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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:


Matthew



-- 
Dianne Patterson, Ph.D.
University of Arizona
SHLS 328
621-5105


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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)
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Saad Jbabdi, 
Postdoctoral Research Assistant,  
Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 222545  (fax 222717)
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--
Dianne Patterson, Ph.D.
[log in to unmask]
University of Arizona
SHLS 328
621-5105