Thanks for the response. I should have been more clear in my first email. I have used tkregister2 in the past to fix talairachs, but this one does not appear to be fixable with the in-plane shifting, scaling, and rotating that is available within the tkregister2 GUI. The moveable appears to be in a different plane than the target. I’m attaching a screenshot from tkregister2.

Is there a different way to fix the talairach or another recon fix (especially considering the apparent brainmask issue) that should be pursued?

Thanks again for your help!

Bryna Goeckner (she/her)

Graduate Student

Meier Lab

Medical College of Wisconsin

Neuroscience Doctoral Program

Date: Fri, 10 Feb 2023 20:48:26 +0000
From: "Huang, Yujing" <YHUANG43@mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all exited with errors
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <MN2PR04MB5982D0100E4EC48D6FD8A2949DDE9@MN2PR04MB5982.namprd04.prod.outlook.com>

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Hi Bryna,

In this tutorial, it talks about how to fix bad output from the talairach registration:

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://urldefense.com/v3/__https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach__;!!H8mHWRdzp34!_l_gOh7Vnn8ovwqfR_EqP1dOfB-MrgDNoaNiCUIahwFJ_aGAOSKGKIk18p6fQDf2snUDr8V7UbYuZ_sgpEWHNY9oikTLS12PI--QGIY$

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Goeckner, Bryna
Sent: Friday, February 10, 2023 3:35 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Recon-all exited with errors

        External Email - Use Caution
Hi All,

I am using FS 7.2.0 and have one subject that exited recon-all with errors (looks like for talairach issues) but I am not able to use tkregister2 to view and make manual adjustments to the talairach since surf/lh.orig was not generated.

I then tried recon-all with the -notal-check flag, which exited "without errors" although the talairach is nowhere near correctly aligned and while aparc & aseg in freeview appear ok, the brainmask appears to have issues (when I turn it off, the entire background displays as white).

I'm including the recon-all logs (original & notal-check flag) and have listed the actual commands used below as well. Any help you can provide in figuring out how to run this subject is greatly appreciated. Thanks!

The original code was:
recon-all -subject subj# \
                -i rawT1.nii.gz \
                -T2 rawT2.nii.gz \
                -T2pial \
                -parallel -openmp 12 \
                -3T \
                -all

And for the second run, -notal-check was added after -all

For tkregister2:
tkregister2 --s subj# --fstal --surf orig

Bryna Goeckner (she/her)
Graduate Student
Meier Lab
Medical College of Wisconsin
Neuroscience Doctoral Program