External Email - Use Caution
Dear experts,
I am running mri_aparc2aseg using two annotations as input (one for each
hemisphere), each with 159 labels, and wish to end up with a single
output segmentation of 318 labels. However, when I run the below, this
is not the case:
mri_aparc2aseg \
--s subject1 \
--annot 500_sym.aparc \
--wmparc-dmax 2 \
--labelwm \
--hypo-as-wm \
--o subject1/mri/parcellation.nii.gz
In fact, the output has 680 labels rather than 318 labels. A few questions.
- How can I see what exactly the 680 label names are (how to extract
from the .nii.gz output file)? Currently, I have just quantified it to
be 680 by doing this in matlab: gunzip('parcellation.nii.gz')
a = MRIread('parcellation.nii');
u = unique(a.vol(:));
length(u) % total number of labels
- I believe the extra labels are from the Freesurfer LUT. How can I make
sure they are not added when running mri_aparc2aseg? (such that only my
annotation labels are included in the output)
Thank you very much,
Ellen
*****
Ellen Ji, PhD
Postdoctoral Research Fellow
Psychiatric University Hospital
University of Zürich
ellen.ji(a)bli.uzh.ch
homanlab.github.io/ellen/
