Hi Alex,
The registered vectors look fine, what version of FSLview are you running? The latest is 3.1.8, it deals with the different conventions. If you have an older version, you will need to update.
Cheers,
Stam
On 1 Jul 2010, at 17:38, Alexander Opitz wrote:
> The upload number is 411811. The DTI and the structural image are indeed in a different convention.
>
> Cheers
> Alex
>
>
> On Thu, 1 Jul 2010 16:36:10 +0100
> Saad Jbabdi <[log in to unmask]> wrote:
>> yep, that's what we thought! we'll find out if you upload the data and the FLIRT transform :)
>>
>> Saad.
>>
>> On 1 Jul 2010, at 16:33, Matt Glasser wrote:
>>
>>> Are your original diffusion images in a different (i.e. neurological or
>>> radiological) convention than your structural images? Perhaps vecreg is not
>>> yet able to handle this conversion.
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>> -----Original Message-----
>>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
>>> Of Alexander Opitz
>>> Sent: Thursday, July 01, 2010 9:15 AM
>>> To: [log in to unmask]
>>> Subject: Re: [FSL] vecreg problem
>>>
>>> Hi Stam
>>>
>>> the original dti_vectors look fine in FSLView
>>>
>>> Cheers ,
>>> Alex
>>>
>>> On Thu, 1 Jul 2010 15:10:49 +0100
>>> Stamatios Sotiropoulos <[log in to unmask]> wrote:
>>>> Hi Alex,
>>>>
>>>> do the original dti vectors (dti_V1) look OK in FSLview or they are
>>> flipped as well?
>>>>
>>>> Cheers,
>>>> Stam
>>>>
>>>>
>>>>
>>>> On 1 Jul 2010, at 14:54, Alexander Opitz wrote:
>>>>
>>>>> Hi
>>>>> I got a problem with the vector registration tool.
>>>>>
>>>>> I registered my FA image (128 x 128 x 72 voxels) to my structural image
>>> (256 x 256 x 256 voxels) using FLIRT and FNIRT. Then I used the vector
>>> registration tool vecreg (version 1.1) to transform the V1 image to
>>> structural space. The transformed color FA image looks fine in FSLView
>>> however looking at the orientation of the lines in the V1_reg at the corpus
>>> callosum I noticed that their orientation was flipped. This happened both
>>> using a linear and a nonlinear transformation. As the correct direction
>>> information is important for me I am wondering if I made a mistake or if
>>> there is a bug in the vecreg tool.
>>>>>
>>>>> Here are my commands:
>>>>>
>>>>> vecreg -i dti_V1.nii.gz -o V1_reg.nii.gz -r struct.nii.gz -t
>>> fa2struct.mat
>>>>>
>>>>> vecreg -i dti_V1.nii.gz -o V1_reg.nii.gz -r struct.nii.gz -w
>>> fa2struct_warp.nii.gz
>>>>>
>>>>> Cheers
>>>>> Alex
>>>>>
>>>
>>
>> --
>> Saad Jbabdi
>> University of Oxford, FMRIB Centre
>>
>> JR Hospital, Headington, OX3 9DU, UK
>> (+44)1865-222466 (fax 717)
>> www.fmrib.ox.ac.uk/~saad
>
|