Hi Nick, Sorry to bother you but I wondered if you had had the time to take a look at my dataset. Thank you very much, Myriam
2011/8/11 Myriam Siefert myriamsiefert@gmail.com
Hi Nick, I just would like to make sure that you had received my data, otherwise I can send it again possibly by another mean if better. Thanks a lot for your help Sincerely, Myriam
2011/8/10 Myriam Siefert myriamsiefert@gmail.com
Hi Bruce and Nick, Thank you so much for taking a look! Right now I'm uploading the set on the anonymous ftp server ( ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming) : talairach_issue.zip. It should appear to you in about 1 hour. It contains 2 versions of the same subject, the only difference is that OK-J-20bis was run with the -use-mritotal flag. Please let me know if there's any problem with the upload or if you need anything else. Sincerely, Myriam
2011/8/10 Bruce Fischl fischl@nmr.mgh.harvard.edu
Hi Myriam Could you send nick a dataset so he can take a look? Thanks Bruce
On Aug 10, 2011, at 10:24 AM, Myriam Siefert myriamsiefert@gmail.com wrote:
Hi freesurfers,
I'm currently re-processing with FS5.1 some data that i had already processed with FS5.0 and am experiencing some unexpected issues with the linear talairach transform.
- While manually checking with Tkregister, I noticed that some off the
subjects had quite unsatisfying transforms , while no talairach failure was detected on the log
- The transforms looked ok for those subjects in FS 5.0
- I re-run autorecon1 using the -use-mritotal flag
- While still no error in the log file, the transforms usually then look
acceptable in Tkregister but completely wrong when talairach.xfm is loaded in tkmedit : transformation in the top or bottom left corners, coronal and transversal views interverted, sagittal views rotated by 90 degrees... This happens for a few (not all) of the subjects that I've re-processed with FS5.1 so far.
I'm probably doing something wrong but can't figure out what nor what to do about it. Any advice would be highly appreciated.
Thanks in advance
Myriam Siefert, MD, MS candidate Visiting scholar in SACNlab Northwestern University
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'm able to replicate what you see in tkmedit when the transform is created using the -use-mritotal flag. i cant explain why this happens, and is a bit unsettling given that the -tal-check portion passed and the transform looks good in tkregister.
the transform created by the default (not using the -use-mritotal flag) seems good enough for freesurfer purposes, and it looks correct in tkmedit (when loading the talairach.xfm), so i would suggest using that one.
n.
On Mon, 2011-08-15 at 11:54 -0500, Myriam Siefert wrote:
Hi Nick, Sorry to bother you but I wondered if you had had the time to take a look at my dataset. Thank you very much, Myriam
2011/8/11 Myriam Siefert myriamsiefert@gmail.com Hi Nick, I just would like to make sure that you had received my data, otherwise I can send it again possibly by another mean if better. Thanks a lot for your help Sincerely, Myriam
2011/8/10 Myriam Siefert <myriamsiefert@gmail.com> Hi Bruce and Nick, Thank you so much for taking a look! Right now I'm uploading the set on the anonymous ftp server (ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming) : talairach_issue.zip. It should appear to you in about 1 hour. It contains 2 versions of the same subject, the only difference is that OK-J-20bis was run with the -use-mritotal flag. Please let me know if there's any problem with the upload or if you need anything else. Sincerely, Myriam 2011/8/10 Bruce Fischl <fischl@nmr.mgh.harvard.edu> Hi Myriam Could you send nick a dataset so he can take a look? Thanks Bruce On Aug 10, 2011, at 10:24 AM, Myriam Siefert <myriamsiefert@gmail.com> wrote: > > Hi freesurfers, > > I'm currently re-processing with FS5.1 some > data that i had already processed with FS5.0 > and am experiencing some unexpected issues > with the linear talairach transform. > > - While manually checking with Tkregister, I > noticed that some off the subjects had quite > unsatisfying transforms , while no talairach > failure was detected on the log > - The transforms looked ok for those > subjects in FS 5.0 > - I re-run autorecon1 using the > -use-mritotal flag > - While still no error in the log file, the > transforms usually then look acceptable in > Tkregister but completely wrong when > talairach.xfm is loaded in tkmedit : > transformation in the top or bottom left > corners, coronal and transversal views > interverted, sagittal views rotated by 90 > degrees... > This happens for a few (not all) of the > subjects that I've re-processed with FS5.1 > so far. > > I'm probably doing something wrong but can't > figure out what nor what to do about it. > Any advice would be highly appreciated. > > Thanks in advance > > Myriam Siefert, MD, MS candidate > Visiting scholar in SACNlab Northwestern > University > > > > _______________________________________________ > 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, I have this problem with quite a few of my subjects, usually the fuzzy transform volume in tkregister looks smaller than the subject's brain. To what extend should I manually edit the xfm (what criterions are mandatory for that transform to be acceptable)?
Actually what puzzles me is that those same subjects' transforms look much better with FS 5.1. What could explain this?
Also, what would be the impact of a bad affine transform on the subcortical volume based stream? (my primary interrests are amygdala and hippocampus volumes).
Thanks for your help, Myriam
2011/8/15 Nick Schmansky nicks@nmr.mgh.harvard.edu
i'm able to replicate what you see in tkmedit when the transform is created using the -use-mritotal flag. i cant explain why this happens, and is a bit unsettling given that the -tal-check portion passed and the transform looks good in tkregister.
the transform created by the default (not using the -use-mritotal flag) seems good enough for freesurfer purposes, and it looks correct in tkmedit (when loading the talairach.xfm), so i would suggest using that one.
n.
On Mon, 2011-08-15 at 11:54 -0500, Myriam Siefert wrote:
Hi Nick, Sorry to bother you but I wondered if you had had the time to take a look at my dataset. Thank you very much, Myriam
2011/8/11 Myriam Siefert myriamsiefert@gmail.com Hi Nick, I just would like to make sure that you had received my data, otherwise I can send it again possibly by another mean if better. Thanks a lot for your help Sincerely, Myriam
2011/8/10 Myriam Siefert <myriamsiefert@gmail.com> Hi Bruce and Nick, Thank you so much for taking a look! Right now I'm uploading the set on the anonymous ftp server (ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming) : talairach_issue.zip. It should appear to you in about 1 hour. It contains 2 versions of the same subject, the only difference is that OK-J-20bis was run with the -use-mritotal flag. Please let me know if there's any problem with the upload or if you need anything else. Sincerely, Myriam 2011/8/10 Bruce Fischl <fischl@nmr.mgh.harvard.edu> Hi Myriam Could you send nick a dataset so he can take a look? Thanks Bruce On Aug 10, 2011, at 10:24 AM, Myriam Siefert <myriamsiefert@gmail.com> wrote: > > Hi freesurfers, > > I'm currently re-processing with FS5.1 some > data that i had already processed with FS5.0 > and am experiencing some unexpected issues > with the linear talairach transform. > > - While manually checking with Tkregister, I > noticed that some off the subjects had quite > unsatisfying transforms , while no talairach > failure was detected on the log > - The transforms looked ok for those > subjects in FS 5.0 > - I re-run autorecon1 using the > -use-mritotal flag > - While still no error in the log file, the > transforms usually then look acceptable in > Tkregister but completely wrong when > talairach.xfm is loaded in tkmedit : > transformation in the top or bottom left > corners, coronal and transversal views > interverted, sagittal views rotated by 90 > degrees... > This happens for a few (not all) of the > subjects that I've re-processed with FS5.1 > so far. > > I'm probably doing something wrong but can't > figure out what nor what to do about it. > Any advice would be highly appreciated. > > Thanks in advance > > Myriam Siefert, MD, MS candidate > Visiting scholar in SACNlab Northwestern > University > > > > _______________________________________________ > 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.
Sorry I meant those same subjects' transforms look much better with *FS 5.0* .
2011/8/15 Myriam Siefert myriamsiefert@gmail.com
Hi Nick, I have this problem with quite a few of my subjects, usually the fuzzy transform volume in tkregister looks smaller than the subject's brain. To what extend should I manually edit the xfm (what criterions are mandatory for that transform to be acceptable)?
Actually what puzzles me is that those same subjects' transforms look much better with FS 5.1. What could explain this?
Also, what would be the impact of a bad affine transform on the subcortical volume based stream? (my primary interrests are amygdala and hippocampus volumes).
Thanks for your help, Myriam
2011/8/15 Nick Schmansky nicks@nmr.mgh.harvard.edu
i'm able to replicate what you see in tkmedit when the transform is created using the -use-mritotal flag. i cant explain why this happens, and is a bit unsettling given that the -tal-check portion passed and the transform looks good in tkregister.
the transform created by the default (not using the -use-mritotal flag) seems good enough for freesurfer purposes, and it looks correct in tkmedit (when loading the talairach.xfm), so i would suggest using that one.
n.
On Mon, 2011-08-15 at 11:54 -0500, Myriam Siefert wrote:
Hi Nick, Sorry to bother you but I wondered if you had had the time to take a look at my dataset. Thank you very much, Myriam
2011/8/11 Myriam Siefert myriamsiefert@gmail.com Hi Nick, I just would like to make sure that you had received my data, otherwise I can send it again possibly by another mean if better. Thanks a lot for your help Sincerely, Myriam
2011/8/10 Myriam Siefert <myriamsiefert@gmail.com> Hi Bruce and Nick, Thank you so much for taking a look! Right now I'm uploading the set on the anonymous ftp server (ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming) : talairach_issue.zip. It should appear to you in about 1 hour. It contains 2 versions of the same subject, the only difference is that OK-J-20bis was run with the -use-mritotal flag. Please let me know if there's any problem with the upload or if you need anything else. Sincerely, Myriam 2011/8/10 Bruce Fischl <fischl@nmr.mgh.harvard.edu> Hi Myriam Could you send nick a dataset so he can take a look? Thanks Bruce On Aug 10, 2011, at 10:24 AM, Myriam Siefert <myriamsiefert@gmail.com> wrote: > > Hi freesurfers, > > I'm currently re-processing with FS5.1 some > data that i had already processed with FS5.0 > and am experiencing some unexpected issues > with the linear talairach transform. > > - While manually checking with Tkregister, I > noticed that some off the subjects had quite > unsatisfying transforms , while no talairach > failure was detected on the log > - The transforms looked ok for those > subjects in FS 5.0 > - I re-run autorecon1 using the > -use-mritotal flag > - While still no error in the log file, the > transforms usually then look acceptable in > Tkregister but completely wrong when > talairach.xfm is loaded in tkmedit : > transformation in the top or bottom left > corners, coronal and transversal views > interverted, sagittal views rotated by 90 > degrees... > This happens for a few (not all) of the > subjects that I've re-processed with FS5.1 > so far. > > I'm probably doing something wrong but can't > figure out what nor what to do about it. > Any advice would be highly appreciated. > > Thanks in advance > > Myriam Siefert, MD, MS candidate > Visiting scholar in SACNlab Northwestern > University > > > >
> 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 Myriam,
did you check the aseg? Unless the talairach.xfm is *really* off I don't think it will have much impact, but you should visually inspect them.
cheers Bruce On Mon, 15 Aug 2011, Myriam Siefert wrote:
Hi Nick, I have this problem with quite a few of my subjects, usually the fuzzy transform volume in tkregister looks smaller than the subject's brain. To what extend should I manually edit the xfm (what criterions are mandatory for that transform to be acceptable)?
Actually what puzzles me is that those same subjects' transforms look much better with FS 5.1. What could explain this?
Also, what would be the impact of a bad affine transform on the subcortical volume based stream? (my primary interrests are amygdala and hippocampus volumes).
Thanks for your help, Myriam
2011/8/15 Nick Schmansky nicks@nmr.mgh.harvard.edu i'm able to replicate what you see in tkmedit when the transform is created using the -use-mritotal flag. i cant explain why this happens, and is a bit unsettling given that the -tal-check portion passed and the transform looks good in tkregister.
the transform created by the default (not using the -use-mritotal flag) seems good enough for freesurfer purposes, and it looks correct in tkmedit (when loading the talairach.xfm), so i would suggest using that one. n.On Mon, 2011-08-15 at 11:54 -0500, Myriam Siefert wrote:
Hi Nick, Sorry to bother you but I wondered if you had had the time to take a look at my dataset. Thank you very much, Myriam
2011/8/11 Myriam Siefert myriamsiefert@gmail.com Hi Nick, I just would like to make sure that you had received my
data,
otherwise I can send it again possibly by another mean if better. Thanks a lot for your help Sincerely, Myriam
2011/8/10 Myriam Siefert myriamsiefert@gmail.com Hi Bruce and Nick, Thank you so much for taking a look! Right now I'm uploading the set on the anonymous ftp server (ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming)
:
talairach_issue.zip. It should appear to you in
about
1 hour. It contains 2 versions of the same subject, the only difference is that OK-J-20bis was run with the -use-mritotal flag. Please let me know if there's any problem with the upload or if you need anything else. Sincerely, Myriam
2011/8/10 Bruce Fischl fischl@nmr.mgh.harvard.edu
Hi Myriam
Could you send nick a dataset so he can take
a
look? Thanks Bruce
On Aug 10, 2011, at 10:24 AM, Myriam Siefert myriamsiefert@gmail.com wrote:
> > Hi freesurfers, > > I'm currently re-processing with FS5.1
some
> data that i had already processed with
FS5.0
> and am experiencing some unexpected issues > with the linear talairach transform. > > - While manually checking with Tkregister,
I
> noticed that some off the subjects had
quite
> unsatisfying transforms , while no
talairach
> failure was detected on the log > - The transforms looked ok for those > subjects in FS 5.0 > - I re-run autorecon1 using the > -use-mritotal flag > - While still no error in the log file,
the
> transforms usually then look acceptable in > Tkregister but completely wrong when > talairach.xfm is loaded in tkmedit : > transformation in the top or bottom left > corners, coronal and transversal views > interverted, sagittal views rotated by 90 > degrees... > This happens for a few (not all) of the > subjects that I've re-processed with FS5.1 > so far. > > I'm probably doing something wrong but
can't
> figure out what nor what to do about it. > Any advice would be highly appreciated. > > Thanks in advance > > Myriam Siefert, MD, MS candidate > Visiting scholar in SACNlab Northwestern > University > > > >
> 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.
fyi, a change from 5.0 to 5.1 pertaining to this is that the talairach stage is now run before the nu_correct stage, so that creation of nu.mgz can benefit from talairach.xfm. this means talairach uses orig.mgz as input, which seems to be affecting your results. the next release of freesurfer will have an option to run talairach using nu.mgz as input, to handle cases like yours where nu.mgz works better.
n.
On Mon, 2011-08-15 at 16:00 -0400, Bruce Fischl wrote:
Hi Myriam,
did you check the aseg? Unless the talairach.xfm is *really* off I don't think it will have much impact, but you should visually inspect them.
cheers Bruce On Mon, 15 Aug 2011, Myriam Siefert wrote:
Hi Nick, I have this problem with quite a few of my subjects, usually the fuzzy transform volume in tkregister looks smaller than the subject's brain. To what extend should I manually edit the xfm (what criterions are mandatory for that transform to be acceptable)?
Actually what puzzles me is that those same subjects' transforms look much better with FS 5.1. What could explain this?
Also, what would be the impact of a bad affine transform on the subcortical volume based stream? (my primary interrests are amygdala and hippocampus volumes).
Thanks for your help, Myriam
2011/8/15 Nick Schmansky nicks@nmr.mgh.harvard.edu i'm able to replicate what you see in tkmedit when the transform is created using the -use-mritotal flag. i cant explain why this happens, and is a bit unsettling given that the -tal-check portion passed and the transform looks good in tkregister.
the transform created by the default (not using the -use-mritotal flag) seems good enough for freesurfer purposes, and it looks correct in tkmedit (when loading the talairach.xfm), so i would suggest using that one. n.On Mon, 2011-08-15 at 11:54 -0500, Myriam Siefert wrote:
Hi Nick, Sorry to bother you but I wondered if you had had the time to take a look at my dataset. Thank you very much, Myriam
2011/8/11 Myriam Siefert myriamsiefert@gmail.com Hi Nick, I just would like to make sure that you had received my
data,
otherwise I can send it again possibly by another mean if better. Thanks a lot for your help Sincerely, Myriam 2011/8/10 Myriam Siefert <myriamsiefert@gmail.com> Hi Bruce and Nick, Thank you so much for taking a look! Right now I'm uploading the set on the anonymous ftp server (ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming):
talairach_issue.zip. It should appear to you inabout
1 hour. It contains 2 versions of the same subject, the only difference is that OK-J-20bis was run with the -use-mritotal flag. Please let me know if there's any problem with the upload or if you need anything else. Sincerely, Myriam 2011/8/10 Bruce Fischl <fischl@nmr.mgh.harvard.edu> Hi Myriam Could you send nick a dataset so he can takea
look? Thanks Bruce On Aug 10, 2011, at 10:24 AM, Myriam Siefert <myriamsiefert@gmail.com> wrote: > > Hi freesurfers, > > I'm currently re-processing with FS5.1some
> data that i had already processed withFS5.0
> and am experiencing some unexpected issues > with the linear talairach transform. > > - While manually checking with Tkregister,I
> noticed that some off the subjects hadquite
> unsatisfying transforms , while notalairach
> failure was detected on the log > - The transforms looked ok for those > subjects in FS 5.0 > - I re-run autorecon1 using the > -use-mritotal flag > - While still no error in the log file,the
> transforms usually then look acceptable in > Tkregister but completely wrong when > talairach.xfm is loaded in tkmedit : > transformation in the top or bottom left > corners, coronal and transversal views > interverted, sagittal views rotated by 90 > degrees... > This happens for a few (not all) of the > subjects that I've re-processed with FS5.1 > so far. > > I'm probably doing something wrong butcan't
> figure out what nor what to do about it. > Any advice would be highly appreciated. > > Thanks in advance > > Myriam Siefert, MD, MS candidate > Visiting scholar in SACNlab Northwestern > University > > > >
> 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 wassent
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@nmr.mgh.harvard.edu
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Bruce Fischl -
Myriam Siefert -
Nick Schmansky