Why does ITK Snap automatically transpose my scans?

[JM]

I was provided with some brain scans that once I display them on ITK-SNAP they automatically get transposed.

When I run from the terminal (Ubuntu) "itksnap scan.nii" I get some information in the terminal that says "Transpose of 1179648 by 2 matrix computed in 0.178418 sec.".

I was thinking that maybe the nifti files have some parameters that make ITK to transpose them. However, I opened a file in python using nibabel library to read and write a new nifti file without any additional information except for the intensity values but ITK still transposes them.

scan = nib.load("scan.nii").get_data()

nib.save(nib.Nifti1Image(scan,np.eye(4)), "output.nii")

Both scan.nii and output.nii get transposed when I display them on ITK-SNAP.

Why is this and how can I stop it to do that?

[Paul Yushkevich]

JM

If the images are transposed in ITK-SNAP, then the NIFTI header is incorrect. You can modify the orientation using Tools->Reorient Image. You can also do it using c3d with the -orient command.

Best,

Paul

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Paul A. Yushkevich, Ph.D.
Associate Professor
Penn Image Computing and Science Laboratory
Department of Radiology
University of Pennsylvania