Thank you. I will try using a cost weighting image.
Crystal
On 2/8/12 4:07 PM, "Mark Jenkinson" <[log in to unmask]> wrote:
>Hi,
>
>If you have substantial distortion in your images then it will be
>difficult/impossible
>to get a very good registration with a rigid registration. However, you
>could try
>using a cost weighting image that is one in all voxels except those in
>*and around*
>the ventricles (you need to include some of the surrounding tissue to get
>the border)
>where the values should be large (say 1000, although try 100, 10000 and
>100000
>too). This will have the effect of making the registration concentrate
>much more on
>the ventricle alignment, at the expense of cortical alignment. If you
>can't get a good
>registration this way then you probably have too much distortion in the
>images, and
>really need a fieldmap.
>
>To run FLIRT with the cost function weighting image you need to make the
>image
>yourself (by hand in FSLView or via fslmaths and segmentation tools) and
>then
>take your original FLIRT results (the matrix) and use this as the -init
>argument,
>together with -nosearch and either -refweight (if the weighting image is
>aligned
>with the reference image) or -inweight (if it is aligned with the input
>image).
>
>I would also recommend going from DTI to T1 space, and then inverting the
>output if you need to transform in the opposite direction. My experience
>is that
>the T1 works better as the reference image, especially when using the
>(default)
>correlation ratio cost function.
>
>All the best,
> Mark
>
>
>
>On 8 Feb 2012, at 14:04, Franklin, Crystal G wrote:
>
>> I have ran rigid registration in flirt and I am still getting
>>misalignment
>> around the ventricles. We would like to keep the DTI in native space.
>>
>> Thank you,
>> Crystal
>>
>> On 2/7/12 5:54 PM, "Cunningham, Dustin" <[log in to unmask]>
>> wrote:
>>
>>> Hi Crystal,
>>>
>>> Usually you can get satisfactory registration between T1 and b0 in the
>>> same subject using rigid registration in flirt. May I ask why you want
>>>to
>>> register the T1 to DTI and not the other way around? Also, the
>>>ventricles
>>> should look very similar in shape in the T1 and b0 image, which is
>>> essentially T2 weighted.
>>>
>>> Dustin
>>> ________________________________________
>>> From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf Of
>>> Franklin, Crystal G [[log in to unmask]]
>>> Sent: Tuesday, February 07, 2012 4:52 PM
>>> To: [log in to unmask]
>>> Subject: [FSL] T1 to DTI Registration
>>>
>>> Dear FSL,
>>>
>>> I am trying to register my subject's T1 (voxel dimensions of .8x.8x.8)
>>>to
>>> their DTI (voxel dimensions of 1.719x1.719x3). Unfortunately I do not
>>> have a T2 image or field maps. Do you suggest using the FA image or
>>>the
>>> b0? I have tried using both in flirt. The registration looks pretty
>>> good until I get around the ventricles. What is the best way to go
>>>about
>>> correcting this misalignment or the best procedure for registering the
>>>T1
>>> to DTI?
>>>
>>> Thank you,
>>> Crystal
>>
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