Hi Jimbo,

fsl_anat will calculate the registration to MNI space, but it will not apply the registration - those images are still in the native space of each subject.

To transform the pve images into MNI space, you will need to use the applywarp tool (assuming you have used non-linear registration). Somewhere in your fsl_anat output directory should be a file called T1_to_MNI_nonlin_field.nii.gz. You can use it to transform the pve image into MNI152 space with something like this (adjust the file names/paths accordingly)

applywarp -i T1_fast_pve_0.nii.gz -r MNI152_T1_2mm.nii.gz -o T1_fast_pve_02standard.nii.gz -w T1_to_MNI_nonlin_field.nii.gz

Cheers,

Paul

On 10 September 2018 at 18:38, Jimbo Connors <[log in to unmask]> wrote:

Hi Paul,
I assumed they were, since i used fsl_anat which does the registration to MNI.
The pve files I guess they are not MNI space? the dimension in mm are 1x0.4688x0.4688

Is there a quick way with fsl to register the pve file to MNI space?
thanks

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