Is talairach.xfm even used as input for any stage of autorecon2 or 3? (Or, is it just the talairach.lta and talairach.m3z files?)
thanks, Mike H. On Thu, 2007-10-11 at 16:28 -0400, Doug Greve wrote: > It is not that important from a recon standpoint. However, if you intend > to report talairach coods, create an average surface, or use that > talairach transform in any way, it will be a problem. > > doug > > Michael Harms wrote: > > >Hello, > >We are running FS v3.0.5 on some elderly brains, and the talairach > >transform (as assessed via tkregister2 with fstal flag) is inaccurate in > >an appreciable number of the scans we have examined so far. Frequently, > >the inaccuracies involve primarily scaling or translation, although in > >one instance the rotation was way-off (such that the cardinal axes were > >basically swapped). However, even for this worst case, the white and > >pial surfaces, as well as the aseg, look reasonable. (I haven't run > >autorecon3 to create the surface parcellations yet). > > > >To what extent is talairach.xfm important for the autorecon2 & 3 stages? > >If surfaces and aseg look ok, can an inaccurate talairach.xfm just be > >ignored if we are not going to be averaging functional data? Will the > >surface parcellations perhaps be affected somehow? > > > >Looking at ReconAllDevTable it appears that talairach.lta and > >talairach.m3z are the primary inputs to stages 2 and 3. So, I'm > >wondering how the .xfm relates to the .lta and .m3z files...? > > > >Lastly, the particularly bad .xfm under v3.0.5 looks fine when created > >using v4.0.1. If we need or want accurate .xfm's would it be > >appropriate to run autorecon1 under v4 but then switch to v3 for > >autorecon2 & 3 so as to maintain compatibility with other subjects > >processed under v3? > > > >thanks, > >Mike H. > > > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
