That one looks like there was a massive failure of the registration. One
thing you can try is to add -samseg-reg to the command line. This will
use samseg to do this registration, which may be more robust. Is there
anything amiss with your image?
On 2/13/2023 10:25 AM, Goeckner, Bryna wrote:
External Email - Use Caution
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" <yhuan...@mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all exited with errors
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<mn2pr04mb5982d0100e4ec48d6fd8a2949d...@mn2pr04mb5982.namprd04.prod.outlook.com>
Content-Type: text/plain; charset="us-ascii"
Hi Bryna,
In this tutorial, it talks about how to fix bad output from the
talairach registration:
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Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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
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