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Hi,
I'm afraid this doesn't make sense to me.
I think we have a problem with terminology.
In step 2 you say you want to get "normalization with
Image_A which is already coregistered to B with
estimation only". That is, as far as I can understand you,
exactly what I was suggesting.
There are only two options for a pair of images
to be registered. The first is that the transformation
is found which relates the two, and neither image
is changed/resampled/resliced. This is what I
assume you mean by "estimation only". This is
exactly what I'd suggested in step 2 - getting
the transformation between Image_A and the
MNI template without changing/resampling/reslicing
any image.
The other option is to find the transformation *and*
apply it by changing/resampling/reslicing one
image to align it with the other.
I have been assuming that what you want is to
have both Image_A and Image_B aligned with
the MNI template and only apply a single
transformation (and hence interpolation) to
both Image_A and Image_B to get them into
this space. That is exactly what I described
how to do in my previous email.
You say that you do not want to apply to
combined transformation in step 3, but
if you do not then you cannot get Image_B
into the MNI space without multiple
interpolation which would be bad. I am
not saying that the combined transformation
is applied to Image_A - only a single
transformation (that found in step 2) is
applied to Image_A.
The only other possibility I can think of is that
you want to directly register Image_B to
the MNI template, but if Image_B is a PET
image which has poorer contrast and
quality than Image_A then I would very
strongly recommend that you do not do
this, but instead do as I suggested and
register Image_B to Image_A and then
Image_A to the MNI and apply the combined
transformation to Image_B (but the
single transformation to Image_A).
I hope that it is now clear what we mean
by the different steps and that there
is no longer any misunderstanding based
on terminology.
All the best,
Mark
On 3 Mar 2009, at 22:45, Buyean Lee wrote:
> I think the second and third steps are not what I want to do.
>
>
> Step1 - get the transformation matrix relating Image_A to Image_B
> but do not
> resample (reslice) anything - I did it and it is right.
>
> Step 2 - get the transformation (warp field or matrix) relating
> Image_A to the
> MNI template but do not resample - I want to get the
> transformation (warp field or matrix) relating Image_A, which is
> already related to Image_B (without reslicing), to the MNI
> template. In SPM5, I can do this by running normalization with
> Image_A which is already coregistered to B with estimation only!
>
> Step 3 - apply the combined transformations to Image_B to resample
> it into
> MNI space - I want to apply the tranformation matrix acquired Step
> 2, not the combined transformation matrix.
>
> I can run Step 3 if I run Step 2 with resliced Image_A related to
> Image_B.
>
> Thank you,
>
> Buyean
>
> -----Original Message-----
> From: Mark Jenkinson <[log in to unmask]>
> To: [log in to unmask]
> Sent: Tue, 3 Mar 2009 12:50 am
> Subject: Re: [FSL] AW: [FSL] Flirt question
>
> Hi,
>
> I *think* I know what you want to do, but part of the problem is
> the term "normalize" as we call both co-registration and normalization
> just "registration" because that's what they are, just with different
> reference images.
>
> So I think you want the following:
> - get the transformation matrix relating Image_A to Image_B but do
> not
> resample (reslice) anything
> - get the transformation (warp field or matrix) relating Image_A to
> the
> MNI template but do not resample
> - apply the combined transformations to Image_B to resample it into
> MNI space
>
> What I'm still unsure about is whether you want a linear or non-linear
> registration (transformation) from Image_A to the template.
>
> I will describe the linear case here as it is easier (and your subject
> is "Flirt question"):
> - run flirt between Image_B and Image_A with the -omat option to
> save the matrix, but not the -out option (which resamples):
>
> flirt -in Image_B -ref Image_A -dof 6 -omat TransB2A.mat -cost
> mutualinfo
>
> - run flirt between Image_A and the MNI template, again with -omat
> but not with -out:
>
> flirt -in Image_A -ref $FSLDIR/da ta/standard/MNI152_T1_2mm_brain -
> omat TransA2MNI.mat
>
> - run convert_xfm to combine the two matrices that you obtained
> above:
>
> convert_xfm -omat TransB2MNI.mat -concat TransA2MNI.mat TransB2A.mat
>
> - run flirt with -applyxfm to resample Image_B into the MNI space:
>
> flirt -in Image_B -ref $FSLDIR/data/standard/MNI152_T1_2mm_brain -
> applyxfm -init TransB2A.mat
>
> That should do what I described, which I hope is what you want.
> Note that I'm assuming that you've run brain extraction on Image_A
> (and
> Image_B if it makes sense).
>
> If you want to do the same but with a non-linear transformation to
> the MNI template, then you'll need to use fnirt and applywarp instead.
>
> All the best,
> Mark
>
>
> On 2 Mar 2009, at 17:51, Buyean Lee wrote:
>
> > Hi,
> >
> > I will try to explain my original question again.
> >
> > Image_A: T1 MRI for a subject A.
> > Image_B: mean PET image for a subject A.
> > BPmap: binding potential map for a subject A that is in the space
> of > Image_B.
> >
> > Goal: normalize BPmap to MNI space with T1 MRI of the subject.
> >
> > In SPM5, I can achieve this goal using the following steps.
> >
> > 1. Coregister Image_A=2 0to Image_B using 'Estimate only' (I don't
> > generate the resliced Image_A).
> > 2. Normalize the coregistered Image_A (not resliced) to MNI space
> > and at the same time, normalize (and reslice) the BPmap.
> >
> > Basically, I want to know how to do the second step with the >
> coregistered Image_A (but not resliced) in flirt.
> >
> >
> > Thank you,
> >
> > Buyean
> >
> >
> >
> >
> > -----Original Message-----
> > From: Gwenaëlle DOUAUD <[log in to unmask]>
> > To: [log in to unmask]
> > Sent: Mon, 2 Mar 2009 4:18 am
> > Subject: Re: [FSL] AW: [FSL] Flirt question
> >
> > Hi Buyean,
> >
> >
> >
> > if what you want to do is place A in the MNI space without >
> interpolating twice
> >
> > (first to B, then to the MNI space), then what you need to do is >
> determine the
> >
> > transformation from B (presumably a=2
> > 0T1w image) to the MNI space (B_to_MNI)
> >
> > first, then compose the matrix from A (presumably dw, fmri or pet
> > image etc.) to
> >
> > B (A_to_B) with it:
> >
> >
> >
> > convert_xfm -omat <A_to_MNI> -concat <B_to_MNI> <A_to_B>
> >
> >
> >
> > and only then apply the concatenated matrix to A:
> >
> >
> >
> > flirt -in A -ref MNI -out A_in_MNIspace -init A_to_MNI -applyxfm
> >
> >
> >
> > Cheers,
> >
> > Gwenaelle
> >
> >
> >
> >
> >
> >
> >
> > --- En date de : Lun 2.3.09, Buyean Lee <[log in to unmask]> a >
> écrit :
> >
> >
> >
> > > De: Buyean Lee <[log in to unmask]>
> >
> > > Objet: Re: [FSL] AW: [FSL] Flirt question
> >
> > > À: [log in to unmask]
> >
> > > Date: Lundi 2 Mars 2009, 0h09
> >
> > > Hi Andreas,
> >
> > >
> >
> > > I need to spatially normalize the coregistered image A.
> >
> > > ?
> >
> > >
> >
> > >
> >
> > > Therefore, I think the reference image should be a
> >
> > > template (e.g., MNI152_T1_1mm.nii).
> >
> > >
> >
> > > In fact, I can normalized the coregistered image_ A using
> >
> > > the resliced image_A (e.g, r_image_A).
> >
> > > I just want to know if I can normalize the image_A (which
> >
> > > is coregistered to image_B) without using the resliced
> >
> > > image_A.
> >
> > >
> >
> > > Thank you,
> >
> > >
> >
> > > Buyean
> >
> > >
> >
> > >
> >
> > >
> >
> > >
> >
> > >
> >
> > > -----Original Message-----
> >
> > > From: Andreas Bartsch
> >
> > > <[log in to unmask]>
> >
> > > To:=2
> > [log in to unmask]
> >
> > > Sent: Sun, 1 Mar 2009 10:46 am
> >
> > > Subject: [FSL] AW: [FSL] Flirt question
> >
> > >
> >
> > >
> >
> > >
> >
> > >
> >
> > >
> >
> > >
> >
> > >
> >
> > >
> >
> > >
> >
> > >
> >
> > > Hi,
> =0 A>
> > >
> >
> > > just do
> >
> > >
> >
> > > flirt -in image_A -ref image_B -omat A2B.mat
> >
> > >
> >
> > > and change whatever defaults you want to adjust opr
> >
> > > whatever additional options
> >
> > > you may want to use (type the "flirt" command in
> >
> > > the terminal to get the usage).
> >
> > >
> >
> > > Cheers-
> >
> > > Andreas
> >
> > >
> >
> > > ________________________________
> >
> > >
> >
> > > Von: FSL - FMRIB's Software Library im Auftrag von
> >
> > > Buyean Lee
> >
> > > Gesendet: So 01.03.2009 17:20
> >
> > > An: [log in to unmask]
> >
> > > Betreff: [FSL] Flirt question
> >
> > >
> >
> > >
> >
> > > Dear FSL users,
> >
> > >
> >
> > > In SPM5, I can find a transformation matrix for spatial
> >
> > > normalization of an
> >
> > > image_A coregistered to an image_B without reslicing the
> >&n bsp;
> > > image_A.
> >
> > >
> >
> > > Would someone please let me know how to do the same
> >
> > > operation with Flirt?
> >
> > > I have very limited experience in FSL (I don't know
> >
> > > what search word would be
> >
> > > the best for this question).
> >
> > >
> >
> > > Thank you,
> >
> > >
> >
> > > Buyean
> >
> > >
> >
> > >
> >
> > >
> >
> > > ________________________________
> >
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