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Dear Stephen, Thank you for your help again. I read tbss_skeleton.cc as well as your study (2006). I can generally understand the study. However, as a person with very weak "computer" language, it's really hard for me to understand tbss_skeleton.cc. I hope to get your help to find the index for the second "warp", skeleton projection. My understanding is for every subject, the FA will be projected onto the mean skeleton. So I suppose there will be an "warping" parameter for each subject (like the 3 volumes 4D file from fnirt). You recommended me to use -d option of tbss_skeleton. Please forgive me of my poor linux language knowledge, I didn't know the meaning of this option. And, how should we use this option (what's the input when using this option)? What does the output mean? I tried using mean_FA.nii.gz as the input and got a 3 volumes 4D file. I didn't know what it meant. Thank you so much. I really appreciate your help! Mingxia On Thu, Jun 13, 2013 at 8:44 AM, Stephen Smith <[log in to unmask]> wrote: > Hi > > On 12 Jun 2013, at 23:36, zhang mingxia <[log in to unmask]> > wrote: > > One more question: someone suggested me correlating the image (after > registration) of every subject with standard image (there is a correlation > coefficient for every subject), and contrast the correlation coefficients > of two groups. Is that a general way to resolve the "cross cultural brain" > problem? > > > That doesn't make a lot of sense because the final image for each subject > (prior to running randomise) is skeletonised…. > > You would need to have a look at fsl_reg and tbss_skeleton.cc in > $FSLDIR/src/tbss in order to work out how to investigate the warp and > skeleton-projections further. > > Cheers. > > > > > > > On Wed, Jun 12, 2013 at 9:58 AM, Stephen Smith <[log in to unmask]>wrote: > >> Hi - the whole point of TBSS is to minimise the effects of morphology >> changes influencing the results - which it will be in general successful >> with when the changes are shifts in tract locations, but it cannot deal >> with the case where thin tracts are thinner in some groups than others, >> because it is not possible to disambiguate changes in >> thin-tract-partial-voluming vs true-FA-changes. >> >> It is possible to do what you are asking for - but it is complicated, >> because the total TBSS "warp" is a combination of the initial FNIRT warp >> (you can find the warp files in the TBSS output directory), as well as the >> skeleton projection "warp" (you can get information about that with the -d >> debug option - but you'll have to read the source code to understand what >> that's all giving!). >> >> Cheers, Steve. >> >> >> On 12 Jun 2013, at 06:29, zhang mingxia <[log in to unmask]> >> wrote: >> >> Dear FSL experts, >> >> I am doing a cross-cultural TBSS study which includes two groups of >> subjects. The reviewer asked me to contrast the degree to which the TBSS >> software changes original tract locations between the two groups to exclude >> the complication introduced by differences in the overall morphology of the >> cranium across groups. >> >> When I analyzed the data, I used "tbss_2_reg -T" and "tbss_3_postreg -S" >> to runs the nonlinear registration, aligning all FA images to a 1x1x1mm >> standard space. >> >> I saw there were basename_to_target.mat, basename_to_target_warp.msf and >> basename_to_target_warp.nii.gz (three volumes) which were related to >> registration. >> >> My question is: what should I use to index the degree to which the TBSS >> software changes original tract location? >> >> Thanks in advance! >> >> Mingxia Zhang >> >> >> >> >> --------------------------------------------------------------------------- >> 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 >> >> --------------------------------------------------------------------------- >> >> Stop the cultural destruction of Tibet <http://smithinks.net/> >> >> >> >> >> > > > --------------------------------------------------------------------------- > 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 > --------------------------------------------------------------------------- > > Stop the cultural destruction of Tibet <http://smithinks.net> > > > > >