Is that true? I thought one time when I sent an e-mail outlining my steps Steve told me not to use the dti_FA but rather the nodif_brain within the FDT gui. I'd be curious to hear what others think about this since I'm doing something similar to what Ravi is doing. Thanks!
Kristen
-----Original Message-----
From: FSL - FMRIB's Software Library on behalf of Gwenaëlle DOUAUD
Sent: Mon 4/7/2008 8:45 AM
To: [log in to unmask]
Subject: Re: [FSL] T1 and DTI Registration problems
Hi Ravi,
here is my take.
First, Kristen is not right: you should definitely go for the image that shows a better contrast, so the FA rather than the B0 (it's all the more true if you use non-linear registration).
Second, if I understand you correctly, you want to register T1 and FA to possibly draw some ROIs on the T1 and transfer them on the DW space...
So what you should do is:
flirt -in T1 -ref FA -omat T1_to_FA.mat
then:
flirt -in T1 -ref FA -o T1_to_FA -init T1_to_FA.mat -applyxfm (to check first for the flirt registration)
then for your ROIs:
flirt -in my_ROI_on_T1 -ref FA -o my_ROI_on_FA -init T1_to_FA.mat -applyxfm
Hope this helps,
Gwenaelle
--- En date de : Lun 7.4.08, Lindgren, Kristen, Ann <[log in to unmask]> a écrit :
> De: Lindgren, Kristen, Ann <[log in to unmask]>
> Objet: Re: [FSL] T1 and DTI Registration problems
> À: [log in to unmask]
> Date: Lundi 7 Avril 2008, 14h31
> I'm not sure if there's more you should be doing,
> but you shouldn't be using the dti_FA image in FLIRT to
> get the str2diff.mat. Instead you should be using the
> nodif_brain image. Not sure if that will solve your
> problem but it might help. Good luck!
>
> Kristen
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library on behalf of Ravi
> Shetty
> Sent: Mon 4/7/2008 4:40 AM
> To: [log in to unmask]
> Subject: Re: [FSL] T1 and DTI Registration problems
>
> Sorry I am not sure if I quite follow. I have been
> registering my diffusion
> data(dti_FA) to the reference image(T1 weighted) and I
> believe that would
> give me the equivalent of the str2diff.mat. From there I
> use that matrix to
> convert the ROI mask I created on my T1 weighted image into
> diffusion space.
> I then overlay that new diffusion space ROI mask onto my
> original diffusion
> image and see if the images are being registered correctly.
> I use this
> method to check because the images outputed after
> registration always seem
> to line up pretty well but once I run probtrackx my results
> were very off.
> This just seemed a faster way to check the registrations
> accuracy. Please
> let me know if I seem to be missing a step. Thanks.
>
> On Mon, 7 Apr 2008 08:33:21 +0100, Steve Smith
> <[log in to unmask]> wrote:
>
> >Just a quick sanity check - you _are_ inverting the
> DTI->structural
> >transform before using it to transform structural-space
> ROIs back to
> >DTI space?
> >Cheers.
> >
> >
> >On 7 Apr 2008, at 03:03, Ravi Shetty wrote:
> >> Hi I have been using FLIRT to register my T1 and
> DTI images to each
> >> other but keep running into
> >> problems. The registered images produced are
> always very close to
> >> what they should be when I
> >> overlay them onto the T1 image. The problem I have
> is the matrixes
> >> don't always reflect the
> >> registration image. I create a CC ROI mask on the
> T1 image/
> >> registered image and use the matrix I
> >> produced to convert it back into difusion space.
> Now when I do this
> >> with some subjects the ROI will
> >> be spot on the CC and for others it will be off
> somewhere in the
> >> cortex or even just into the black
> >> void. I can't seem to find any rhyme or reason
> for this and the
> >> variation of how off the matrix is does
> >> not seem to be consistent, any help figuring this
> out would be
> >> appreciated. Thanks.
> >>
> >
> >
> >---------------------------------------------------------------------------
> >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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