I would like to normalize PET image (binding potential image) to the MNI space so that I can run statistical parametric analysis (group effect and correlation with other measures).
Buyean
-----Original Message-----
From: Brian Patenaude <[log in to unmask]>
To: [log in to unmask]
Sent: Fri, 20 Mar 2009 1:48 pm
Subject: Re: [FSL] Better spatial normalization of subcortial regions with FSL FIRST?
Hi,
> Can someone tell if I need to use a MNI template or the same individual's
> normalized image generated by 'flirt_first' (x${flirt_ref}_to_std_sub, in
> the following script)?
>
Use it specifically for what ?
Cheers,
Brian
>
> Hi FSL users,
>
> I am trying to normalize PET images with FSL FIRST hoping to get better
> registration.
>
> Although I posted the same question several days ago, but I didn't get any
> reply ( I guess it is too simple question).
> I am not sure which reference image I need to use to generate final
> normalized PET image (the last step of the following script '# generate
> the normalized image w${flirt_in}.nii').
>
> Can someone tell if I need to use a MNI template or the same individual's
> normalized image generated by 'flirt_first' (x${flirt_ref}_to_std_sub, in
> the following script)?
>
>
>
>
>
>
> I adapted the detailed instruction that Mark replied a while ago (see the
> end of email if you want see it).
>
>
>
> #!/bin/sh
> # Use direction: xfm_ff image1.nii (or img) image2.nii (or img)
>
> # image1: input image for flirt: BP image.
>
> # image2: reference image for flirt: structural MRI.
>
>
>
> # Extract the basename of the input images and give them to the
> corresponding variables.
> flirt_in=$($FSLDIR/bin/remove_ext $1)
>
> flirt_ref=$($FSLDIR/bin/remove_ext $2)
>
>
>
> #run flirt (BP image to sMRI)
>
> flirt -in $flirt_in -ref $flirt_ref -omat ${flirt_in}1.mat -bins 256 -cost
> mutualinfo -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 6
>
>
>
> #run first_flirt of FSL First.
>
> echo "starting first_flirt ${flirt_ref}"
>
> first_flirt $flirt_ref x${flirt_ref}_to_std_sub
>
>
>
> # generate ${flirt_in}_final.mat - combined transformation matrix
> f4=x${flirt_ref}_to_std_sub
>
> convert_xfm -omat ${flirt_in}_final.mat -concat $f4.mat ${flirt_in}1.mat
>
>
>
> # generate the normalized image w${flirt_in}.nii"
>
> flirt -in $flirt_in -ref $FSLDIR/data/standard/MNI152_T1_1mm_brain
> -applyxfm -init ${flirt_in}_final.mat -out w${flirt_in}.nii -paddingsize
> 0.0 -interp sinc -sincwidth 7 -sincwindow hanning -v
>
>
>
> Thank you,
>
>
>
> Buyean
>
>
>
> ** email from Mark
>
> 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
>
>
>
>
>
>
>
>
>
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