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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 T1w 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: [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
> 
> 
> 
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