Hi - have you checked the results of the registration between
structural space and diffusion native space?
Cheers.
On 27 Jul 2007, at 08:56, Ravi Shetty wrote:
> 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
>> ---------------------------------------------------------------------
>> ---
>> ---
------------------------------------------------------------------------
---
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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