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 >> > > >> > > >> > > >> > > >> _______________________________________________ >> > > 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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