Hi All,
I don't want to complicate this issue, but I'm also interested in
registering diffusion with anatomical image in the absence of field map
to correct image distortion retrospectively. I read some where in the
list where Jesper was saying it's "too permissive" of an approach to
register EPI with anatomical image this way. This is because the
correction should be done along phase encoding direction only.
From what I understand, EPI image is distorted along phase encoding
direction(typically vertical axis) making a sphere look like an egg
shape (ellipsoid). To register the ellipsoid with the sphere, I think
there are more than one ways to do this. One of the ways is to shrink
the ellipsoid along the y-axis to match the sphere. Alternatively, it
can also be shrunk by shrinking along x,y, and z axis. Thus non-linear
registration between EPI and anatomical image should be done with some
restrictions, and I'm not sure if FNIRT has an option to warp along
prescribed axis. Please let me know if this is feasible with FNIRT.
There are papers written about EPI distortion correction without use of
field map like this one
Geometric Distortion Correction of High-Resolution 3 T Diffusion Tensor
Brain Images
Siamak Ardekani1 and Usha Sinha, MRM 2005
Hope this helps?
Hedok
Gwenaëlle DOUAUD wrote:
> Hi Anastasia,
>
> I think Jesper would have a better insight on the question, but I don't think that registering dw images to T1w images should be a problem.
>
> Having said that, I am not surprised that non-linearly registering b0 images to T1 scans don't work (see previous threads on the question). There is not enough contrast in this image to properly match the structures. Try generating the FA map and then fnirt it to the T1 with the default settings. It should work fine.
>
> Cheers,
> Gwen
>
>
>
>
>
> --- En date de : Mer 20.8.08, Matt Glasser <[log in to unmask]> a écrit :
>
>
>> De: Matt Glasser <[log in to unmask]>
>> Objet: Re: [FSL] FNIRT bzero to T1
>> À: [log in to unmask]
>> Date: Mercredi 20 Août 2008, 21h05
>> Nonlinear registration like FNIRT is not really appropriate
>> for cross
>> modality registrations. It is better to properly unwarp
>> your diffusion
>> weighted images using a field map and fugue or some other
>> method and then
>> use rigid body registration (FLIRT -dof 6) to register each
>> subject's FA map
>> to their T1 scan.
>>
>> Peace,
>>
>> Matt.
>>
>> -----Original Message-----
>> From: FSL - FMRIB's Software Library
>> [mailto:[log in to unmask]] On Behalf
>> Of Anastasia Ford
>> Sent: Wednesday, August 20, 2008 12:39 PM
>> To: [log in to unmask]
>> Subject: [FSL] FNIRT bzero to T1
>>
>> Hello,
>>
>> I am wondering if anyone is using FNIRT to register DWI
>> volumes and
>> anatomical scans. I
>> tried doing so by changing the configuration files provided
>> in the new FSL
>> package but have
>> not found a set of parameters that would enable a good
>> registration.
>>
>> Sincerely,
>>
>> Anastasia
>>
>
>
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