[Neuroimaging] OrthoSlicer3D

[Christopher Markiewicz]

Hi Dalton,

Without seeing the file or a screenshot, my best guess is that your affine matrix indicates the "center" of the image is in a corner and that the edges of the image are empty. Try clicking in the middle of each square to select different voxels. If there is content in the middle of your image, selecting a voxel in the center should reveal it.

If you're calling `OrthoSlicer3D` directly, then your origin will be at (i, j, k) = (0, 0, 0), which will cause the situation I describe above. It will also treat your voxels as isotropic 1mm, which may not be correct. For NIfTI and other volumetric files, I would recommend the alternative `img.orthoview()`, which will pass the correct affine matrix by default.

Also a quick note that OrthoSlicer3D doesn't work well on OSX. That may be another source of problems.

Chris
________________________________
From: Neuroimaging <neuroimaging-bounces+markiewicz=stanford.edu at python.org> on behalf of Dalton Sakthivadivel <dalton.sakthi at gmail.com>
Sent: Thursday, April 25, 2019 12:04 AM
To: neuroimaging at python.org
Subject: [Neuroimaging] OrthoSlicer3D

Dear nipy team,

Can you describe to me some of the limitations on function that OrthoSlicer3D has? Is it limited to accepting images that are of the brain, or arrays of a certain size?

OrthoSlicer3D does not work for my data and I can’t make heads nor tails of it. Rather than a typical output, it plots four black squares, as though I hadn’t put any data in at all. It may be an issue that my .nii file contains images which are not of the human brain. Otherwise I am at a loss. I can attach my code to this email at a later time.

I would very much appreciate any help you had to give in this matter, including alternative suggestions for displaying typical 4D nifti images contained in .nii files.

Thank you,

Dalton Sakthivadivel
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