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Hi Maria,

Your command looks fine. Can you share what your ctab looks like, sample of your label files, version of Freesurfer you are running?

Best,

Yujing From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Maria Czarnecka Sent: Tuesday, June 27, 2023 9:07 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mris_label2annot

External Email - Use Caution Dear Sisters and Brothers in neuroscience,

I am trying to make my own annotation file that will include only occipital cortex labels from the a2009s atlas. Is it possible?

I am trying to do that with:

mris_label2annot --ctab lh.my-color-table.txt --a my-annot-name --h lh --s fsaverage --l lh.S_calcarine.label --l lh.S_parieto_occipita.label --l lh.G_cuneus.label --l lh.G_oc-temp_med-Lingual.label --l lh.S_collat_transv_post.label --l lh.G_and_S_occipital_inf.label --l lh.Pole_occipital.label --l lh.G_occipital_middle.label --l lh.S_oc_middle_and_Lunatus.label --l lh.S_oc_sup_and_transversal.label --l lh.G_occipital_sup.label --l lh.S_oc-temp_med_and_Lingual.label --l lh.G_oc-temp_lat-fusifor.label --l lh.S_oc-temp_lat.label

If i run it i get:

0 0 1 -1 NOT_FOUND 2 -1 NOT_FOUND 3 -1 NOT_FOUND 4 -1 NOT_FOUND 5 -1 NOT_FOUND 6 -1 NOT_FOUND 7 -1 NOT_FOUND 8 -1 NOT_FOUND 9 -1 NOT_FOUND 10 -1 NOT_FOUND 11 -1 NOT_FOUND 12 -1 NOT_FOUND 13 -1 NOT_FOUND Writing annot to...

The file is saved and it is empty. Where is my mistake?

I will be grateful for your help, Best, Maria Czarnecka