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Thankyou for the details...one more question, wrt probtrackx, I have never used the waytotal (to my knowledge). I run probtrack like this: probtrackx --network --mode=seedmask -x cst_l/masks.txt -l -c 0.2 -S 2000 --steplength=0.5 -P 5000 --avoid=cst_l_exclusion_diff.nii.gz --forcedir -f --opd -s Bed.bedpostX/merged -m Bed.bedpostX/nodif_brain_mask --dir=cst_l Rerunning probtrackx for all the subjects would be a monumental task...I don't currently get any waytotal file in the directory...should I be planning to spend several months rerunning probtrackx?? Thanks, Dianne On Thu, Aug 14, 2008 at 1:30 AM, Saad Jbabdi <[log in to unmask]> wrote: > The changes to FDT are all minor: > > - dtifit: . sets the correct min-max intensity range of all outputs to > make fslview visualisation easier > . output the mode and the tensor components > - probtrackx: . fix waytotal bug (it was underestimating the number of > connecting tracts) --> need to re-run subjects if previous version used. > . the seed masks and target masks no longer need to be binarised > - bedpostx: . none. > > > Cheers, > Saad. > > > > On 14 Aug 2008, at 07:37, Steve Smith wrote: > > Hi - I don't think that the probtrackx stuff has changed significantly, > Saad can comment if I"m wrong. > Cheers. > > > On 13 Aug 2008, at 18:27, Dianne Patterson wrote: > > Dear Group, > > I don't want to treat new subjects differently than the old ones... > I have been using FDT and doing probability tracking. > I've used flirt a lot as well, and > I've also been experimenting with Nudge > > Is there any reason I should avoid moving from the most recent FSL 4.0 to > FSL 4.1? > > Thankyou! > > Dianne > > On Wed, Aug 13, 2008 at 9:54 AM, Matthew Webster <[log in to unmask]> > wrote: > Fsl 4.1.0 has been released and is now ready for download, new features > include: > > • FNIRT - FMRIB's Nonlinear Image Registration Tool. The first release of > an accurate and yet fast nonlinear registration tool. This replaces IRTK, > and is based on a similar warp field representation, but a) includes > relative bias field modelling for improved accuracy and b) is very fast > because of explicit computation of the cost function Hessian. FEAT, MELODIC, > TBSS and FSL-VBM have all been updated to use FNIRT. > • FEAT v5.98. Various improvements, including FNIRT nonlinear registration, > outlier modelling in higher-level analysis and higher-level voxelwise > covariates (e.g., for structural confound modelling). A new script > feat_gm_prepare makes it easy to process structural data for use as a > higher-level voxelwise confound covariate. > • randomise v2.1. Various improvements, including improved handling of > confounds, TFCE optimisation for TBSS and parallelisation over multiple > computers. > • FAST v4.1 is now the default tissue-type segmentation program, and FAST > v3 has been removed from FSL. Hence all programs including SIENA/SIENAX now > use FAST v4. > • FIRST subcortical segmentation is now considerably faster, has improved > boundary correction and now includes a cerebellum model. > • The outputting of ANALYZE files is no longer supported as the format is > now strongly discouraged. > > The binaries, sources and test data can be downloaded from: > > http://www.fmrib.ox.ac.uk/fsldownloads/ > > Matthew > > > > -- > Dianne Patterson, Ph.D. > [log in to unmask] > University of Arizona > SHLS 328 > 621-5105 > > > > --------------------------------------------------------------------------- > 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<http://www.fmrib.ox.ac.uk/%7Esteve> > --------------------------------------------------------------------------- > > > --------------------------------------------------------------------------- > Saad Jbabdi, > Postdoctoral Research Assistant, > Oxford University FMRIB Centre > > FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > +44 (0) 1865 222545 (fax 222717) > [log in to unmask] http://www.fmrib.ox.ac.uk/~saad<http://www.fmrib.ox.ac.uk/%7Esaad> > --------------------------------------------------------------------------- > > > > > -- Dianne Patterson, Ph.D. [log in to unmask] University of Arizona SHLS 328 621-5105