Unexpected behaviour of sliceViewer 'SliceDirection'

I'm not really sure how to reconcile the 'SliceDirection' in sliceViewer. Matlab's documentation says SliceDirection = [0 1 0] slices along the second dimension. But this is clearly not the case. In the MWE SliceViewer shows a line in the middle slice, and black everywhere else. I would expect each slice to have a bright spot in the middle. The imshow() outputs the expected result, a single bright pixel.

matlab sliceViewer documentation says:

Character VectorLogical VectorDescription

'X' [1 0 0] Browse in X direction

'Y' [0 1 0] Browse in Y direction

'Z' (default) [0 0 1] Browse in Z direction"

MWE:

clear all; clc;
N = 40;
full_vol = zeros(N, N, N, 'uint8');
full_vol(N/2, :, N/2) = 255;

figure(); sliceViewer(full_vol, 'SliceDirection', [0 1 0], 'SliceNumber', N/2);
figure(); imshow(squeeze(full_vol(:, N/2, :)))

[Jacques]

Please correct me if there is a mistake here, but I'm thinking the problem was:

It was a misunderstanding of the convention (using [x y z] for 'SliceDirection' makes it confusing).

Using 'SliceDirection' [0 1 0] will slice along the first dimension, because matlab defines the first dimension as y, the second dimension as x and the third as z.

Answer 1

[Kautuk Raj]

Hello @Jacques,

This is arising from how MATLAB indexes arrays and how sliceViewer interprets the 'SliceDirection' parameter. In MATLAB, a 3D array is indexed as (row, column, page), which corresponds to (Y, X, Z).

When you use 'SliceDirection', [0 1 0], you are moving through the first dimension (Y, or rows), so each slice is an X-Z plane at a fixed Y. In your example, only the slice at Y = N/2 (i.e., SliceNumber = N/2) shows the line you set; all other slices are black.

So, your code is behaving as expected according to MATLAB's conventions.