Thanks Nick very much for your suggestion.
Unfortunately it did not fix the error.
I run the mri_nu_correct command trying several -n values (1, 5, 20), then I -talairach, but the output is always the same. Talairach finish but when I check it the brain and standars are slided down to the bottom of the window. See a new output attached.
What can be happening here? Any idea to fix it?
thanks
Daniel
2012/10/17 Nick Schmansky nicks@nmr.mgh.harvard.edu
Daniel,
See this page which i just created which describes a workaround to a problem some people are having with the Talairach stage in the v5.1 release:
https://surfer.nmr.mgh.harvard.edu/fswiki/TalFailV5.1
Nick
On Wed, 2012-10-17 at 08:24 +0200, Daniel Ferreira wrote:
Dear experts,
Please, I'm getting the Talairach Failure Detection problem in one of my subjects (message enclosed below).
I tried to follow the tutorial to fix a bad Talairach with:
- tkregister2 --mgz -s <id> --fstal --> not green lines appear, I
attach a screenshot. Both the standard and my MRI are slided down to the bottom of the window. See also attached tkmedit file.
- Anyway, I tried also -notal-check to see if something changed in
spite Talairach failed, but it fails also (off course).
- I used -use-mritotal but I still get the same. However, this time
processing finishes without errors, but my MRI is still at the bottom of the window and output cut all what is between middle temporal regions and neck.
Please, any idea?
Thanks a lot
Daniel
#@# Talairach Failure Detection Wed Oct 10 09:08:27 CEST 2012 /home/daniel/FreeSurfer/subjects/N001511_d2/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
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. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux siv 2.6.32-33-generic #72-Ubuntu SMP Fri Jul 29 21:07:13 UTC 2011 x86_64 GNU/Linux
recon-all -s N001511_d2 exited with ERRORS at Wed Oct 10 09:08:27 CEST 2012
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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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 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.
Hi Daniel
what was your original data format? Did you start with dicoms? Bruce On Thu, 18 Oct 2012, Daniel Ferreira wrote:
Thanks Nick very much for your suggestion. Unfortunately it did not fix the error.
I run the mri_nu_correct command trying several -n values (1, 5, 20), then I -talairach, but the output is always the same. Talairach finish but when I check it the brain and standars are slided down to the bottom of the window. See a new output attached.
What can be happening here? Any idea to fix it?
thanks
Daniel
2012/10/17 Nick Schmansky nicks@nmr.mgh.harvard.edu Daniel,
See this page which i just created which describes a workaround to a problem some people are having with the Talairach stage in the v5.1 release: https://surfer.nmr.mgh.harvard.edu/fswiki/TalFailV5.1 Nick On Wed, 2012-10-17 at 08:24 +0200, Daniel Ferreira wrote: > Dear experts, > > Please, I'm getting the Talairach Failure Detection problem in one of > my subjects (message enclosed below). > > > I tried to follow the tutorial to fix a bad Talairach with: > > > 1) tkregister2 --mgz -s <id> --fstal --> not green lines appear, I > attach a screenshot. Both the standard and my MRI are slided down to > the bottom of the window. See also attached tkmedit file. > > > 2) Anyway, I tried also -notal-check to see if something changed in > spite Talairach failed, but it fails also (off course). > > > 3) I used -use-mritotal but I still get the same. However, this time > processing finishes without errors, but my MRI is still at the bottom > of the window and output cut all what is between middle temporal > regions and neck. > > > Please, any idea? > > > Thanks a lot > > > Daniel > > > > #@# Talairach Failure Detection Wed Oct 10 09:08:27 CEST 2012 > /home/daniel/FreeSurfer/subjects/N001511_d2/mri > > talairach_afd -T 0.005 -xfm transforms/talairach.xfm > > 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. > See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach > Linux siv 2.6.32-33-generic #72-Ubuntu SMP Fri Jul 29 21:07:13 UTC > 2011 x86_64 GNU/Linux > > recon-all -s N001511_d2 exited with ERRORS at Wed Oct 10 09:08:27 CEST > 2012 > > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > >
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Hi,
I did recon-all -i <dicoms> -s <id>
and then what Nick posted.
2012/10/18 Bruce Fischl fischl@nmr.mgh.harvard.edu
Hi Daniel
what was your original data format? Did you start with dicoms? Bruce
On Thu, 18 Oct 2012, Daniel Ferreira wrote:
Thanks Nick very much for your suggestion.
Unfortunately it did not fix the error.
I run the mri_nu_correct command trying several -n values (1, 5, 20), then I -talairach, but the output is always the same. Talairach finish but when I check it the brain and standars are slided down to the bottom of the window. See a new output attached.
What can be happening here? Any idea to fix it?
thanks
Daniel
2012/10/17 Nick Schmansky nicks@nmr.mgh.harvard.edu Daniel,
See this page which i just created which describes a workaround to a problem some people are having with the Talairach stage in the v5.1 release: https://surfer.nmr.mgh.**harvard.edu/fswiki/TalFailV5.1<https://surfer.nmr.mgh.harvard.edu/fswiki/TalFailV5.1> Nick On Wed, 2012-10-17 at 08:24 +0200, Daniel Ferreira wrote: > Dear experts, > > Please, I'm getting the Talairach Failure Detection problem in one of > my subjects (message enclosed below). > > > I tried to follow the tutorial to fix a bad Talairach with: > > > 1) tkregister2 --mgz -s <id> --fstal --> not green lines appear, I > attach a screenshot. Both the standard and my MRI are slided down to > the bottom of the window. See also attached tkmedit file. > > > 2) Anyway, I tried also -notal-check to see if something changed in > spite Talairach failed, but it fails also (off course). > > > 3) I used -use-mritotal but I still get the same. However, this time > processing finishes without errors, but my MRI is still at the bottom > of the window and output cut all what is between middle temporal > regions and neck. > > > Please, any idea? > > > Thanks a lot > > > Daniel > > > > #@# Talairach Failure Detection Wed Oct 10 09:08:27 CEST 2012 > /home/daniel/FreeSurfer/**subjects/N001511_d2/mri > > talairach_afd -T 0.005 -xfm transforms/talairach.xfm > > 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. > See http://surfer.nmr.mgh.harvard.**edu/fswiki/FsTutorial/**Talairach<http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach> > Linux siv 2.6.32-33-generic #72-Ubuntu SMP Fri Jul 29 21:07:13 UTC > 2011 x86_64 GNU/Linux > > recon-all -s N001511_d2 exited with ERRORS at Wed Oct 10 09:08:27 CEST > 2012 > > To report a problem, see > http://surfer.nmr.mgh.harvard.**edu/fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > >______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://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.
what does orig.mgz look like in tkmedit?
n.
On Thu, 2012-10-18 at 18:44 +0200, Daniel Ferreira wrote:
Hi,
I did recon-all -i <dicoms> -s <id>
and then what Nick posted.
2012/10/18 Bruce Fischl fischl@nmr.mgh.harvard.edu Hi Daniel
what was your original data format? Did you start with dicoms? Bruce On Thu, 18 Oct 2012, Daniel Ferreira wrote: Thanks Nick very much for your suggestion. Unfortunately it did not fix the error. I run the mri_nu_correct command trying several -n values (1, 5, 20), then I -talairach, but the output is always the same. Talairach finish but when I check it the brain and standars are slided down to the bottom of the window. See a new output attached. What can be happening here? Any idea to fix it? thanks Daniel 2012/10/17 Nick Schmansky <nicks@nmr.mgh.harvard.edu> Daniel, See this page which i just created which describes a workaround to a problem some people are having with the Talairach stage in the v5.1 release: https://surfer.nmr.mgh.harvard.edu/fswiki/TalFailV5.1 Nick On Wed, 2012-10-17 at 08:24 +0200, Daniel Ferreira wrote: > Dear experts, > > Please, I'm getting the Talairach Failure Detection problem in one of > my subjects (message enclosed below). > > > I tried to follow the tutorial to fix a bad Talairach with: > > > 1) tkregister2 --mgz -s <id> --fstal --> not green lines appear, I > attach a screenshot. Both the standard and my MRI are slided down to > the bottom of the window. See also attached tkmedit file. > > > 2) Anyway, I tried also -notal-check to see if something changed in > spite Talairach failed, but it fails also (off course). > > > 3) I used -use-mritotal but I still get the same. However, this time > processing finishes without errors, but my MRI is still at the bottom > of the window and output cut all what is between middle temporal > regions and neck. > > > Please, any idea? > > > Thanks a lot > > > Daniel > > > > #@# Talairach Failure Detection Wed Oct 10 09:08:27 CEST 2012 > /home/daniel/FreeSurfer/subjects/N001511_d2/mri > > talairach_afd -T 0.005 -xfm transforms/talairach.xfm > > 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. > See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach > Linux siv 2.6.32-33-generic #72-Ubuntu SMP Fri Jul 29 21:07:13 UTC > 2011 x86_64 GNU/Linux > > recon-all -s N001511_d2 exited with ERRORS at Wed Oct 10 09:08:27 CEST > 2012 > > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > _______________________________________________ > 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.
Hi Nick,
Here comes attached the tkmedit orig.mgz
thanks
Daniel
2012/10/22 Nick Schmansky nicks@nmr.mgh.harvard.edu
what does orig.mgz look like in tkmedit?
n.
On Thu, 2012-10-18 at 18:44 +0200, Daniel Ferreira wrote:
Hi,
I did recon-all -i <dicoms> -s <id>
and then what Nick posted.
2012/10/18 Bruce Fischl fischl@nmr.mgh.harvard.edu Hi Daniel
what was your original data format? Did you start with dicoms? Bruce On Thu, 18 Oct 2012, Daniel Ferreira wrote: Thanks Nick very much for your suggestion. Unfortunately it did not fix the error. I run the mri_nu_correct command trying several -n values (1, 5, 20), then I -talairach, but the output is always the same. Talairach finish but when I check it the brain and standars are slided down to the bottom of the window. See a new output attached. What can be happening here? Any idea to fix it? thanks Daniel 2012/10/17 Nick Schmansky <nicks@nmr.mgh.harvard.edu> Daniel, See this page which i just created which describes a workaround to a problem some people are having with the Talairach stage in the v5.1 release: https://surfer.nmr.mgh.harvard.edu/fswiki/TalFailV5.1 Nick On Wed, 2012-10-17 at 08:24 +0200, Daniel Ferreira wrote: > Dear experts, > > Please, I'm getting the Talairach Failure Detection problem in one of > my subjects (message enclosed below). > > > I tried to follow the tutorial to fix a bad Talairach with: > > > 1) tkregister2 --mgz -s <id> --fstal --> not green lines appear, I > attach a screenshot. Both the standard and my MRI are slided down to > the bottom of the window. See also attached tkmedit file. > > > 2) Anyway, I tried also -notal-check to see if something changed in > spite Talairach failed, but it fails also (off course). > > > 3) I used -use-mritotal but I still get the same. However, this time > processing finishes without errors, but my MRI is still at the bottom > of the window and output cut all what is between middle temporal > regions and neck. > > > Please, any idea? > > > Thanks a lot > > > Daniel > > > > #@# Talairach Failure Detection Wed Oct 10 09:08:27 CEST 2012 > /home/daniel/FreeSurfer/subjects/N001511_d2/mri > > talairach_afd -T 0.005 -xfm transforms/talairach.xfm > > 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. > Seehttp://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
> Linux siv 2.6.32-33-generic #72-Ubuntu SMP Fri Jul 29 21:07:13 UTC > 2011 x86_64 GNU/Linux > > recon-all -s N001511_d2 exited with ERRORS at Wed Oct 10 09:08:27 CEST > 2012 > > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > _______________________________________________ > 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.
Hi Daniel
it looks like you have too much wrap in your image, with a significant amount of brain wrapping to the top. Nothing will work on this
sorry Bruce
On Tue, 23 Oct 2012, Daniel Ferreira wrote:
Hi Nick, Here comes attached the tkmedit orig.mgz
thanks
Daniel
2012/10/22 Nick Schmansky nicks@nmr.mgh.harvard.edu what does orig.mgz look like in tkmedit?
n. On Thu, 2012-10-18 at 18:44 +0200, Daniel Ferreira wrote: > Hi, > > > I did recon-all -i <dicoms> -s <id> > > > and then what Nick posted. > > > > 2012/10/18 Bruce Fischl <fischl@nmr.mgh.harvard.edu> > Hi Daniel > > what was your original data format? Did you start with dicoms? > Bruce > > On Thu, 18 Oct 2012, Daniel Ferreira wrote: > > Thanks Nick very much for your suggestion. > Unfortunately it did not fix the error. > > I run the mri_nu_correct command trying several -n > values (1, 5, 20), then I > -talairach, but the output is always the same. > Talairach finish but when I > check it the brain and standars are slided down to the > bottom of the window. > See a new output attached. > > What can be happening here? Any idea to fix it? > > thanks > > Daniel > > > > 2012/10/17 Nick Schmansky <nicks@nmr.mgh.harvard.edu> > Daniel, > > See this page which i just created which > describes a > workaround to a > problem some people are having with the > Talairach stage in > the v5.1 > release: > > > https://surfer.nmr.mgh.harvard.edu/fswiki/TalFailV5.1 > > Nick > > > On Wed, 2012-10-17 at 08:24 +0200, Daniel > Ferreira wrote: > > Dear experts, > > > > Please, I'm getting the Talairach Failure > Detection > problem in one of > > my subjects (message enclosed below). > > > > > > I tried to follow the tutorial to fix a bad > Talairach > with: > > > > > > 1) tkregister2 --mgz -s <id> --fstal --> > not green > lines appear, I > > attach a screenshot. Both the standard and my > MRI are > slided down to > > the bottom of the window. See also attached > tkmedit > file. > > > > > > 2) Anyway, I tried also -notal-check to see if > something > changed in > > spite Talairach failed, but it fails also (off > course). > > > > > > 3) I used -use-mritotal but I still get the > same. > However, this time > > processing finishes without errors, but my MRI > is still > at the bottom > > of the window and output cut all what is > between middle > temporal > > regions and neck. > > > > > > Please, any idea? > > > > > > Thanks a lot > > > > > > Daniel > > > > > > > > #@# Talairach Failure Detection Wed Oct 10 > 09:08:27 CEST > 2012 > > > /home/daniel/FreeSurfer/subjects/N001511_d2/mri > > > > talairach_afd -T 0.005 -xfm > transforms/talairach.xfm > > > > 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. > > See > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach > > Linux siv 2.6.32-33-generic #72-Ubuntu SMP Fri > Jul 29 > 21:07:13 UTC > > 2011 x86_64 GNU/Linux > > > > recon-all -s N001511_d2 exited with ERRORS at > Wed Oct 10 > 09:08:27 CEST > > 2012 > > > > To report a problem, see > > > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > > > > > _______________________________________________ > > 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. > > > > >
Hi,
I see. But why does it happen? If I look at the initial Dicom it is normal, no wrapped, as usually looks like.
thanks
2012/10/23 Bruce Fischl fischl@nmr.mgh.harvard.edu
Hi Daniel
it looks like you have too much wrap in your image, with a significant amount of brain wrapping to the top. Nothing will work on this
sorry Bruce
On Tue, 23 Oct 2012, Daniel Ferreira wrote:
Hi Nick,
Here comes attached the tkmedit orig.mgz
thanks
Daniel
2012/10/22 Nick Schmansky nicks@nmr.mgh.harvard.edu what does orig.mgz look like in tkmedit?
n. On Thu, 2012-10-18 at 18:44 +0200, Daniel Ferreira wrote: > Hi, > > > I did recon-all -i <dicoms> -s <id> > > > and then what Nick posted. > > > > 2012/10/18 Bruce Fischl <fischl@nmr.mgh.harvard.edu> > Hi Daniel > > what was your original data format? Did you start withdicoms? > Bruce > > On Thu, 18 Oct 2012, Daniel Ferreira wrote: > > Thanks Nick very much for your suggestion. > Unfortunately it did not fix the error. > > I run the mri_nu_correct command trying several -n > values (1, 5, 20), then I > -talairach, but the output is always the same. > Talairach finish but when I > check it the brain and standars are slided down to the > bottom of the window. > See a new output attached. > > What can be happening here? Any idea to fix it? > > thanks > > Daniel > > > > 2012/10/17 Nick Schmansky < nicks@nmr.mgh.harvard.edu> > Daniel, > > See this page which i just created which > describes a > workaround to a > problem some people are having with the > Talairach stage in > the v5.1 > release: > > > https://surfer.nmr.mgh.** harvard.edu/fswiki/TalFailV5.1https://surfer.nmr.mgh.harvard.edu/fswiki/TalFailV5.1 > > Nick > > > On Wed, 2012-10-17 at 08:24 +0200, Daniel > Ferreira wrote: > > Dear experts, > > > > Please, I'm getting the Talairach Failure > Detection > problem in one of > > my subjects (message enclosed below). > > > > > > I tried to follow the tutorial to fix a bad > Talairach > with: > > > > > > 1) tkregister2 --mgz -s <id> --fstal --> > not green > lines appear, I > > attach a screenshot. Both the standard and my > MRI are > slided down to > > the bottom of the window. See also attached > tkmedit > file. > > > > > > 2) Anyway, I tried also -notal-check to see if > something > changed in > > spite Talairach failed, but it fails also (off > course). > > > > > > 3) I used -use-mritotal but I still get the > same. > However, this time > > processing finishes without errors, but my MRI > is still > at the bottom > > of the window and output cut all what is > between middle > temporal > > regions and neck. > > > > > > Please, any idea? > > > > > > Thanks a lot > > > > > > Daniel > > > > > > > > #@# Talairach Failure Detection Wed Oct 10 > 09:08:27 CEST > 2012 > > > /home/daniel/FreeSurfer/** subjects/N001511_d2/mri > > > > talairach_afd -T 0.005 -xfm > transforms/talairach.xfm > > > > 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. > > See > > http://surfer.nmr.mgh.harvard.** edu/fswiki/FsTutorial/**Talairachhttp://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach > > Linux siv 2.6.32-33-generic #72-Ubuntu SMP Fri > Jul 29 > 21:07:13 UTC > > 2011 x86_64 GNU/Linux > > > > recon-all -s N001511_d2 exited with ERRORS at > Wed Oct 10 > 09:08:27 CEST > > 2012 > > > > To report a problem, see > > > http://surfer.nmr.mgh.harvard.** edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > > > > > ______________________________** _________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.** edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://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. > > > > >
really? In what viewer? Does it happen in the rawavg.mgz?
On Tue, 30 Oct 2012, Daniel Ferreira wrote:
Hi, I see. But why does it happen? If I look at the initial Dicom it is normal, no wrapped, as usually looks like.
thanks
2012/10/23 Bruce Fischl fischl@nmr.mgh.harvard.edu Hi Daniel
it looks like you have too much wrap in your image, with a significant amount of brain wrapping to the top. Nothing will work on this sorry Bruce On Tue, 23 Oct 2012, Daniel Ferreira wrote: Hi Nick, Here comes attached the tkmedit orig.mgz thanks Daniel 2012/10/22 Nick Schmansky <nicks@nmr.mgh.harvard.edu> what does orig.mgz look like in tkmedit? n. On Thu, 2012-10-18 at 18:44 +0200, Daniel Ferreira wrote: > Hi, > > > I did recon-all -i <dicoms> -s <id> > > > and then what Nick posted. > > > > 2012/10/18 Bruce Fischl <fischl@nmr.mgh.harvard.edu> > Hi Daniel > > what was your original data format? Did you start with dicoms? > Bruce > > On Thu, 18 Oct 2012, Daniel Ferreira wrote: > > Thanks Nick very much for your suggestion. > Unfortunately it did not fix the error. > > I run the mri_nu_correct command trying several -n > values (1, 5, 20), then I > -talairach, but the output is always the same. > Talairach finish but when I > check it the brain and standars are slided down to the > bottom of the window. > See a new output attached. > > What can be happening here? Any idea to fix it? > > thanks > > Daniel > > > > 2012/10/17 Nick Schmansky <nicks@nmr.mgh.harvard.edu> > Daniel, > > See this page which i just created which > describes a > workaround to a > problem some people are having with the > Talairach stage in > the v5.1 > release: > > > https://surfer.nmr.mgh.harvard.edu/fswiki/TalFailV5.1 > > Nick > > > On Wed, 2012-10-17 at 08:24 +0200, Daniel > Ferreira wrote: > > Dear experts, > > > > Please, I'm getting the Talairach Failure > Detection > problem in one of > > my subjects (message enclosed below). > > > > > > I tried to follow the tutorial to fix a bad > Talairach > with: > > > > > > 1) tkregister2 --mgz -s <id> --fstal --> > not green > lines appear, I > > attach a screenshot. Both the standard and my > MRI are > slided down to > > the bottom of the window. See also attached > tkmedit > file. > > > > > > 2) Anyway, I tried also -notal-check to see if > something > changed in > > spite Talairach failed, but it fails also (off > course). > > > > > > 3) I used -use-mritotal but I still get the > same. > However, this time > > processing finishes without errors, but my MRI > is still > at the bottom > > of the window and output cut all what is > between middle > temporal > > regions and neck. > > > > > > Please, any idea? > > > > > > Thanks a lot > > > > > > Daniel > > > > > > > > #@# Talairach Failure Detection Wed Oct 10 > 09:08:27 CEST > 2012 > > > /home/daniel/FreeSurfer/subjects/N001511_d2/mri > > > > talairach_afd -T 0.005 -xfm > transforms/talairach.xfm > > > > 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. > > See > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach > > Linux siv 2.6.32-33-generic #72-Ubuntu SMP Fri > Jul 29 > 21:07:13 UTC > > 2011 x86_64 GNU/Linux > > > > recon-all -s N001511_d2 exited with ERRORS at > Wed Oct 10 > 09:08:27 CEST > > 2012 > > > > To report a problem, see > > > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > > > > > _______________________________________________ > > 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. > > > > >
Well, in the PACs looks fine. When converting to nii it is already wrapped.
I will go to the machine again and see.
Thanks!
2012/10/30 Bruce Fischl fischl@nmr.mgh.harvard.edu
really? In what viewer? Does it happen in the rawavg.mgz?
On Tue, 30 Oct 2012, Daniel Ferreira wrote:
Hi,
I see. But why does it happen? If I look at the initial Dicom it is normal, no wrapped, as usually looks like.
thanks
2012/10/23 Bruce Fischl fischl@nmr.mgh.harvard.edu Hi Daniel
it looks like you have too much wrap in your image, with a significant amount of brain wrapping to the top. Nothing will work on this sorry Bruce On Tue, 23 Oct 2012, Daniel Ferreira wrote: Hi Nick, Here comes attached the tkmedit orig.mgz thanks Daniel 2012/10/22 Nick Schmansky <nicks@nmr.mgh.harvard.edu> what does orig.mgz look like in tkmedit? n. On Thu, 2012-10-18 at 18:44 +0200, Daniel Ferreira wrote: > Hi, > > > I did recon-all -i <dicoms> -s <id> > > > and then what Nick posted. > > > > 2012/10/18 Bruce Fischl <fischl@nmr.mgh.harvard.edu> > Hi Daniel > > what was your original data format? Did you start with dicoms? > Bruce > > On Thu, 18 Oct 2012, Daniel Ferreira wrote: > > Thanks Nick very much for your suggestion. > Unfortunately it did not fix the error. > > I run the mri_nu_correct command trying several -n > values (1, 5, 20), then I > -talairach, but the output is always the same. > Talairach finish but when I > check it the brain and standars are slided down to the > bottom of the window. > See a new output attached. > > What can be happening here? Any idea to fix it? > > thanks > > Daniel > > > > 2012/10/17 Nick Schmansky <nicks@nmr.mgh.harvard.edu> > Daniel, > > See this page which i just created which > describes a > workaround to a > problem some people are having with the > Talairach stage in > the v5.1 > release: > > > https://surfer.nmr.mgh.**harvard.edu/fswiki/TalFailV5.1<https://surfer.nmr.mgh.harvard.edu/fswiki/TalFailV5.1> > > Nick > > > On Wed, 2012-10-17 at 08:24 +0200, Daniel > Ferreira wrote: > > Dear experts, > > > > Please, I'm getting the Talairach Failure > Detection > problem in one of > > my subjects (message enclosed below). > > > > > > I tried to follow the tutorial to fix a bad > Talairach > with: > > > > > > 1) tkregister2 --mgz -s <id> --fstal --> > not green > lines appear, I > > attach a screenshot. Both the standard and my > MRI are > slided down to > > the bottom of the window. See also attached > tkmedit > file. > > > > > > 2) Anyway, I tried also -notal-check to see if > something > changed in > > spite Talairach failed, but it fails also (off > course). > > > > > > 3) I used -use-mritotal but I still get the > same. > However, this time > > processing finishes without errors, but my MRI > is still > at the bottom > > of the window and output cut all what is > between middle > temporal > > regions and neck. > > > > > > Please, any idea? > > > > > > Thanks a lot > > > > > > Daniel > > > > > > > > #@# Talairach Failure Detection Wed Oct 10 > 09:08:27 CEST > 2012 > > > /home/daniel/FreeSurfer/**subjects/N001511_d2/mri > > > > talairach_afd -T 0.005 -xfm > transforms/talairach.xfm > > > > 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. > > See > > http://surfer.nmr.mgh.harvard.**edu/fswiki/FsTutorial/**Talairach http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach > > Linux siv 2.6.32-33-generic #72-Ubuntu SMP Fri > Jul 29 > 21:07:13 UTC > > 2011 x86_64 GNU/Linux > > > > recon-all -s N001511_d2 exited with ERRORS at > Wed Oct 10 > 09:08:27 CEST > > 2012 > > > > To report a problem, see > > > http://surfer.nmr.mgh.harvard.**edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > > > > > ______________________________**_________________ > > Freesurfer mailing list > > 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/**compliancelinehttp://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@nmr.mgh.harvard.edu
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Bruce Fischl -
Daniel Ferreira -
Nick Schmansky