Hi - yes, I guess FDT doesn't generate registration evaluation output
images.
You can apply the diff2str.mat to the nodif image using the ApplyXFM
GUI and then load this in along with the structural into FSLView to
check the registration.
Cheers.
On 27 Jul 2007, at 09:21, Ravi Shetty wrote:
> 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
>> ---------------------------------------------------------------------
>> ---
>> ---
>> ===========================================================
> ==============
------------------------------------------------------------------------
---
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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