Vina,

See this tutorial page:

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData

namely, you use this command:

tkmedit <subj> brainmask.mgz lh.white \ -aux T1.mgz -aux-surface rh.white \ -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt

which loads the surfaces creates by recon-all on top of the skull-stripped volume (brainmask.mgz). You would step through the slices to confirm that the pial and white surfaces are correct.

Nick

On Tue, 2008-08-19 at 13:07 -0500, Vina Goghari wrote:

Hello, I used recon-all on my subjects as I didn't expect majority of subjects to have a problem. However, what are the core steps (output images) I should check through for every subject?

Thanks, Vina _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Hi Tim,

the thickness is stored in the ?h.thickness file for every vertex on each hemisphere (*not* for every voxel). YOu can convert it to an ascii format with mris_convert, or the aparc.stats file tabulates it by region.

cheers, Bruce On Wed, 20 Aug 2008, [GB2312] ÀîÈÕ wrote:

Hi: I have run the recon-all command and it finished without error. And now I am interested with the thickness, I want to select a region of interest and get information of every voxel,including the coordinate ,the thickness of this voxel.Also , I want to put these information into a file. Does anyone know how to do this? Thank you very much.

Tim