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Thank you all for the reply. Paul ==============Original message text=============== On Sun, 10 Feb 2008 9:47:54 am CST Steve Smith wrote: Thanks Matt, Yes - I presume you mean the TBSS-derived nonlinear warp fields, which certainly will help. Note though that the final "alignment" stage in TBSS (the tract-centre to skeleton projection) would not be easily usable in this context, and so my concern would still stand to some extent. Cheers, Steve. On 10 Feb 2008, at 15:38, Matt Glasser wrote: > In the past, I have applied the registration matrices generated by > TBSS to > align tractography results before averaging them. You also might > consider > this approach to improve tract alignment. > > Peace, > > Matt. > > -----Original Message----- > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On > Behalf > Of Steve Smith > Sent: Sunday, February 10, 2008 10:24 AM > To: [log in to unmask] > Subject: Re: [FSL] t-test for tractography > > Hi - I guess you're feeding in the fdt_paths image from each subject > into a group-wise t-test? There are various dangers here. > > The obvious one is that you will not have very good alignment between > subjects for such a voxelwise test. This is the primary issue that > TBSS attempts to resolve. However, if you accept this danger (and, > maybe smooth a lot......), you can run the voxelwise t-test on the > tractography output.... > > Which brings you to a second danger, which is that it will be hard to > correct for multiple comparisons across space, as the spatial > autocorrelation structure will be high and complex. However, you can > probably get over that by using randomise correctly. > > I'm sure that Tim/Saad may have further caveats with this.... > > Cheers, Steve. > > > > > On 7 Feb 2008, at 21:06, Paul Geha wrote: > >> Dear FSL users, >> >> >> I am running proabilistic tractography (using a mask identified from >> TBSS) >> on a group of patients and age matched controls. Is it >> statisitcally sound >> to do an unpaired t-test between the 2 groups on the tracts maps >> obtained ? >> >> thanks >> Paul >> >> >> >> Paul Geha M.D. >> Northwestern University >> The Feinberg School of Medicine >> Department of Physiology M211 >> 303 E. Chicago Ave. >> Chicago, IL 60611 >> Tel:312-503 2886 >> Fax: 312-503-5101 >> > > > --------------------------------------------------------------------------- > 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> --------------------------------------------------------------------------- > --------------------------------------------------------------------------- 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--------------------------------------------------------------------------- ===========End of original message text=========== Paul Geha M.D. Northwestern University The Feinberg School of Medicine Department of Physiology M211 303 E. Chicago Ave. Chicago, IL 60611 Tel:312-503 2886 Fax: 312-503-5101