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:
External Email - Use CautionDear 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@bli.uzh.ch homanlab.github.io/ellen/
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