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
Sun, 15 Apr 2018, Michelle
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:
mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz
However, the result is very odd. The aseg boundaries appear correct in the
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
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!!
PhD student in Psychology
Developmental Affective Neuroscience Lab
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