Hello Keren,
fslreorient2std effectively just “swaps” the x,y,z axes around to find the closest match to MNI space, no registration/interpolation will occur. To deoblique your images ( which will involve interpolation ) you will either need to use flirt ( to register to MNI or some other space ) or you could use the Nudge tool to manually rotate the images. If you want to perform a “minimal” registration with flirt you could use rigid-body ( 6 dof ) mode, which will rotate/translate your images to ( e.g.) MNI space, but will not rescale/shear.
Hope this helps,
Kind Regards,
Matthew
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Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
> On 10 Sep 2017, at 14:28, Keren Lesinger <[log in to unmask]> wrote:
>
> Hi
>
> I have anatomical images from an open datasource. Currently, I ran fsl_anat on the anatomical scans without registration to MNI (in the near future I am interested in creating my own anatomical common space using ANTs, therefore I skipped the MNI registration). Some of the original images are a little bit oblique and even though I ran fslreorient2std as part fsl_anat the output remained oblique, how is it possible to deoblique the anatomical scans without registration to MNI?
>
> Thanks in advance,
> Keren
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