Hi Yolanda,

the first command maps the aseg from the "conformed" voxel geometry back to the voxel geometry on the scanner, and the second extracts the caudate from that volume. If you want the caudate in the conformed space, just use aseg.mgz in the mri_extract_label command instead of aseg-in-rawavg.mgz

cheers
Bruce

On Thu, 10 Feb 2011, Yolanda Vives wrote:

Dear freesurfer's,

I have run a conventional recon-all process and I am interested in isolating
the caudate from my subjects. I have applied the following commands:

*./mri_label2vol --seg $SUBJECTS_DIR/$subj/mri/aseg.mgz --temp
$SUBJECTS_DIR/$subj/mri/rawavg.mgz --o
$SUBJECTS_DIR/$subj/mri/aseg-in-rawavg.mgz --regheader
$SUBJECTS_DIR/$subj/mri/aseg.mgz
*
*./mri_extract_label $SUBJECTS_DIR/$subj/mri/aseg-in-rawavg.mgz 11
$PROJDIR/$subj.nii.gz
*

I had seen in the wiki that these commands should be used when we need the
images in native space. ¿Does it mean that my caudates are "denormalized" or
on the contrary, that the images have only been resliced to the original
size? If it is the second case, how could I obtain the caudates from the
original image?

Thank you for your help,
Yolanda

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