how are you verifying that it is not in the right place? You should view it on the 2mm MNI152 using freeview. Also, your label should be a label in fsaverage space.

On 3/27/18 9:52 AM, gj wrote:

Hi,

Newbie question....I want to take FreeSurfer labels (from an atlas in fsaverage space) and convert it into a volumetric NIFTI mask. I ran the following command, but I must be missing something because the output is not in the right space (far too posterior):

$FREESURFER_HOME/bin/mri_label2vol \

--label $ll \ --temp $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \ --reg $FREESURFER_HOME/average/mni152.register.dat \ --fillthresh .5 \ --o $wd/${ll}.nii

Am I perhaps supposed to first create the volumetric file without mapping into MNI space and then use tkregister2?

Thanks in advance for any help or advice! Gina _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer