flip dimensions in OrthoSlicer3D

[pelednoam]

Hey,
I'm loading sample subject (from freesurfer) T1.mgz file, both using OrthoSlicer3D and freeview (same slice: 133, 84, 122). It looks like in the coronal and axial views, the left and right are flipped:

OrthoSlicer3D:

freeview:

Any idea why?
Thanks!

[effigies]

I'm replicating this issue, so I'd say it's either a bug in nibabel or in freeview...

Edit: Freeview is consistent with fslview, so I'm going to call this a nibabel bug.

[pelednoam]

I've loaded a CT of an epileptic patient with depth electrodes, and it can be seen clearly from the electrodes locations that it's a nibabel bug.

[effigies]

I'm going to generate a series of images with different orientations to check whether it's always LR flipped or just in some orientations. Hopefully it's always, because that'll be the easiest to fix. (The logic of this feature is not easy to follow.)

[pelednoam]

Yes, I used this code to support slices view in my visualization software (mmvt), and indeed, it was quite hard to follow. In the end, I've just flipped this dimension. From what I checked, it seems to be always LR flipped.

[effigies]

Thanks. Feel free to submit a PR with your modification. Otherwise I will, when I get a few more minutes.

[pelednoam]

Well, for now, in my code I've just added this line:
`flips[0] = not flips[0]
Not sure it's the best solution... Maybe a further investigation is needed to understand why the first item in flips is flipped on the first place...

[matthew-brett]

Sorry to be superficial - but can the difference be explained by differences in display conventions? Nibabel does display the left on the left - neurological convention. Maybe Freesurfer does right on the left - radiological? Or am I missing something?

[matthew-brett]

@pelednoam - yes - the visualization code needs to be refactored. It's been on my to-do list for a while ...

[effigies]

The L and R labels need to be swapped, then.

…

On Oct 14, 2017 07:58, "Matthew Brett" ***@***.***> wrote: Sorry to be superficial - but can the difference be explained by differences in display conventions? Nibabel does display the left on the left - neurological convention. Maybe Freesurfer does right on the left - radiological? Or am I missing something? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#559 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAFF8gIJtzorax6SoXozEjlXwFkBsQP9ks5ssKHUgaJpZM4Pnw6e> .

[pelednoam]

@matthew-brett, I don't think it's conventions issue, because both in nibabel and freeview, in those two perspectives, the label R is on the right and L is on the left. I could understand the flip if also the labels were flipped.
Refactored or not, your code is really great, and saved me so much work! Thanks to you, I could add a slicer viewer into my Blender addon:

Thanks!