[Freesurfer] mri_vol2surf

2013-12-01 Thread Arash Nazeri
Hi all, I wanted to make sure how one could assign intensities from the subjacent white matter voxels to the cortical surfaces using mri_vol2surf. Based on the documentation page --projfrac, if used with negative values, would assign white matter values to the surface. I was wondering if this

Re: [Freesurfer] FW: recon -all in FS version 5.3 CentOS 6

2013-12-01 Thread Douglas Greve
Others (Nick, Zeke) correct me if I'm wrong, but you will get different answers with the two operating systems, so I would just analyze them on a single OS. doug On 11/27/13 3:46 PM, pablo najt wrote: Dear FS experts, I am forwarding a message I sent yesterday that my got lost in the lon

Re: [Freesurfer] Fwd: converting to fsaverage space

2013-12-01 Thread Douglas Greve
Don't go through fsaverage. Instead use mni152reg to create a registration matrix from an individual to the 152 (stored in $SUBJECTS_DIR/$subject/mri/transforms). Then use the command below with this registration matrix instead of mni152.register.dat doug On 11/27/13 2:57 PM, Paul Beach wr

Re: [Freesurfer] Volume differences after corrections

2013-12-01 Thread Douglas Greve
Hi Gari, this is expected because of the way that we estimate intracranial volume (based on registration to talairach space). But even in theory, you are only changing what is brain and not what is skull so eICV should not change. doug On 11/28/13 11:52 AM, Garikoitz Lerma-Usabiaga wrote: