[Freesurfer] extra brain tiussue

Dear FS experts, I want to extra the extra brain tissue. Is it correct to subtract orig.mgz from aparc+aseg? Is this provide accurate estimates forrhe space between the brain tissue and the skull. Kindly, do you suggest me better solution? Thanks for any advice! J_

[Freesurfer] how to get intrinsic/gaussian curvature in custom FMRI ROI?

Hi, i would like to use an FMRI ROI as a label from which to extract some curvature metrics in single subjects. all my FMRI ROIs are in nifti volume format, in the same space as my freesurfer segmentations. i've tried this tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalT

Re: [Freesurfer] Issue with Freesurfer installation

Thanks, Andrew. That seems to have done the trick! On Thu, Dec 14, 2017 at 9:43 PM, Hoopes, Andrew wrote: > Hi Scott, > > It looks like "/Users/scottpruett/sample-001.mgz" doesn’t exist because > your cp command never ran (you have to specify a destination). Try: > cp $FREESURFER_HOME/subjects/s

Re: [Freesurfer] surface/volume conversion

Hi Martin you can use the ribbon.mgz for this I guess. The surfaces can't be represented perfectly in the volume since the volume is discretized and the surfaces live in a continuum. cheers Bruce On Fri, 15 Dec 2017, Strebl, Martin Georg wrote: > > Hi all, > > > Is there an existing matrix

[Freesurfer] surface/volume conversion

Hi all, Is there an existing matrix that I could use to transform the surface files (white/pial) back into the volume coordinate system so that they're registered with the fsaverage volume in another visualization tool like AMIRA? Currently they seem to be in totally different spaces. Best,

[Freesurfer] mri_gtmpvc & mri_gtmseg errors - failed tissue type check

Hi Doug, I ran mri_gtmseg on a subject & got no errors, and the gtmseg.mgz/apas+head.mgz outputs looked fine: $Id: mri_gtmseg.c,v 1.9.2.1 2016/08/02 21:07:49 greve Exp $ mri_gtmseg --s $s etc, exited fine Then I tried running mri_gtmpvc, and got a 'failed tissue type check' error: [weckl:FDG_201

[Freesurfer] local Gyrification Index

Hi: To compute local Gyrification Index is necessary Matlab... Complete installation or only runtime? Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 C

[Freesurfer] extract surface area for singe vertex

Dear Freesurfer experts, I've run a longitudinal two stage model of 2 time points to look at the rate of change in surface area and whether my two groups change differently. I find a superior parietal cluster in the right hemisphere. So far I've already run the mri_glmfit-sim to get the value

[Freesurfer] Finding correlation between Cth and clinical data

Dear Experts: I am very new to freesurfer glmfit and this post may seem dumb. I want to find the correlation between Cth and Education for each of HC and RRMS group regressing out the effect of gender and (demeaned) age. My fsgd file is something like below. GroupDescriptorFile 1 Title

Re: [Freesurfer] Nonlinear CVS registration into average brain for coordinates

Hey David, Have you managed to find a solution for that? Best, Noam From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Zhou, David Wei Sent: Thursday, April 7, 2016 3:10:38 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Nonlinear CVS reg