#@# Talairach Failure Detection Wed Nov 2 02:03:32 EDT 2011 /home/virtualuser/freesurfer/subjects/test005/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
I am receiving the error (pasted below) on about half of my scans, despite all cans using same protocol. I detect no obvious issue with the quality of the images. I have original dicoms, and am using mri_convert to save into a single .mgz (or .nii, doesn't neem to make a difference), and the unpredictability of the error makes diagnosis problematic. TKMedit2 reveals absolutely wacky registrations. I am processing on Freesurfer 5.1, and have replicated issue on two different installations. I am designing a new longitudinal study inheriting the same imaging protocol and I do not want to get in a situation demanding manual editing of the talairach. Can anyone help me out? Thanks, Joshua
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0030, 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 FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux
recon-all -s test005 exited with ERRORS at Wed Nov 2 02:03:32 EDT 2011
For more details, see the log file /home/virtualuser/freesurfer/subjects/test005/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
- Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805
Small Update: Error Disappears if Using Freesurfer version 5.0 instead of 5.1. However, since I am keenly interested in the hippocampal-subfield segmentation capabilities of the most recent version, I am loathe to regress to an earlier version of FreeSurfer - Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805
On Wed, Nov 2, 2011 at 2:29 AM, Joshua Lee jkilee@ucdavis.edu wrote:
#@# Talairach Failure Detection Wed Nov 2 02:03:32 EDT 2011 /home/virtualuser/freesurfer/subjects/test005/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
I am receiving the error (pasted below) on about half of my scans, despite all cans using same protocol. I detect no obvious issue with the quality of the images. I have original dicoms, and am using mri_convert to save into a single .mgz (or .nii, doesn't neem to make a difference), and the unpredictability of the error makes diagnosis problematic. TKMedit2 reveals absolutely wacky registrations. I am processing on Freesurfer 5.1, and have replicated issue on two different installations. I am designing a new longitudinal study inheriting the same imaging protocol and I do not want to get in a situation demanding manual editing of the talairach. Can anyone help me out? Thanks, Joshua
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0030, 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 FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux
recon-all -s test005 exited with ERRORS at Wed Nov 2 02:03:32 EDT 2011
For more details, see the log file /home/virtualuser/freesurfer/subjects/test005/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805
can you send us an example that works in 5.0 and fails in 5.1?
thanks Bruce On Wed, 2 Nov 2011, Joshua Lee wrote:
Small Update: Error Disappears if Using Freesurfer version 5.0 instead of 5.1. However, since I am keenly interested in the hippocampal-subfield segmentation capabilities of the most recent version, I am loathe to regress to an earlier version of FreeSurfer
Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805
On Wed, Nov 2, 2011 at 2:29 AM, Joshua Lee jkilee@ucdavis.edu wrote: #@# Talairach Failure Detection Wed Nov 2 02:03:32 EDT 2011 /home/virtualuser/freesurfer/subjects/test005/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm I am receiving the error (pasted below) on about half of my scans, despite all cans using same protocol. I detect no obvious issue with the quality of the images. I have original dicoms, and am using mri_convert to save into a single .mgz (or .nii, doesn't neem to make a difference), and the unpredictability of the error makes diagnosis problematic. TKMedit2 reveals absolutely wacky registrations. I am processing on Freesurfer 5.1, and have replicated issue on two different installations. I am designing a new longitudinal study inheriting the same imaging protocol and I do not want to get in a situation demanding manual editing of the talairach. Can anyone help me out? Thanks, Joshua ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0030, 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 FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all -s test005 exited with ERRORS at Wed Nov 2 02:03:32 EDT 2011 For more details, see the log file /home/virtualuser/freesurfer/subjects/test005/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805
joshua,
try adding -use-mritotal to the end of your recon-all command. it will use an alternate way to compute the talairach.xfm which works better on some data.
the change from v5.0 to v5.1 in the talairach stage was that in v5.1, the talairach.xfm is needed to compute nu.mgz, so the talairach stage needs to precede the nu_correct stage. this means the talairach stage can no longer use nu.mgz as input, which seems to work better than orig.mgz for some data (and is the case for your data).
in the next release of freesurfer, recon-all will automatically try the alternate method (mritotal) if the default talairach_avi method fails the tal-check.
n.
On Wed, 2011-11-02 at 08:45 -0400, Bruce Fischl wrote:
can you send us an example that works in 5.0 and fails in 5.1?
thanks Bruce On Wed, 2 Nov 2011, Joshua Lee wrote:
Small Update: Error Disappears if Using Freesurfer version 5.0 instead of 5.1. However, since I am keenly interested in the hippocampal-subfield segmentation capabilities of the most recent version, I am loathe to regress to an earlier version of FreeSurfer
Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805
On Wed, Nov 2, 2011 at 2:29 AM, Joshua Lee jkilee@ucdavis.edu wrote: #@# Talairach Failure Detection Wed Nov 2 02:03:32 EDT 2011 /home/virtualuser/freesurfer/subjects/test005/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm I am receiving the error (pasted below) on about half of my scans, despite all cans using same protocol. I detect no obvious issue with the quality of the images. I have original dicoms, and am using mri_convert to save into a single .mgz (or .nii, doesn't neem to make a difference), and the unpredictability of the error makes diagnosis problematic. TKMedit2 reveals absolutely wacky registrations. I am processing on Freesurfer 5.1, and have replicated issue on two different installations. I am designing a new longitudinal study inheriting the same imaging protocol and I do not want to get in a situation demanding manual editing of the talairach. Can anyone help me out? Thanks, Joshua ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0030, 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 FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all -s test005 exited with ERRORS at Wed Nov 2 02:03:32 EDT 2011 For more details, see the log file /home/virtualuser/freesurfer/subjects/test005/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Nick,
Is use-mritotal equivalent to what version 5.0 does by default?
Also, any suggestions on why this talairach error would occur only on a portion of my data, despite all being collected with the same imaging protocol, same conversions from dicom, etc? - Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805
On Wed, Nov 2, 2011 at 4:02 PM, Nick Schmansky nicks@nmr.mgh.harvard.eduwrote:
joshua,
try adding -use-mritotal to the end of your recon-all command. it will use an alternate way to compute the talairach.xfm which works better on some data.
the change from v5.0 to v5.1 in the talairach stage was that in v5.1, the talairach.xfm is needed to compute nu.mgz, so the talairach stage needs to precede the nu_correct stage. this means the talairach stage can no longer use nu.mgz as input, which seems to work better than orig.mgz for some data (and is the case for your data).
in the next release of freesurfer, recon-all will automatically try the alternate method (mritotal) if the default talairach_avi method fails the tal-check.
n.
On Wed, 2011-11-02 at 08:45 -0400, Bruce Fischl wrote:
can you send us an example that works in 5.0 and fails in 5.1?
thanks Bruce On Wed, 2 Nov 2011, Joshua Lee wrote:
Small Update: Error Disappears if Using Freesurfer version 5.0 instead
of
5.1. However, since I am keenly interested in the hippocampal-subfield segmentation capabilities of the most recent version, I am loathe to
regress
to an earlier version of FreeSurfer
Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805
On Wed, Nov 2, 2011 at 2:29 AM, Joshua Lee jkilee@ucdavis.edu wrote: #@# Talairach Failure Detection Wed Nov 2 02:03:32 EDT 2011 /home/virtualuser/freesurfer/subjects/test005/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm I am receiving the error (pasted below) on about half of my scans, despite all cans using same protocol. I detect no obvious issue with the quality of the images. I have original dicoms, and am using mri_convert to save into a single .mgz (or .nii, doesn't neem to make a difference), and the unpredictability of the error makes diagnosis problematic. TKMedit2 reveals absolutely wacky registrations. I am processing on Freesurfer 5.1, and have replicated issue on two different installations. I am designing a new longitudinal study inheriting the same imaging protocol and I do not want to get in a situation demanding manual editing of the talairach. Can anyone help me out? Thanks, Joshua ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0030, 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 FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all -s test005 exited with ERRORS at Wed Nov 2 02:03:32 EDT 2011 For more details, see the log file/home/virtualuser/freesurfer/subjects/test005/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805
_______________________________________________ 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.
no, v5.0 uses nu.mgz as input to the talairach_avi routine, whereas v5.1 uses orig.mgz.
its hard to say why it would fail for some subjects but not others, other than head positioning and to some degree ventricle size makes a difference.
n.
On Wed, 2011-11-02 at 16:10 -0400, Joshua Lee wrote:
Thanks Nick,
Is use-mritotal equivalent to what version 5.0 does by default?
Also, any suggestions on why this talairach error would occur only on a portion of my data, despite all being collected with the same imaging protocol, same conversions from dicom, etc?
Joshua Lee
Graduate Student Center for Mind and Brain &
Department of Psychology
University of California, Davis 530.747.3805
On Wed, Nov 2, 2011 at 4:02 PM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote: joshua,
try adding -use-mritotal to the end of your recon-all command. it will use an alternate way to compute the talairach.xfm which works better on some data. the change from v5.0 to v5.1 in the talairach stage was that in v5.1, the talairach.xfm is needed to compute nu.mgz, so the talairach stage needs to precede the nu_correct stage. this means the talairach stage can no longer use nu.mgz as input, which seems to work better than orig.mgz for some data (and is the case for your data). in the next release of freesurfer, recon-all will automatically try the alternate method (mritotal) if the default talairach_avi method fails the tal-check. n. On Wed, 2011-11-02 at 08:45 -0400, Bruce Fischl wrote: > can you send us an example that works in 5.0 and fails in 5.1? > > thanks > Bruce > On Wed, 2 Nov > 2011, Joshua Lee wrote: > > > Small Update: Error Disappears if Using Freesurfer version 5.0 instead of > > 5.1. However, since I am keenly interested in the hippocampal-subfield > > segmentation capabilities of the most recent version, I am loathe to regress > > to an earlier version of FreeSurfer > > - > > Joshua Lee > > Graduate Student > > Center for Mind and Brain & > > Department of Psychology > > University of California, Davis > > 530.747.3805 > > > > > > On Wed, Nov 2, 2011 at 2:29 AM, Joshua Lee <jkilee@ucdavis.edu> wrote: > > #@# Talairach Failure Detection Wed Nov 2 02:03:32 EDT 2011 > > /home/virtualuser/freesurfer/subjects/test005/mri > > > > talairach_afd -T 0.005 -xfm transforms/talairach.xfm > > > > I am receiving the error (pasted below) on about half of my > > scans, despite all cans using same protocol. I detect no obvious > > issue with the quality of the images. I have original dicoms, > > and am using mri_convert to save into a single .mgz (or .nii, > > doesn't neem to make a difference), and the unpredictability of > > the error makes diagnosis problematic. TKMedit2 reveals > > absolutely wacky registrations. I am processing on Freesurfer > > 5.1, and have replicated issue on two different installations. I > > am designing a new longitudinal study inheriting the same > > imaging protocol and I do not want to get in a situation > > demanding manual editing of the talairach. Can anyone help me > > out? Thanks, Joshua > > > > ERROR: talairach_afd: Talairach Transform: > > transforms/talairach.xfm ***FAILED*** (p=0.0030, 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 FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 > > 01:57:59 UTC 2009 i686 GNU/Linux > > > > recon-all -s test005 exited with ERRORS at Wed Nov 2 02:03:32 > > EDT 2011 > > > > For more details, see the log file > > /home/virtualuser/freesurfer/subjects/test005/scripts/recon-all.log > > To report a problem, see > > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > - > > Joshua Lee > > Graduate Student > > Center for Mind and Brain & > > Department of Psychology > > University of California, Davis > > 530.747.3805 > > > > > > > > > _______________________________________________ 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.
OK, now I understand better. One further question: Would the use of MRI-total degrade quality of the Freesurfer segmentations substantively, and would using it only on a portion of my data introduce a systematic bias to the data set? Josh
On Wed, Nov 2, 2011 at 4:15 PM, Nick Schmansky nicks@nmr.mgh.harvard.eduwrote:
no, v5.0 uses nu.mgz as input to the talairach_avi routine, whereas v5.1 uses orig.mgz.
its hard to say why it would fail for some subjects but not others, other than head positioning and to some degree ventricle size makes a difference.
n.
On Wed, 2011-11-02 at 16:10 -0400, Joshua Lee wrote:
Thanks Nick,
Is use-mritotal equivalent to what version 5.0 does by default?
Also, any suggestions on why this talairach error would occur only on a portion of my data, despite all being collected with the same imaging protocol, same conversions from dicom, etc?
Joshua Lee
Graduate Student Center for Mind and Brain &
Department of Psychology
University of California, Davis 530.747.3805
On Wed, Nov 2, 2011 at 4:02 PM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote: joshua,
try adding -use-mritotal to the end of your recon-all command. it will use an alternate way to compute the talairach.xfm which works better on some data. the change from v5.0 to v5.1 in the talairach stage was that in v5.1, the talairach.xfm is needed to compute nu.mgz, so the talairach stage needs to precede the nu_correct stage. this means the talairach stage can no longer use nu.mgz as input, which seems to work better than orig.mgz for some data (and is the case for your data). in the next release of freesurfer, recon-all will automatically try the alternate method (mritotal) if the default talairach_avi method fails the tal-check. n. On Wed, 2011-11-02 at 08:45 -0400, Bruce Fischl wrote: > can you send us an example that works in 5.0 and fails in 5.1? > > thanks > Bruce > On Wed, 2 Nov > 2011, Joshua Lee wrote: > > > Small Update: Error Disappears if Using Freesurfer version 5.0 instead of > > 5.1. However, since I am keenly interested in the hippocampal-subfield > > segmentation capabilities of the most recent version, I am loathe to regress > > to an earlier version of FreeSurfer > > - > > Joshua Lee > > Graduate Student > > Center for Mind and Brain & > > Department of Psychology > > University of California, Davis > > 530.747.3805 > > > > > > On Wed, Nov 2, 2011 at 2:29 AM, Joshua Lee <jkilee@ucdavis.edu> wrote: > > #@# Talairach Failure Detection Wed Nov 2 02:03:32 EDT 2011 > > /home/virtualuser/freesurfer/subjects/test005/mri > > > > talairach_afd -T 0.005 -xfm transforms/talairach.xfm > > > > I am receiving the error (pasted below) on about half of my > > scans, despite all cans using same protocol. I detect no obvious > > issue with the quality of the images. I have original dicoms, > > and am using mri_convert to save into a single .mgz (or .nii, > > doesn't neem to make a difference), and the unpredictability of > > the error makes diagnosis problematic. TKMedit2 reveals > > absolutely wacky registrations. I am processing on Freesurfer > > 5.1, and have replicated issue on two different installations. I > > am designing a new longitudinal study inheriting the same > > imaging protocol and I do not want to get in a situation > > demanding manual editing of the talairach. Can anyone help me > > out? Thanks, Joshua > > > > ERROR: talairach_afd: Talairach Transform: > > transforms/talairach.xfm ***FAILED*** (p=0.0030, 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 FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 > > 01:57:59 UTC 2009 i686 GNU/Linux > > > > recon-all -s test005 exited with ERRORS at Wed Nov 2 02:03:32 > > EDT 2011 > > > > For more details, see the log file > >/home/virtualuser/freesurfer/subjects/test005/scripts/recon-all.log
> > To report a problem, see > > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > - > > Joshua Lee > > Graduate Student > > Center for Mind and Brain & > > Department of Psychology > > University of California, Davis > > 530.747.3805 > > > > > > > > > _______________________________________________ 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.
it should not change the quality of the subcortical or cortical streams at all. the talairach.xfm is used for reporting purposes in the gui tools, and for group averaging (in some instances, qdec not being one of them). so i would not worry about introducing a bias. if you are concerned about a bias, the thing to do (which ought to be done as a QA step anyway) is to run:
tkregister --s <subjid> --fstal --surfs
on all your subjects after recon-all has finished (or after -autorecon1 as long as you exclude the --surfs flag) and make sure the alignment is 'good enough'.
n.
On Wed, 2011-11-02 at 16:22 -0400, Joshua Lee wrote:
OK, now I understand better. One further question: Would the use of MRI-total degrade quality of the Freesurfer segmentations substantively, and would using it only on a portion of my data introduce a systematic bias to the data set? Josh
On Wed, Nov 2, 2011 at 4:15 PM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote: no, v5.0 uses nu.mgz as input to the talairach_avi routine, whereas v5.1 uses orig.mgz.
its hard to say why it would fail for some subjects but not others, other than head positioning and to some degree ventricle size makes a difference. n. On Wed, 2011-11-02 at 16:10 -0400, Joshua Lee wrote: > Thanks Nick, > > Is use-mritotal equivalent to what version 5.0 does by default? > > Also, any suggestions on why this talairach error would occur only on > a portion of my data, despite all being collected with the same > imaging protocol, same conversions from dicom, etc? > - > > Joshua Lee > > Graduate Student > Center for Mind and Brain & > > Department of Psychology > > University of California, Davis > 530.747.3805 > > > On Wed, Nov 2, 2011 at 4:02 PM, Nick Schmansky > <nicks@nmr.mgh.harvard.edu> wrote: > joshua, > > try adding -use-mritotal to the end of your recon-all > command. it will > use an alternate way to compute the talairach.xfm which works > better on > some data. > > the change from v5.0 to v5.1 in the talairach stage was that > in v5.1, > the talairach.xfm is needed to compute nu.mgz, so the > talairach stage > needs to precede the nu_correct stage. this means the > talairach stage > can no longer use nu.mgz as input, which seems to work better > than > orig.mgz for some data (and is the case for your data). > > in the next release of freesurfer, recon-all will > automatically try the > alternate method (mritotal) if the default talairach_avi > method fails > the tal-check. > > n. > > > > On Wed, 2011-11-02 at 08:45 -0400, Bruce Fischl wrote: > > can you send us an example that works in 5.0 and fails in > 5.1? > > > > thanks > > Bruce > > On Wed, 2 Nov > > 2011, Joshua Lee wrote: > > > > > Small Update: Error Disappears if Using Freesurfer version > 5.0 instead of > > > 5.1. However, since I am keenly interested in the > hippocampal-subfield > > > segmentation capabilities of the most recent version, I am > loathe to regress > > > to an earlier version of FreeSurfer > > > - > > > Joshua Lee > > > Graduate Student > > > Center for Mind and Brain & > > > Department of Psychology > > > University of California, Davis > > > 530.747.3805 > > > > > > > > > On Wed, Nov 2, 2011 at 2:29 AM, Joshua Lee > <jkilee@ucdavis.edu> wrote: > > > #@# Talairach Failure Detection Wed Nov 2 02:03:32 > EDT 2011 > > > /home/virtualuser/freesurfer/subjects/test005/mri > > > > > > talairach_afd -T 0.005 -xfm > transforms/talairach.xfm > > > > > > I am receiving the error (pasted below) on about > half of my > > > scans, despite all cans using same protocol. I > detect no obvious > > > issue with the quality of the images. I have > original dicoms, > > > and am using mri_convert to save into a single .mgz > (or .nii, > > > doesn't neem to make a difference), and the > unpredictability of > > > the error makes diagnosis problematic. TKMedit2 > reveals > > > absolutely wacky registrations. I am processing on > Freesurfer > > > 5.1, and have replicated issue on two different > installations. I > > > am designing a new longitudinal study inheriting the > same > > > imaging protocol and I do not want to get in a > situation > > > demanding manual editing of the talairach. Can > anyone help me > > > out? Thanks, Joshua > > > > > > ERROR: talairach_afd: Talairach Transform: > > > transforms/talairach.xfm ***FAILED*** (p=0.0030, > 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 FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP > Fri Apr 17 > > > 01:57:59 UTC 2009 i686 GNU/Linux > > > > > > recon-all -s test005 exited with ERRORS at Wed Nov > 2 02:03:32 > > > EDT 2011 > > > > > > For more details, see the log file > > > > /home/virtualuser/freesurfer/subjects/test005/scripts/recon-all.log > > > To report a problem, see > > > > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > - > > > Joshua Lee > > > Graduate Student > > > Center for Mind and Brain & > > > Department of Psychology > > > University of California, Davis > > > 530.747.3805 > > > > > > > > > > > > > > > _______________________________________________ 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,
What was the reason for this switch? Intuitively it seems that a bias-corrected image is likely to get a better registration (since I assume the target has essentially uniform intensities).
Michael
On Wed, Nov 2, 2011 at 1:15 PM, Nick Schmansky nicks@nmr.mgh.harvard.eduwrote:
no, v5.0 uses nu.mgz as input to the talairach_avi routine, whereas v5.1 uses orig.mgz.
its hard to say why it would fail for some subjects but not others, other than head positioning and to some degree ventricle size makes a difference.
n.
On Wed, 2011-11-02 at 16:10 -0400, Joshua Lee wrote:
Thanks Nick,
Is use-mritotal equivalent to what version 5.0 does by default?
Also, any suggestions on why this talairach error would occur only on a portion of my data, despite all being collected with the same imaging protocol, same conversions from dicom, etc?
Joshua Lee
Graduate Student Center for Mind and Brain &
Department of Psychology
University of California, Davis 530.747.3805
On Wed, Nov 2, 2011 at 4:02 PM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote: joshua,
try adding -use-mritotal to the end of your recon-all command. it will use an alternate way to compute the talairach.xfm which works better on some data. the change from v5.0 to v5.1 in the talairach stage was that in v5.1, the talairach.xfm is needed to compute nu.mgz, so the talairach stage needs to precede the nu_correct stage. this means the talairach stage can no longer use nu.mgz as input, which seems to work better than orig.mgz for some data (and is the case for your data). in the next release of freesurfer, recon-all will automatically try the alternate method (mritotal) if the default talairach_avi method fails the tal-check. n. On Wed, 2011-11-02 at 08:45 -0400, Bruce Fischl wrote: > can you send us an example that works in 5.0 and fails in 5.1? > > thanks > Bruce > On Wed, 2 Nov > 2011, Joshua Lee wrote: > > > Small Update: Error Disappears if Using Freesurfer version 5.0 instead of > > 5.1. However, since I am keenly interested in the hippocampal-subfield > > segmentation capabilities of the most recent version, I am loathe to regress > > to an earlier version of FreeSurfer > > - > > Joshua Lee > > Graduate Student > > Center for Mind and Brain & > > Department of Psychology > > University of California, Davis > > 530.747.3805 > > > > > > On Wed, Nov 2, 2011 at 2:29 AM, Joshua Lee <jkilee@ucdavis.edu> wrote: > > #@# Talairach Failure Detection Wed Nov 2 02:03:32 EDT 2011 > > /home/virtualuser/freesurfer/subjects/test005/mri > > > > talairach_afd -T 0.005 -xfm transforms/talairach.xfm > > > > I am receiving the error (pasted below) on about half of my > > scans, despite all cans using same protocol. I detect no obvious > > issue with the quality of the images. I have original dicoms, > > and am using mri_convert to save into a single .mgz (or .nii, > > doesn't neem to make a difference), and the unpredictability of > > the error makes diagnosis problematic. TKMedit2 reveals > > absolutely wacky registrations. I am processing on Freesurfer > > 5.1, and have replicated issue on two different installations. I > > am designing a new longitudinal study inheriting the same > > imaging protocol and I do not want to get in a situation > > demanding manual editing of the talairach. Can anyone help me > > out? Thanks, Joshua > > > > ERROR: talairach_afd: Talairach Transform: > > transforms/talairach.xfm ***FAILED*** (p=0.0030, 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 FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 > > 01:57:59 UTC 2009 i686 GNU/Linux > > > > recon-all -s test005 exited with ERRORS at Wed Nov 2 02:03:32 > > EDT 2011 > > > > For more details, see the log file > >/home/virtualuser/freesurfer/subjects/test005/scripts/recon-all.log
> > To report a problem, see > > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > - > > Joshua Lee > > Graduate Student > > Center for Mind and Brain & > > Department of Psychology > > University of California, Davis > > 530.747.3805 > > > > > > > > > _______________________________________________ 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
Hi Michael
we found that the conversion to unsigned character sometimes compressed the brain into only a couple of bits of the dynamic range. We know use the talairach xform to locate the center of the brain and make sure that a ball centered at the tal origin occupies a lot of the histogram. This helped in a number of cases, but maybe the makes the tal xform more sensitive to bias fields and strange intensity scalings.
Bruce On Wed, 2 Nov 2011, Michael Waskom wrote:
Hi, What was the reason for this switch? Intuitively it seems that a bias-corrected image is likely to get a better registration (since I assume the target has essentially uniform intensities).
Michael
On Wed, Nov 2, 2011 at 1:15 PM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote: no, v5.0 uses nu.mgz as input to the talairach_avi routine, whereas v5.1 uses orig.mgz.
its hard to say why it would fail for some subjects but not others, other than head positioning and to some degree ventricle size makes a difference. n.On Wed, 2011-11-02 at 16:10 -0400, Joshua Lee wrote:
Thanks Nick,
Is use-mritotal equivalent to what version 5.0 does by default?
Also, any suggestions on why this talairach error would occur only on a portion of my data, despite all being collected with the same imaging protocol, same conversions from dicom, etc?
Joshua Lee
Graduate Student Center for Mind and Brain &
Department of Psychology
University of California, Davis 530.747.3805
On Wed, Nov 2, 2011 at 4:02 PM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote: joshua,
try adding -use-mritotal to the end of your recon-all command. it will use an alternate way to compute the talairach.xfm which works better on some data.
the change from v5.0 to v5.1 in the talairach stage was that in v5.1, the talairach.xfm is needed to compute nu.mgz, so the talairach stage needs to precede the nu_correct stage. this means the talairach stage can no longer use nu.mgz as input, which seems to work better than orig.mgz for some data (and is the case for your data).
in the next release of freesurfer, recon-all will automatically try the alternate method (mritotal) if the default talairach_avi method fails the tal-check.
n.
On Wed, 2011-11-02 at 08:45 -0400, Bruce Fischl wrote: > can you send us an example that works in 5.0 and fails in 5.1? > > thanks > Bruce > On Wed, 2 Nov > 2011, Joshua Lee wrote: > > > Small Update: Error Disappears if Using Freesurfer version 5.0 instead of > > 5.1. However, since I am keenly interested in the hippocampal-subfield > > segmentation capabilities of the most recent version, I am loathe to regress > > to an earlier version of FreeSurfer > > - > > Joshua Lee > > Graduate Student > > Center for Mind and Brain & > > Department of Psychology > > University of California, Davis > > 530.747.3805 > > > > > > On Wed, Nov 2, 2011 at 2:29 AM, Joshua Lee jkilee@ucdavis.edu wrote: > > #@# Talairach Failure Detection Wed Nov 2 02:03:32 EDT 2011 > > /home/virtualuser/freesurfer/subjects/test005/mri > > > > talairach_afd -T 0.005 -xfm transforms/talairach.xfm > > > > I am receiving the error (pasted below) on about half of my > > scans, despite all cans using same protocol. I detect no obvious > > issue with the quality of the images. I have original dicoms, > > and am using mri_convert to save into a single .mgz (or .nii, > > doesn't neem to make a difference), and the unpredictability of > > the error makes diagnosis problematic. TKMedit2 reveals > > absolutely wacky registrations. I am processing on Freesurfer > > 5.1, and have replicated issue on two different installations. I > > am designing a new longitudinal study inheriting the same > > imaging protocol and I do not want to get in a situation > > demanding manual editing of the talairach. Can anyone help me > > out? Thanks, Joshua > > > > ERROR: talairach_afd: Talairach Transform: > > transforms/talairach.xfm ***FAILED*** (p=0.0030, 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 FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 > > 01:57:59 UTC 2009 i686 GNU/Linux > > > > recon-all -s test005 exited with ERRORS at Wed Nov 2 02:03:32 > > EDT 2011 > > > > For more details, see the log file > > /home/virtualuser/freesurfer/subjects/test005/scripts/recon-all.log > > To report a problem, see > > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > - > > Joshua Lee > > Graduate Student > > Center for Mind and Brain & > > Department of Psychology > > University of California, Davis > > 530.747.3805 > > > > > > > >
> _______________________________________________ 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.
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Dear FreeSurfur Gurus, It appears that the using -use-mritotal worked to get past the talairach error.
Thank you for all your help. We really appreciate it.
Joshua
On Wed, Nov 2, 2011 at 7:01 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Michael
we found that the conversion to unsigned character sometimes compressed the brain into only a couple of bits of the dynamic range. We know use the talairach xform to locate the center of the brain and make sure that a ball centered at the tal origin occupies a lot of the histogram. This helped in a number of cases, but maybe the makes the tal xform more sensitive to bias fields and strange intensity scalings.
Bruce
On Wed, 2 Nov 2011, Michael Waskom wrote:
Hi,
What was the reason for this switch? Intuitively it seems that a bias-corrected image is likely to get a better registration (since I assume the target has essentially uniform intensities).
Michael
On Wed, Nov 2, 2011 at 1:15 PM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote: no, v5.0 uses nu.mgz as input to the talairach_avi routine, whereas v5.1 uses orig.mgz.
its hard to say why it would fail for some subjects but not others, other than head positioning and to some degree ventricle size makes a difference. n.On Wed, 2011-11-02 at 16:10 -0400, Joshua Lee wrote:
Thanks Nick,
Is use-mritotal equivalent to what version 5.0 does by default?
Also, any suggestions on why this talairach error would occur only on a portion of my data, despite all being collected with the same imaging protocol, same conversions from dicom, etc?
Joshua Lee
Graduate Student Center for Mind and Brain &
Department of Psychology
University of California, Davis 530.747.3805
On Wed, Nov 2, 2011 at 4:02 PM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote: joshua,
try adding -use-mritotal to the end of your recon-all command. it will use an alternate way to compute the talairach.xfm which works better on some data. the change from v5.0 to v5.1 in the talairach stage was that in v5.1, the talairach.xfm is needed to compute nu.mgz, so the talairach stage needs to precede the nu_correct stage. this means the talairach stage can no longer use nu.mgz as input, which seems to work better than orig.mgz for some data (and is the case for your data). in the next release of freesurfer, recon-all will automatically try the alternate method (mritotal) if the default talairach_avi method fails the tal-check. n. On Wed, 2011-11-02 at 08:45 -0400, Bruce Fischl wrote: > can you send us an example that works in 5.0 and fails in 5.1? > > thanks > Bruce > On Wed, 2 Nov > 2011, Joshua Lee wrote: > > > Small Update: Error Disappears if Using Freesurfer version 5.0 instead of > > 5.1. However, since I am keenly interested in the hippocampal-subfield > > segmentation capabilities of the most recent version, I am loathe to regress > > to an earlier version of FreeSurfer > > - > > Joshua Lee > > Graduate Student > > Center for Mind and Brain & > > Department of Psychology > > University of California, Davis > > 530.747.3805 > > > > > > On Wed, Nov 2, 2011 at 2:29 AM, Joshua Lee <jkilee@ucdavis.edu> wrote: > > #@# Talairach Failure Detection Wed Nov 2 02:03:32 EDT 2011 > > /home/virtualuser/freesurfer/**subjects/test005/mri > > > > talairach_afd -T 0.005 -xfm transforms/talairach.xfm > > > > I am receiving the error (pasted below) on about half of my > > scans, despite all cans using same protocol. I detect no obvious > > issue with the quality of the images. I have original dicoms, > > and am using mri_convert to save into a single .mgz (or .nii, > > doesn't neem to make a difference), and the unpredictability of > > the error makes diagnosis problematic. TKMedit2 reveals > > absolutely wacky registrations. I am processing on Freesurfer > > 5.1, and have replicated issue on two different installations. I > > am designing a new longitudinal study inheriting the same > > imaging protocol and I do not want to get in a situation > > demanding manual editing of the talairach. Can anyone help me > > out? Thanks, Joshua > > > > ERROR: talairach_afd: Talairach Transform: > > transforms/talairach.xfm ***FAILED*** (p=0.0030, 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 FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 > > 01:57:59 UTC 2009 i686 GNU/Linux > > > > recon-all -s test005 exited with ERRORS at Wed Nov 2 02:03:32 > > EDT 2011 > > > > For more details, see the log file > > /home/virtualuser/freesurfer/**subjects/test005/scripts/**recon-all.log
> > To report a problem, see > > http://surfer.nmr.mgh.harvard.**edu/fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > > - > > Joshua Lee > > Graduate Student > > Center for Mind and Brain & > > Department of Psychology > > University of California, Davis > > 530.747.3805 > > > > > > > > > ______________________________**_________________ 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/**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/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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