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
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