On 11/9/2020 3:58 PM, Hyon, Justin J. wrote:
External Email - Use CautionHello,
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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