Resample all histological images to 0.2x0.2x0.5 resolution

[valosekj]

Description

This PR updates histological atlas to 0.2x0.2x0.5 resolution.

Note: The real resolution is 0.199074x0.198795x0.5 due to rounding. Context: spinalcordtoolbox/spinalcordtoolbox#4077

Resulting dim and pixdim for all histological images:

valosek@macbook-pro:~/code/PAM50/histology$ for file in *.gz;do echo ${file};sct_image -i ${file} -header | grep dim | head -3;echo "";done
PAM50_200um_AVF.nii.gz
dim		[3, 108, 83, 205, 1, 1, 1, 1]
pixdim		[-1.0, 0.199074, 0.198795, 0.5, 0.0, 0.0, 0.0, 0.0]
phase_dim	0

PAM50_200um_Eccentricity.nii.gz
dim		[3, 108, 83, 205, 1, 1, 1, 1]
pixdim		[-1.0, 0.199074, 0.198795, 0.5, 0.0, 0.0, 0.0, 0.0]
phase_dim	0

PAM50_200um_EquivDiameter.nii.gz
dim		[3, 108, 83, 205, 1, 1, 1, 1]
pixdim		[-1.0, 0.199074, 0.198795, 0.5, 0.0, 0.0, 0.0, 0.0]
phase_dim	0

PAM50_200um_EquivDiameter14.nii.gz
dim		[3, 108, 83, 205, 1, 1, 1, 1]
pixdim		[-1.0, 0.199074, 0.198795, 0.5, 0.0, 0.0, 0.0, 0.0]
phase_dim	0

PAM50_200um_EquivDiameter48.nii.gz
dim		[3, 108, 83, 205, 1, 1, 1, 1]
pixdim		[-1.0, 0.199074, 0.198795, 0.5, 0.0, 0.0, 0.0, 0.0]
phase_dim	0

PAM50_200um_MVF.nii.gz
dim		[3, 108, 83, 205, 1, 1, 1, 1]
pixdim		[-1.0, 0.199074, 0.198795, 0.5, 0.0, 0.0, 0.0, 0.0]
phase_dim	0

PAM50_200um_Naxons.nii.gz
dim		[3, 108, 83, 205, 1, 1, 1, 1]
pixdim		[-1.0, 0.199074, 0.198795, 0.5, 0.0, 0.0, 0.0, 0.0]
phase_dim	0

Note that a modified version of resampling.py was used to set img.header["pixdim"][4:] = 0; context here.

The size is 31M, which is under the 50M threshold proposed by Julien in #7.

valosek@macbook-pro:~/code/PAM50/histology$ du -h
 31M	.

Related issues/PRs

Fixes #7
Fixes #8

[joshuacwnewton]

In the 2023-03-30 meeting, we discussed whether the 0.199074x0.198795x0.5 is acceptable. Due to the complicated nature of achieving exactly 0.2x0.2x0.5 resolution (see @mguaypaq's comment in spinalcordtoolbox/spinalcordtoolbox#4077 (comment)), we decided to stick with the slightly-off resolution for now.

The size is 31M

Additionally, since this PR greatly decreases the file size of each file, merging this PR will address #7 as well. So, I've updated the description to link that issue to this PR.

I think we're good to merge! 🎉