Hi Kourosh,

you can ask the freesurfer list for these kind of questions. I believe that the ras coordinates are not changed, so reslicing everyhting as the original inputs will be sufficient (no transform, only based on the header information) e.g. mri_convert -rt nearest -rl youroriginialinput.mgz labels.mgz labelsinorig.mgz if it is labels (e.g. aseg.mgz) you are mapping, use nearest neighbor, else use -rt cubic (in the dev version) in stable versions (5.1 and earlier) just stick with linear (default).

Best, Martin

----- Original Message ----- From: "Kourosh Jafari-Khouzani" kjafari@nmr.mgh.harvard.edu To: "Martin Reuter" mreuter@nmr.mgh.harvard.edu Sent: Thursday, April 19, 2012 10:04 AM Subject: Question about FreeSurfer

Hi Martin,

I have a question about FreeSurfer subcortical segmentation: FreeSurfer reslices an image and makes the voxel 1 mm isotropic and then segments it. Is there a command to map the labels back to the original image?

In case you don't know the answer, do you know anyone who may know it?

Thanks! Kourosh