Hi Maria,

There are some assumptions to run mris_label2annot with Freesurfer 7.3.2:

1. label id 0 is reserved for Unknown, can you change your first line to ‘0 Unknown 0 0 0 0’?

2. the rest of your label ids need to be sequentially numbered

3. each label needs to have unique color scheme

4. the label files listed in your command line need to in the same order of the label appear in LUT

Say you first label has id=11102, specify ‘—offset 11102’ on your command line.

Can you give it a try?

Best,

Yujing

ps. the dev version of mris_label2annot has a different assumption. It doesn’t require #2 and #4. But it requires the <labelname> are embedded in label file names (?h_<labelname>.label) – the <labelname> need to be found in LUT.

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Maria Czarnecka
Sent: Friday, June 30, 2023 10:59 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_label2annot

External Email - Use Caution

Dear Yujing,

Thank you so much for your answer.

My ctab looks like this:

11100 Unknown 0 0 0 0
11102 G_and_S_occipital_inf 0 0 0 0
11111 G_cuneus 0 0 0 0
11119 G_occipital_middle 221 60 60 0
11120 G_occipital_sup 0 0 0 0
11121 G_oc-temp_lat-fusifor 0 0 0 0
11122 G_oc-temp_med-Lingual 0 0 0 0
11130 G_precuneus 0 0 0 0
11143 Pole_occipital 221 60 60 0
11145 S_calcarine 221 60 60 0
11158 S_oc_middle_and_Lunatus 0 0 0 0
11160 S_occipital_ant 0 0 0 0
11161 S_oc-temp_lat 20 180 140 0
11162 S_oc-temp_med_and_Lingual 0 0 0 0

11166 S_parieto_occipital 221 60 60 0

a sample of one of my label files:

#!ascii label , from subject fsaverage vox2ras=TkReg
1630
139 -4.532 -75.888 20.953 0.0000000000
300 -15.423 -72.840 16.348 0.0000000000
301 -15.452 -76.689 23.049 0.0000000000
571 -15.631 -67.683 9.887 0.0000000000
573 -4.258 -84.880 12.147 0.0000000000

version of FreeSurfer:
freesurfer-linux-centos7_x86_64-7.3.2-20220804-6354275