mri_cor2label does work for extracting vectors with FreesurferColorLUT.txt label numbers from .mgz volumes.

The documentation at http://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2label states:

--id labelid

0-255 value in COR volume

The attached pdf shows the number of vectors which were extracted from each of 5 volumes for labels 1-255.

You can see that volumes aseg, aparc+aseg, and wmparc yield nearly identical results.  I ran several file pairs through spot checks and the vectors were identical in the ones I checked.

Volume filled.mgz contains vectors for only 3 labels while volume T1.mgz contained vectors for all of them and in most cases, the numbers were higher.

Questions:

1. Can mri_cor2label handle labelIDs > 255?

2. Is there a tool determining which labelIDs are represented in a .mgz volume?

3. Are there other volumes which I should be using for vector extraction for these labels.

4. Is there a way to extract labels with ids > 255? I assume that mri_cor2label is an older tool and the new approach is generate .annot files and then use mri_annotation2label.

5. How are .annot files created? I have been unable to find this even though it must be staring me in the face.

Thanks,

Don