Hi I am using probtrack and pre processed the data using BET and FDT. The FA maps look great
after using DTIFit and I got through DTIFit and bedposting with no problems. And like I said
before I can get very nice probability maps when using only diffusion data in probtrack but when I
try and create the seed mask in structural space using the anatomy files is when I get odd results.
Also i've noticed that if I use avwstats on the fdt_paths from the str2diff sets I get the exact same
value for the number of voxels and volume whereas if I use avwstats on the fdt_paths from
diffusion only data I get different values for #voxels and volume. I have recently turned verbose on
and have been seeing this error whenver I run probtrack.
Errors: basename /home/ravi/Desktop/dti/8.bedpost/merged maskfile
/home/ravi/Desktop/dti/8.bedpost/nodif_brain_mask seeds
/home/ravi/Desktop/dti/8/mprage-mask.nii.gz
output fdt_paths
verbose 1
nparticles 1000
nsteps 2000
usef 0
rseed 12345
Thanks again for your help.
-Ravi
On Fri, 27 Jul 2007 08:22:36 +0100, Steve Smith <[log in to unmask]> wrote:
>Hi - I'm afraid it's not at all clear what analysis you are trying to
>do - which FSL tools are you using to generate "probability maps"?
>Cheers, Steve.
>
>
>On 26 Jul 2007, at 23:59, Ravi Shetty wrote:
>
>> Hi I am currently trying to create some probability maps of stroke
>> subjects
>> through the corpus callosum yet when I create them between
>> structural and
>> diffusion images I get weird maps (Maps going through the
>> ventricles). If I
>> use the diffusion images alone (mean_fsamples) I get a nice
>> probability map.
>> I checked the orientation to see if they were in radiological
>> coordinates
>> and they both were. I used dcm2nii to convert the original par/rec
>> files to
>> nifti format. Is there something I am doing wrong here? Thanks.
>>
>> -Ravi
>
>
>------------------------------------------------------------------------
>---
>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
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