 |
 |
Thank you Andreas & Steve for your feedback! This was very helpful. --Ryan On May 26 2010, Stephen Smith wrote: > HI - yes this makes sense - thought I suspect that there probably isn't a > huge difference between working in a 'mid' space for the within-subject > affine registrations vs just taking one of the timepoints as a target, > given that probably the main advantage of doing a custom approach with > multiple timepoints will probably be the joint use (across all timepoints > wihtin-subject) of a single warp field. > >Cheers. > > >On 25 May 2010, at 22:43, Andreas Bartsch wrote: > >> Hi, >> >> what you could try is the following: >> i) affinely register the individual FA maps to a template >> ii) apply 'midtrans' to the 3 *.mat-files produced by flirt >> iii) get the inverse using convert_xfm >> iv) apply that to the template to get a midspace FA >> >> You would then have to re-register the individual FAs and potentially >> average these prior to fnirting (to get a uniform non-linear reg across >> the 3 time points). >> >> However, having said that I think even theoretically we have no >> "optimal" way or uniform gold standard to register longitudinal data >> yet. It all depends on the assumptions you are willing to make and the >> data you have. For example, if people were repositioned distortions may >> vary quite a bit. Then the best processing depends on the distortion >> correction and how good it works. Even signal loss can vary, e.g. you >> will observe less signal loss from adjacent sinuses if a subject comes >> in with sinusitis at one time point. >> >> Essentially, you need to decide whether affine registration of the >> individual time points to each other for a given subject is really the >> way to go and at how many DOFs. But Steve has already indicated that the >> FMRIB crew is going into that. >> >> Any comments, Steve / MJ / Jesper? >> >> Cheers- >> Andreas >> >> ________________________________________ >> Von: FSL - FMRIB's Software Library [[log in to unmask]] im Auftrag von >> Ryan Muetzel [[log in to unmask]] >> Gesendet: Dienstag, 25. Mai 2010 22:05 >> An: [log in to unmask] >> Betreff: [FSL] 3+ time point longidtudinal data >> >> Hello, >> >> We are conducting a longitudinal study and are using TBSS to warp each FA >> map to standard space. With our DTI data, we've found slightly more >> intra-subject variability in the nonlinear warp than we were expecting. >> >> In an attempt to address this variability, prior to running tbss_2, we >> align the time-1 and time-2 data into a half-way space (just as is done >> in >> SIENA). From there, we compute an average FA map for each subject >> (time-1 + >> time2/2) and feed that image into tbss_2 to determine the nonlinear warp. >> We can then apply this warp to the individual time-point images using >> tbss_non_FA. This method seems to reduce the intra-subject variability by >> using the same nonlinear warp for each time point. >> >> My question then is, is there a way to find the "mid point" among 3+ >> scans, >> just as is done in SIENA with 2 scans? >> >> Best, >> >> Ryan > > >--------------------------------------------------------------------------- >Stephen M. Smith, Professor of Biomedical Engineering >Associate Director, Oxford University FMRIB Centre > >FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK >+44 (0) 1865 222726 (fax 222717) >[log in to unmask] http://www.fmrib.ox.ac.uk/~steve >--------------------------------------------------------------------------- > > > > -- ============================================================= Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. =============================================================