Hi Michelle

from the mri dir I think you can run:

mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg.rawavg.mgz

-rl = "reslice like"
-rt = "resample type"


p.s. I think your problem is probably that you used trilinear resampling. YOu could change the resampling in mri_vol2vol and it would work as well On Sun, 15 Apr 2018, Michelle VanTieghem wrote:

Hi Freesurfer experts, 

I am trying to convert the aseg back into native space of the anatomical T1 
image. I followed the
instructions as in the webpage:

specifically this line of code:

cd $SUBJECTS_DIR/<subjid>/mri
mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz 
--regheader aseg.mgz
However, the result is very odd. The aseg boundaries appear correct in the 
subcortical regions.
however, at the gray mater boundaries, there are single voxels incorrectly 
labeled as different
subcortical-regions. As a result, in the viewer, the gray matter boundaries 
look multicolored. 

This is problematic, as I would like to extract a mask of specific ROIs (e.g. 
right amygdala) but
there are many other voxels labeled '54' in addition to the right amygdala. 

See attached images. I would greatly appreciate your assistance!! 

Thank you, 

Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University 

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