 |
 |
Hi Steve, I read this note with some concern, given that a couple of my colleagues are using TBSS to evaluate hemispheric FA asymmetries. In looking over their results, I think they have found too many significant voxels (including a large number of the highest possible significance). What biases one might expect if they used the publically released TBSS scripts to perform a hemispheric FA asymmetry study? Thanks, Matt. -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Steve Smith Sent: Thursday, May 14, 2009 11:23 AM To: [log in to unmask] Subject: Re: [FSL] Symmetrical TBSS skeleton Hi, Yes - when you want "tbss_skeleton" to use a specific skeleton rather than one derived from the 4D data you feed in, you need to use the -s flag (see the usage). Also, you need to explicitly force the skeleton to be symmetric and not just derive it from a symmetric mean FA image (the skeletonisation will not necessarily give an _exactly_ symmetric skeleton when fed a symmetric image). We have a script for doing asymmetry analyses which we will clean up and make available soon - hopefully next week. Cheers. > Hi, > > Just to correct my last post - what I get at the end of this > processing > pipeline is an 4d all_FA_skeleton file that IS symmetrical but does > not > quite fit my original "symmetrised" mean_FA_skeleton in that there are > additional/missing voxels in places. > > Is this a reasonable method to achieve what I am after, or is there an > alternative method. > > Thanks. > > Pete > On 11 May 2009, at 12:44, Pete Goodman wrote: > Dear All, > > I am trying to use TBSS to derive asymmetry indices. To do this I > have, > > 1) Made the FA template symmetrical by creating a flipped version > (fslswapdim applied) and averaging the flipped and unflipped versions > 2) Registered all data to new template using tbss scripts 1, 2 and 3 > 3) Taken the mean FA skeleton and made this symmetrical using the same > method as above > 4) Fed my all_FA data into tbss 4 together with the new symmetrical > skeleton > - here I was expecting voxels from each subject to be projected onto > the > symmetrical skeleton which I could then flip again and use > (unflipped minus > flipped) to derive AI. > > However, the all_FA_skeletonised output I get is not quite > symmetrical. The > deprojection step seems to have ignored the use of the new symmetrical > skeleton, and instead used the old, unsymmetrical one. > > Any help, tips as to a better method would be welcome. > > Thanks. > > Pete > --------------------------------------------------------------------------- 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 ---------------------------------------------------------------------------