On 08/06/2014 11:40 AM, Krieger, Donald N. wrote:
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 http://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2label states:
--id labelid
0-255 value in COR volume
That is probably old documentation (try running it with --help)
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?
yes
2.Is there a tool determining which labelIDs are represented in a .mgz volume?
mri_segstats will do it (see the --sum output)
3.Are there other volumes which I should be using for vector extraction for these labels.
I'm not sure what labels you want.
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.
mri_cor2label
5.How are .annot files created? I have been unable to find this even though it must be staring me in the face.
mris_ca_label during recon-all
Thanks,
Don
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer