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:
https://secure-web.cisco.com/1AsdowaGUQbpsRB4dUWGRiDD2RdKWB-n1kUwwmPwq1WQ9YeKKqov5FFLfo7EJ1tkbdCb8krY7nQttKhgmNZCXK5L94ZpFhJkWTFUHHIAx2IOPV6NdbjrrR8l5to2eYyjf7f73q0gxzvGRqPjFYJSbx6RnU2e6Y0Y845X5iZK0gJjKf0ocZfzbtnDxSQPa9rAacjR4rEiApsikJTcm8bqKneABuY85pIGXSVGaAlmOYhwc2jnJOim5ip-CHBIWC6YBOUNw73onOe9612EeLkDlFEN7mTxvA6ddcLM4B5FXXvr0imuo4Q0yko_o4jFQXiRG_YNEBEk4HApUCE4KmVHr2w/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTalairach__;!!H8mHWRdzp34!_l_gOh7Vnn8ovwqfR_EqP1dOfB-MrgDNoaNiCUIahwFJ_aGAOSKGKIk18p6fQDf2snUDr8V7UbYuZ_sgpEWHNY9oikTLS12PI--QGIY$<https://secure-web.cisco.com/1YTUJIwB-u_KNhoI17IHgKhkMu-K4cxIGnnOeSiooClREnWme11f5wwS_mX9Rx4UP523Br2Cnzb57bqvcJ2PLBpiR5k410ksn7Q23xaG_tnK045KUyPlp2rv7s6Kq2pte4t73E-NqHvoLJFuWAySX2iOqlRGRmOaLPmHkm5Vk9y5Jj5SO3Ndt8nUQS657skk6jrPN5DJXr8S4FayfpfrGAxz9djtI9_5v63yyeGK9B7IHShMLkrd7mOgTgg91nQQ8j57F_1qykXxnrxZ1SEHy714L5pyC2GzySNFbxWd0_mqGSYYIxDNNLByDVDIEeNVktgup-0CUh10JQIsW5HhPUQ/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTalairach__;!!H8mHWRdzp34!_l_gOh7Vnn8ovwqfR_EqP1dOfB-MrgDNoaNiCUIahwFJ_aGAOSKGKIk18p6fQDf2snUDr8V7UbYuZ_sgpEWHNY9oikTLS12PI--QGIY$>
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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
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.
