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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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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
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