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 > > > > > > > > _______________________________________________ > > 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
