You should get labels for both cortex and WM (159*2*2) plus labels for subcortical, which should bring it up to about 680. The numbering is going to depend on the order of the labels in the colortable in 500_sym.aparc. You can extract the color table with mris_anatomical_stats with the -c option (see recon-all.log for a command line). For lh cortex, prepend ctx-lh- to the name and add 1000 to the number For rh cortex, prepend ctx-rh- to the name and add 2000 to the number For lh wm, prepend wm-lh- to the name and add 3000 to the number For rh wm, prepend wm-lh- to the name and add 4000 to the number

On 7/30/2020 11:39 AM, Ellen Ji wrote:

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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

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Ellen Ji, PhD Postdoctoral Research Fellow Psychiatric University Hospital University of Zürich ellen.ji@bli.uzh.ch homanlab.github.io/ellen/

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