On 11/9/2020 3:58 PM, Hyon, Justin J. wrote:

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Hello,

I’m new to Freesurfer and am trying to learn the steps to manually label some brain regions for use in source localization in MNE. So far my understanding is that I have to create label files which contain the list of coordinates for the vertices in each region, and a color lookup table which has a list of these labels and their corresponding RGB values for display. However, there are a few pieces missing in my understanding. How would I create the label files for each brain region? For example, if I wish to combine several regions found in the Desikan-Killiany atlas, how would I get from the label files generated via ?h.aparc.annot to new label files combining several labels?

Use mri_annotation2label to break up the labels in to pieces, then use mri_mergelabels to merge the labels you want into a single label. If you need a new annot, then you can use mris_label2annot

Also, in order to create a source space in MNE I need a single segmented .mgz output such as aparc.a2009s+aseg.mgz. If I create a new .annot based on my new label files and lookup table, how would I obtain this volume?

If you are using v6, then use mri_aparc2aseg. If you are using v7, then use mri_surf2volseg. Look in the recon-all.cmd file for example command lines (but make sure to change the output so that you don't overwrite)

Thank You!

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