Sorry I meant those same subjects' transforms look much better with *FS 5.0*
.


2011/8/15 Myriam Siefert <myriamsief...@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 <ni...@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 <myriamsief...@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 <myriamsief...@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 <fis...@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
>> >                         <myriamsief...@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
>> >                         >
>> >                         >
>> >                         >
>> >                         >
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