[Freesurfer] FIR analysis

Hi experts, I was wondering if there is any tutorial or example on FIR analysis. I don't know where to start. I need to look at the time course of some voxels. I have a localizer session and the main experiment. I am intending to find the ROIs in the localizer scans and then extract their time co

[Freesurfer] ROI extraction using functional masks

Dear FS experts, I am trying to extract values for cortical thickness, surface area and volumes, from different functional ROIs. These cortical ROIs have been defined using SPM tools, and are in .nii format. My scans have been processed using FS v5.3. Although the conversion seems to go well, t

Re: [Freesurfer] QDEC Set Up

Since I have 4 groups here: X1-M, X2-M, X1-F and X2-F, so can someone please confirm if this is identical to this example: https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V If so, then I can follow instructions on this page and set up my contrast files accordingly. Thanks. On Mon, Feb 12, 2018

[Freesurfer] QDEC Set Up

Hi FS experts, I have two population groups X1 (controls) and X2 (patients). I am interested in calculating impact of sex (F or M) on causing difference between both groups e.g. I am interested in following 4 contrasts: X1 (F) > X1 (M) X2 (F) > X2 (M) X1 (F) > X2 (F) X1 (M) > X2 (M) X1 (M+F) > X2

Re: [Freesurfer] Removing labels after extending parcellation into white matter

Hi Doug, Thanks - this is extremely helpful! With regard to the first command: mri_binarize --replace 1001 3001 --i aparc+aseg+2mm.masked.nii.gz --o aparc+aseg+2mm.masked.merged.nii.gz Since I'd like to replace every cortical label with its corresponding WM label on both hemispheres, is there a m

Re: [Freesurfer] Problems running LGI

Hi Dusan, I’ll take a look at this and get back to you soon. I think this issue is related to the matlab version. best Andrew On February 10, 2018 at 4:27:11 PM, Dusan Hirjak (dusanhir...@hotmail.com) wrote: Dear Freesurfer Experts, I am currently trying to