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/data/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 to 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,
>
> >
>
> > 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
>
> > 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
>
> >
>
> >
>
> >
>
> > ________________________________
>
> >
>
> > A Good Credit Score is 700 or Above. See
> yours in just 2
>
> > easy steps!
>
> > <http://pr.atwola.com/promoclk/100126575x1218822736x1201267884/aol?redir=http:%2F%2Fwww.freecreditreport.com%2Fpm%2Fdefault.aspx%3Fsc%3D668072%26hmpgID%3D62%26bcd%3DfebemailfooterNO62
> >
>
>
>
>
>
>
>
>
> A Good Credit Score is 700 or Above. See yours in just 2 easy steps!
|