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Dear  Jesper,

Thank you for your reply, but my template is a  betted  image. Is the input
of fnirt also should be an image non-betted?

And I don't want to get the deformation field from the template to the
subject space , I want to get the deformation field from the template to the*
linearly registered image(flirt_T1)*.So, I tried like this after fnirt:

*fnirtfileutils --in=warp_coef.nii.gz --ref=Colin27_Template.nii.gz
--out=fnirtfileutils_field*

*invwarp --ref=flirt_T1.nii.gz --warp=fnirtfileutils_field.nii.gz
--out=invfileutils_mni2flirt*

I want to know if the *'invfileutils_mni2flirt'* file I got is the
deformation field of the image I want from the template to the
linear registered image(flirt_T1)?


ping









Jesper Andersson <[log in to unmask]> 于2019年6月20日周四 下午5:01写道:

> Dear Ping,
>
> the warp field that takes the template into subject space should be the
> same size as the subject image (T1 image of the original space), so that is
> absolutely correct.
>
> But there are a couple of other problems with your commands below
>
>
>         I want to get the warp_field from the standard space template to
> the linearly registered T1 image. How should I perform invwarp?
>         I have tried to do this as follows,
>
> "flirt -ref Template -in struc_brain.nii.gz -omat flirt_transf.mat -out
> flirt_brain
> fnirt --in=struc_brain.nii.gz --aff=flirt_transf.mat
> --cout=fnirt_transfcoef --ref=Template
>
>
> When you run fnirt you should _not_ use the brain extracted (betted) data.
> You should use the non-betted (original) images and warp them to the
> non-betted template (typically the MNI152_T1_2mm.nii.gz image)
>
> You should also use a suitable configuration file. For T1-weighted human
> images we recommend the T1_2_MNI152_2mm.cnf file. If using it for other
> types of data that file still provides a good starting point for defining
> ones own configuration file.
>
> Jesper
>
>
> applywarp --ref=Template --in=struc_brain.nii.gz --warp=fnirt_transfcoef
> --out=fnirt_brain
> invwarp --ref=struc_brain.nii.gz --warp=fnirt_transfcoef.nii.gz
> --out=warpfield_into_struc_ space"
>
>        But the resulting warp_field is the same size as the T1 image of
> the original space. This should not be the warp_field from the template to
> the linear registration image I want to get. So, what should I do for this?
>        Your help is greatly appreciated.
>
> ping
>
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