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Try using Check Reg between the two images.  It's possible that the DICOM to NIfTI converter you used deals with the different orientations.  If it didn't, then you could try the DICOM import button of SPM.

If the images appear to be aligned in Check reg, then it should be possible to use the reslice only option of coregister, to reslice one of the images to match the other (if this is actually what you need).

Best regards,
-John


On 5 April 2017 at 15:06, Jeffrey Crawford <[log in to unmask]> wrote:

Hello everyone!

 

I have two types of scans of the same participant. One was an Axial scan (Image 1) and the other is a Cortical Scan (Image 2), both with the same dimensions (256 by 256 by 124). As you can see, the orientation of the axial scan has the coronal in the top left, the sagittal in the top right, and the axial below. The coronal scan has the axial in the top left, the sagittal in the top right (in an odd orientation) and the cortical on the bottom.

 

Is it possible in SPM to convert the cortical scan, so that it presents itself in the same order and orientation as the axial scan?

 

I realize that this would mean that the converted cortical scan would have different dimensions, but I think that is just fine for my purposes.

 

I would much appreciate any and all opinions,

Jeff