Re: [Freesurfer] Recon-all exited without errors

2023-03-06 Thread Douglas N. Greve 
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 +
From: "Huang, Yujing" 
Subject: Re: [Freesurfer] Recon-all exited with errors
To: Freesurfer support list 
Message-ID:


Content-Type: text/plain; charset="us-ascii"

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-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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Re: [Freesurfer] Recon-all exited without errors

2023-02-13 Thread Goeckner, Bryna 
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 +
From: "Huang, Yujing" 
Subject: Re: [Freesurfer] Recon-all exited with errors
To: Freesurfer support list 
Message-ID:



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$

Best,

Yujing



From: 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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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 
 .
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.