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Freesurfer Version: 7.4.1
R Studio Version: 2022.07.1
R Version: 4.4.1
Operating System: macOS Tahoe 26.6.2

I also went back through the output in terminal and there is an indexing error. Here is the start of what gets printed into the terminal: 

subject sub-F03019_ses-30D_T1W
hemi    lh
SUBJECTS_DIR /Volumes/SHRedMRI/01-CodeFiles/FinishedCode/FreeViewImageGeneration/SignificanceMap
ColorTable /Volumes/SHRedMRI/01-CodeFiles/FinishedCode/FreeViewImageGeneration/SignificanceMap/SecondErrorTest_editedColour.txt
AnnotName  ctab.hand.edited.R.output2
nlables 34
LabelThresh 0 0.000000
Loading /Volumes/SHRedMRI/01-CodeFiles/FinishedCode/FreeViewImageGeneration/SignificanceMap/sub-F03019_ses-30D_T1W/surf/lh.orig
Index Offset 0
0 reading /Volumes/SHRedMRI/01-CodeFiles/FinishedCode/FreeViewImageGeneration/SignificanceMap/aparc-labels-left/lh.bankssts.label
 1 10657952 caudalanteriorcingulate
1 reading /Volumes/SHRedMRI/01-CodeFiles/FinishedCode/FreeViewImageGeneration/SignificanceMap/aparc-labels-left/lh.caudalanteriorcingulate.label
 2 10723488 caudalmiddlefrontal
2 reading /Volumes/SHRedMRI/01-CodeFiles/FinishedCode/FreeViewImageGeneration/SignificanceMap/aparc-labels-left/lh.caudalmiddlefrontal.label
 3 10854560 cuneus
3 reading /Volumes/SHRedMRI/01-CodeFiles/FinishedCode/FreeViewImageGeneration/SignificanceMap/aparc-labels-left/lh.cuneus.label
 4 10920096 entorhinal
4 reading /Volumes/SHRedMRI/01-CodeFiles/FinishedCode/FreeViewImageGeneration/SignificanceMap/aparc-labels-left/lh.entorhinal.label
 5 10985632 fusiform

What I can't figure out is where the mis-indexed numbers are coming from because I can't see anything in the text file , this is what the first few rows of that looks like (this is a version with colours edited but the same issue happens when I use autogenerated colours):

0 unknown 160 160 160 0
1 bankssts 160 160 161 0
2 caudalanteriorcingulate 160 160 162 0
3 caudalmiddlefrontal 160 160 163 0
4 corpuscallosum 160 160 164 0
5 cuneus 160 160 165 0
6 entorhinal 255 239 0 0
7 fusiform 160 160 167 0
8 inferiorparietal 160 160 168 0
9 inferiortemporal 160 160 169 0

If I figure out anything else I will update this thread.

Thanks

Rachel

Rachel J. Sharkey, Ph.D. (she/her)
Research Associate, Sport Injury Prevention Research Centre 
Faculty of Kinesiology, University of Calgary

I would like to acknowledge that I reside within the traditional territories of the peoples of Treaty 7, which includes the Blackfoot Confederacy, comprising the Siksika, Piikani, and Kainai First Nations, the Tsuut¡¯ina First Nation, the Stoney Nakoda First Nations, including the Chiniki, Bearspaw, and Wesley First Nations.  The City of Calgary is also home to M¨¦tis Nation of Alberta, Region III.

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Date: Thu, 03 Sep 2026 22:50:21 +0200
From: fsbuild <fsbuild@contbay.com>
Subject: [Freesurfer] Re: mris_label2annot generates the wrong labels
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        External Email - Use Caution

It would be useful to know the version of freesurfer you are running as well as the operating system version. &nbsp;The behavior might not be the same in different (more recent) freesurfer versions.
- R.
On Sep 3, 2026, at 16:14, Rachel Sharkey &lt;rachel.sharkey1@ucalgary.ca&gt; wrote:

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