Hello,
Hope this message finds you well.
I was beginning to run recon-all on a dataset and was encountering a problem with the talairach registration. I've encountered this error before here and there, but I've been receiving the same error for every scan that I've been trying to run, and I'm not sure why. It's also the first time I've used NIFTI files as the input - not sure if that's a contributing factor. I've also tried the -use-mritotal flag without any luck.
These are the errors I receive:
WARNING: neither NIfTI-1 qform or sform are valid
WARNING: your volume will probably be incorrectly oriented
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)
Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test,
making sure the -notal-check flag follows -all
or -autorecon1 in the command string.
I would appreciate your help. Thank you!
Warmly, Ariana
That means that geometry information (ie, what is left and right, anterior or posterior) is not part of the nifti file. Without that information, the anatomical analysis cannot be done. You will either have to fix it yourself (ie, imbed that info into the file) or, better, recreate the file with the proper geometry info
On 09/11/2017 01:52 PM, Ariana Vajdi wrote:
Hello,
Hope this message finds you well.
I was beginning to run recon-all on a dataset and was encountering a problem with the talairach registration. I've encountered this error before here and there, but I've been receiving the same error for every scan that I've been trying to run, and I'm not sure why. It's also the first time I've used NIFTI files as the input - not sure if that's a contributing factor. I've also tried the -use-mritotal flag without any luck.
These are the errors I receive:
WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string.I would appreciate your help. Thank you!
Warmly, Ariana
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Ah, I see - how would I be able to do either of those? And would I have to check the geometry of each scan individually? Not sure how that works, but I have a substantially large dataset.
Thank you for your response!
On Mon, Sep 11, 2017 at 1:02 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
That means that geometry information (ie, what is left and right, anterior or posterior) is not part of the nifti file. Without that information, the anatomical analysis cannot be done. You will either have to fix it yourself (ie, imbed that info into the file) or, better, recreate the file with the proper geometry info
On 09/11/2017 01:52 PM, Ariana Vajdi wrote:
Hello,
Hope this message finds you well.
I was beginning to run recon-all on a dataset and was encountering a problem with the talairach registration. I've encountered this error before here and there, but I've been receiving the same error for every scan that I've been trying to run, and I'm not sure why. It's also the first time I've used NIFTI files as the input - not sure if that's a contributing factor. I've also tried the -use-mritotal flag without any luck.
These are the errors I receive:
WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string.I would appreciate your help. Thank you!
Warmly, Ariana
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.
I don't know how you (or someone else) generated the nifti files in the first place, so I can't help there. If you did not generate them, then talk to the person who did. I do not really recommend trying to do it by hand. You can get AP and SI correctly, but you'll never know whether they are LR reversed or not
On 09/11/2017 04:12 PM, Ariana Vajdi wrote:
Ah, I see - how would I be able to do either of those? And would I have to check the geometry of each scan individually? Not sure how that works, but I have a substantially large dataset.
Thank you for your response!
On Mon, Sep 11, 2017 at 1:02 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
That means that geometry information (ie, what is left and right, anterior or posterior) is not part of the nifti file. Without that information, the anatomical analysis cannot be done. You will either have to fix it yourself (ie, imbed that info into the file) or, better, recreate the file with the proper geometry info On 09/11/2017 01:52 PM, Ariana Vajdi wrote: > Hello, > > Hope this message finds you well. > > I was beginning to run recon-all on a dataset and was encountering a > problem with the talairach registration. I've encountered this error > before here and there, but I've been receiving the same error for > every scan that I've been trying to run, and I'm not sure why. It's > also the first time I've used NIFTI files as the input - not sure if > that's a contributing factor. I've also tried the -use-mritotal flag > without any luck. > > These are the errors I receive: > > WARNING: neither NIfTI-1 qform or sform are valid > > WARNING: your volume will probably be incorrectly oriented > > > ERROR: talairach_afd: Talairach Transform: > transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < > threshold=0.0050) > > Manual Talairach alignment may be necessary, or > > include the -notal-check flag to skip this test, > > making sure the -notal-check flag follows -all > > or -autorecon1 in the command string. > > > I would appreciate your help. Thank you! > > Warmly, > Ariana > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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
Ok - thank you! I will speak to the person who generated the files then.
On Mon, Sep 11, 2017 at 1:56 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
I don't know how you (or someone else) generated the nifti files in the first place, so I can't help there. If you did not generate them, then talk to the person who did. I do not really recommend trying to do it by hand. You can get AP and SI correctly, but you'll never know whether they are LR reversed or not
On 09/11/2017 04:12 PM, Ariana Vajdi wrote:
Ah, I see - how would I be able to do either of those? And would I have to check the geometry of each scan individually? Not sure how that works, but I have a substantially large dataset.
Thank you for your response!
On Mon, Sep 11, 2017 at 1:02 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
That means that geometry information (ie, what is left and right, anterior or posterior) is not part of the nifti file. Without that information, the anatomical analysis cannot be done. You will either have to fix it yourself (ie, imbed that info into the file) or, better, recreate the file with the proper geometry info On 09/11/2017 01:52 PM, Ariana Vajdi wrote: > Hello, > > Hope this message finds you well. > > I was beginning to run recon-all on a dataset and was encounteringa
> problem with the talairach registration. I've encountered thiserror
> before here and there, but I've been receiving the same error for > every scan that I've been trying to run, and I'm not sure why. It's > also the first time I've used NIFTI files as the input - not sureif
> that's a contributing factor. I've also tried the -use-mritotalflag
> without any luck. > > These are the errors I receive: > > WARNING: neither NIfTI-1 qform or sform are valid > > WARNING: your volume will probably be incorrectly oriented > > > ERROR: talairach_afd: Talairach Transform: > transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < > threshold=0.0050) > > Manual Talairach alignment may be necessary, or > > include the -notal-check flag to skip this test, > > making sure the -notal-check flag follows -all > > or -autorecon1 in the command string. > > > I would appreciate your help. Thank you! > > Warmly, > Ariana > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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
-- 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
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve