Re: [Freesurfer] Thalamus ROI

Subject: Re: [Freesurfer] Thalamus ROI Hi Sara sure, you can look up the thalamus labels in FreeSurferColorLUT.txt (10 and 49 for lh and rh), then use either mri_extract_labels or mri_binarize to pull our ROIs. cheers Bruce On Mon, 7 Aug 2017, sarai...@alumni.ubc.ca wrote: > Hi Freesurfer t

[Freesurfer] Thalamus ROI

Hi Freesurfer team, Is it possible to extract Thalamus as an ROI from aseg.mgz to be used for tractography in FSL. If so, what command I have to use to extract it. Can I use the LUT table to extract thalamus? Thanks, Sara ___ Freesurfer mailing list

[Freesurfer] FSL-compatible surfaces

Hi Freesurfer team, I am trying to use Freesurfer surfaces to do tractography in FSL. I extracted two ROIs, one of which is the output of the following command: label2surf –s lh.white.gii –o lh.prefrontal.gii –l lh.prefrontal.txt and the other is the output of: mri_tessellate aseg.mgz 46

[Freesurfer] Using Freesurfer for skull stripping then reorienting images to use in FSL

Hello, We are using freesurfer to skull strip T1 images on a high-motion pediatric sample. We want to use freesurfer to get brain-only images and then do further analysis using FSL. The problem is that, in freesurfer, the images are in a different orientation than those in FSL. For example,