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"
cheers Bruce
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: https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
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
-- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu