Hello FreeSurfer experts,
I have been running into a consistent problem of Talairach alignment error in my recon-all for some of my subjects, even though I was able to get a completed recon-all for other subjects by using the same procedure to obtain my nifti files. I have attached the recon-all logs of a successful and a Talairach failed subject respectively, and as I try to understand the difference, in the successful one this was tried the last: INFO: Trying MINC mritotal to perform Talairach align... then failed, then there is a "New invocation of recon-all " which succeeded. I do not think I made that invocation. Could someone help me figure out what I am missing, and how can I make recon-all continue as I somehow did previously?
Thank you so much! Idil
It is failing the tal registration check. Does the registration look ok? If so, then run with -no-talcheck.
On 08/09/2017 02:24 PM, Yagmur Ozdemir 19 wrote:
Hello FreeSurfer experts,
I have been running into a consistent problem of Talairach alignment error in my recon-all for some of my subjects, even though I was able to get a completed recon-all for other subjects by using the same procedure to obtain my nifti files. I have attached the recon-all logs of a successful and a Talairach failed subject respectively, and as I try to understand the difference, in the successful one this was tried the last: INFO: Trying MINC mritotal to perform Talairach align... then failed, then there is a "New invocation of recon-all " which succeeded. I do not think I made that invocation. Could someone help me figure out what I am missing, and how can I make recon-all continue as I somehow did previously?
Thank you so much! Idil
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I would prefer to have it run with the tal registration, as I am not entirely sure if the registration works ok as it was made in another software, but worst case I will try that option. Thank you!
Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, August 10, 2017 1:18 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach error
It is failing the tal registration check. Does the registration look ok? If so, then run with -no-talcheck.
On 08/09/2017 02:24 PM, Yagmur Ozdemir 19 wrote:
Hello FreeSurfer experts,
I have been running into a consistent problem of Talairach alignment error in my recon-all for some of my subjects, even though I was able to get a completed recon-all for other subjects by using the same procedure to obtain my nifti files. I have attached the recon-all logs of a successful and a Talairach failed subject respectively, and as I try to understand the difference, in the successful one this was tried the last: INFO: Trying MINC mritotal to perform Talairach align... then failed, then there is a "New invocation of recon-all " which succeeded. I do not think I made that invocation. Could someone help me figure out what I am missing, and how can I make recon-all continue as I somehow did previously?
Thank you so much! Idil
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
you can visually check it. Also, it is not super critical
On 08/10/2017 01:45 PM, Yagmur Ozdemir 19 wrote:
I would prefer to have it run with the tal registration, as I am not entirely sure if the registration works ok as it was made in another software, but worst case I will try that option. Thank you!
Idil ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, August 10, 2017 1:18 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach error
It is failing the tal registration check. Does the registration look ok? If so, then run with -no-talcheck.
On 08/09/2017 02:24 PM, Yagmur Ozdemir 19 wrote:
Hello FreeSurfer experts,
I have been running into a consistent problem of Talairach alignment error in my recon-all for some of my subjects, even though I was able to get a completed recon-all for other subjects by using the same procedure to obtain my nifti files. I have attached the recon-all logs of a successful and a Talairach failed subject respectively, and as I try to understand the difference, in the successful one this was tried the last: INFO: Trying MINC mritotal to perform Talairach align... then failed, then there is a "New invocation of recon-all " which succeeded. I do not think I made that invocation. Could someone help me figure out what I am missing, and how can I make recon-all continue as I somehow did previously?
Thank you so much! Idil
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Yagmur Ozdemir 19