External Email - Use Caution
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 Métis Nation of Alberta, Region III.
________________________________ From: freesurfer-request@nmr.mgh.harvard.edu freesurfer-request@nmr.mgh.harvard.edu Sent: September 4, 2026 2:20 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 271, Issue 4
[△EXTERNAL]
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Today's Topics:
1. Re: mris_label2annot generates the wrong labels (fsbuild)
----------------------------------------------------------------------
Message: 1 Date: Thu, 03 Sep 2026 22:50:21 +0200 From: fsbuild fsbuild@contbay.com Subject: [Freesurfer] Re: mris_label2annot generates the wrong labels To: freesurfer@nmr.mgh.harvard.edu Message-ID: ccb75858b67361700c730091c38ad60f@trashmail.com Content-Type: multipart/alternative; boundary="_=_swift_1788468621_85c59db5602a01fe6dfd79a894c93d31_=_"
External Email - Use Caution
It would be useful to know the version of freesurfer you are running as well as the operating system version. The behavior might not be the same in different (more recent) freesurfer versions. - R. On Sep 3, 2026, at 16:14, Rachel Sharkey <rachel.sharkey1@ucalgary.ca> wrote:
-------------- next part -------------- A message part incompatible with plain text digests has been removed ... Name: not available Type: text/html Size: 1214 bytes Desc: not available
------------------------------
Subject: Digest Footer
_______________________________________________ Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu https://secure-web.cisco.com/1SSy-AVc3jCHndfEUPE-ClcbYJ35UQHAsyQn5ysfFSCGjMf...
------------------------------
End of Freesurfer Digest, Vol 271, Issue 4 ****************************************** The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1X4PL_D4Jz-Wht6k3xyROEBaYGjntfWZUHm44oVmLNEx-hO... https://secure-web.cisco.com/1X4PL_D4Jz-Wht6k3xyROEBaYGjntfWZUHm44oVmLNEx-hOgRl6f6eazqEaVzXFv0v_dVRZWNVbkg4jBoSed2nNIwf4fm8KcQAOk2svTUctv5qYBTOpFTyqHe0zsCc87iJv7ybDj_KE2TLEkfTSf-MUSyByEdHZ9WyMEc53xMopif2Ej5mKdgrUY8y884-becZcza5a-DSYa9YGatm4oURDmFol9SY3ahwd7Nl3KVY5v5XjI-PnCyi6Pu1-Za8kaU5T8ewOP6cQjL7fswjpCyQyPkHGoKtMMNI88FVuvvD0kdRskafTaWSlso3Y08Iy5_t625T4vqGhgy2mc7AyN0Cw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.