 5:42 PM, Thomas DeRamus wrote: > That one gives the following error: > > mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --cache-dir &g

Re: [Freesurfer] Running mri_glmfit-sim with pre-computed Monte-Carlo

or --sim) > > On 10/20/2014 05:42 PM, Thomas DeRamus wrote: > > It does not I'm afraid. The error I get says the following: > > > > mri_glmfit-sim --glmdir rh.ALESocial__agevolume.glmdir --cache-dir > > > /media/rkbatch/gyrification/fsaverage/mult-comp-cor/fsaverag

Re: [Freesurfer] Running mri_glmfit-sim with pre-computed Monte-Carlo

-sign abs as well. On Mon, Oct 20, 2014 at 3:15 PM, Douglas N Greve wrote: > > You should not spec --sim. If you do not, does it work? > doug > > On 10/20/2014 04:10 PM, Thomas DeRamus wrote: > > I guess the better term would be to say that I'm not sure if the > >

Re: [Freesurfer] Running mri_glmfit-sim with pre-computed Monte-Carlo

line > and terminal output. Also, are you following these instructions? > > https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo > > > On 10/20/2014 03:50 PM, Thomas DeRamus wrote: > > Dear Freesurfer Experts, > > > > I have a label file of a number of

[Freesurfer] Running mri_glmfit-sim with pre-computed Monte-Carlo

gn value like it wants to compute a monte-carlo from scratch. Could I get an example on how best to direct it to the simulation I've run on it? Thanks much. -Thomas -- *Thomas DeRamus* UAB Department of Psychology, Behavioral Neuroscience Graduate Research Trainee Civitan International

[Freesurfer] White Matter and Pial Edit Question

to 500k compared to the originals. So my question is, would it be feasible or kosher to put the brainmask and wm.mgz values from those skull-stripped images into the problem folders grabbing too much dura and re-running the subjects starting from autorecon2? Thank you. -- *Thomas DeRamu

[Freesurfer] Using Gender as a Covariate in glm_fit

Hello, I am performing an mri_glmfit analysis between my control and my clinical group, and I'm including age and total intracranial volume in the model. However, I'd like to regress out the effects of gender, and I'm curious if the best approach to do this is to group my subjects by their gender