Hi Bruce,

If I *just run the mri_convert command that you provided, it did not work. The result is the same, with randomly labeled voxels along the boundaries of GM.

*Am I supposed to run mri_convert and then also run the mri_vol2vol command?

I don't understand what you mean by trilinear sampling; because freesurfer recon-all resampled the data automatically, I did not control how it was done.

For mri_vol2vol, I just followed the instructions exactly as stated on the FsAnat-to-NativeAnat webpage. Can you please provide more detail as to what exactly I would need to modify in this command to alter the resampling? I have not found this website to be helpful either. https://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2vol#RequiredFlaggedArguments

Thank you,

Michelle

----

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, Apr 15, 2018 at 8:30 PM, Michelle VanTieghem <michelle.vantieghem@gmail.com> 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

Michelle VanTieghem

PhD student in Psychology

Developmental Affective Neuroscience Lab

Columbia University

mrv2115@columbia.edu