Hi. When I convert my T1 DICOM files from the GE Signa MR scanner to nifti format, it produces a result with unwanted rotations and shears, when viewed in SPM with the "World space" setting. I have tried multiple DICOM to nifti converters (SPM's DICOM Import, dcm2nii, Freesurfer), with the same result. When I view the nifti images in SPM with the "Voxel space" setting, the images look correct (no shears or rotations).
Also, in the nifti header, the image scaling does not seem to be correct. Here is an example header matrix for one of my images:
-0.9988 -0.0287 0.0390 124.3288
-0.0201 0.9785 0.2051 -97.2591
0.0441 -0.2041 0.9778 -13.5133
0 0 0 1.0000
Should the scaling be exactly 1?
To get around the problem of the unwanted shears and rotations, I was planning to simply set the nifti header matrix to:
-1 0 0 0
0 1 0 0
0 0 1 0
0 0 0 1
However, I need the scaling to be correct (because I need to measure structures), so I am not sure if this is valid.
I think the nifti header matrix is derived from the "ImagePositionPatient" and "ImageOrientationPatient" fields of the DICOM files, but I am not sure why my images are being distorted. Perhaps the GE scanner DICOM format is not being interpreted correctly by the DICOM to nifti converters.
Any advice would be greatly appreciated.
Thanks
John
