you can try playing with the --reorder flag in mri_convert
On 04/05/2017 10:11 AM, Jeffrey Crawford 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 Freesurfer 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
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