Hi, sorry I am fairly new to using FSL is there a specific way I should go about doing so? This is the
matrix from the str2diff.mat file not sure what it means though.
-0.0265797 -0.0821534 0.839682 52.2631
-0.414014 -0.897735 -0.132488 263.655
0.818242 -0.461883 -0.0249049 6.59096
0 0 0 1
Thanks.
-Ravi
On Fri, 27 Jul 2007 09:04:38 +0100, Steve Smith <[log in to unmask]> wrote:
>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
>------------------------------------------------------------------------
>---
>===========================================================
==============
|