Hi,
I think the best solution for what you want is to use aff2rigid, which uses a 12 DOF affine registration to MNI space to calculate a rigid-body (6 DOF) transformation that will allow you to make your images non-oblique without changing the shape of the image.
So just do:
flirt -in your_brain_extracted_image -ref $FSLDIR/data/standard/MNI152_T1_2mm -dof 12 -omat brain2mni.mat
aff2rigid brain2mni.mat deoblique.mat
flirt -in your_brain_extracted_image -ref $FSLDIR/data/standard/MNI152_T1_2mm -init deoblique.mat -applyxfm -out brain_not_oblique
In the example above I've used a brain extracted image in both lines 1 and 3. It is essential for line 1, but not for line 3 (the non-brain extracted image can be used in line 3).
The reference image in line 3 could be either a 2mm or 1mm MNI space, but you could also use another image, with any resolution, as long as the FOV is large enough (quite often the initial structural does not have a large enough FOV for this, but sometimes it does).
All the best,
Mark
> On 11 Sep 2017, at 07:12, Keren Lesinger <[log in to unmask]> wrote:
>
> thank u for the answers.
> what are the parameters that the flirt option includes fsl_anat? or in order to run the "minimal flirt" I need to run it separately from the fsl_anat?
> thanks again !
> Keren
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