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.