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 > > > > > > > > > > > > _______________________________________________ > > > 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. > > > > > > > > > > > > > >
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