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Subject:

Re: FLIRT with DTI images

From:

Hoang Tran <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Tue, 17 Aug 2004 00:37:57 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (86 lines)

Thank you all for the help and insights. It turns out that the calibration
was for the DTI image was incorrect. After it was corrected, I was able to
successfully register the DTI to the T1 directly without having to BET
first. I'm not too sure if that's going to work on every subject, but at
least it worked on one.

Thanks again,

Hoang

On Sat, 14 Aug 2004 08:59:48 +0100, Tim Behrens <[log in to unmask]>
wrote:

>Hi - I am surprised by this. We do this regularly and, in general, it
>works well.
>
>Some notes -
>1) We register FROM the T2-weighted b=0 images TO the T1-weighted scan.
>
>2) We extract the brain from both images before we start (for exactly the
>reason you suggest)
>NB - bet does not always work well with the defaults with dwi reference
>images, but you can pretty much always tune it by hand to make things
>good - I start off with "-f 0.4" which tends to work better than default.
>
>3) In general, mutual information cost function in flirt tends to work
>best ( but not hugely better than default)
>
>4) Remember that this is a affine registration, and there will be some
>warping between the EPI and the structural image. The worse the warping,
>the worse you can do with affine registration. This will not only affect
>the registration in areas of bad distrotion, but throughout the brain, as
>the global cost function will try to match the local distortion. Hence the
>worse you distortion, the worse your registration will be generally. If
>this is bad, you should think of collecting field maps to help
>registration.
>
>Hope this is useful,
>
>Tim
>
>
>
>---------------------------------------------------------------------------
----
>Tim Behrens
>Centre for Functional MRI of the Brain
>The John Radcliffe Hospital
>Headley Way Oxford OX3 9DU
>Oxford University
>Work 01865 222782
>Mobile 07980 884537
>---------------------------------------------------------------------------
----
>
>On Fri, 13 Aug 2004, Hoang Tran wrote:
>
>> Does anyone have any experience (good or bad) with registering a DTI
image
>> to a T1 image? The images have different spatial resolutions, but are
>> oriented the same way.
>>
>> I've been trying to do so, but the results are terrible. I've tried the
>> following methods so far:
>>
>> 1) Registered full head DTI (b=0) with full head T1 => poorly registered
>> because DTI image does not have enough contrast on the skull and skin,
i.e.
>> those areas are relatively dark in the DTI relative to the brain. In the
>> T1, that's not the case.
>>
>> 2) Registered brain DTI (b=0) with brain T1 (brains were extracted using
>> BET with some post BET editing) => poorly registered but have no idea why
>> it should be
>>
>> Any suggestions or insights would be much appreciated.
>>
>> Hoang Tran
>> Neurobehavioral Research, Inc.
>> 201 Tamal Vista Blvd.
>> Corte Madera, California  94925
>> 415.927.6627 (Office)
>> 415-924-2903 (Fax)
>> [log in to unmask]
>>

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