Closed valosekj closed 1 year ago
This PR updates histological atlas to 0.2x0.2x0.5 resolution.
Note: The real resolution is 0.199074x0.198795x0.5 due to rounding. Context: https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/4077
Resulting dim and pixdim for all histological images:
dim
pixdim
valosek@macbook-pro:~/code/PAM50/histology$ for file in *.gz;do echo ${file};sct_image -i ${file} -header | grep dim | head -3;echo "";done PAM50_200um_AVF.nii.gz dim [3, 108, 83, 205, 1, 1, 1, 1] pixdim [-1.0, 0.199074, 0.198795, 0.5, 0.0, 0.0, 0.0, 0.0] phase_dim 0 PAM50_200um_Eccentricity.nii.gz dim [3, 108, 83, 205, 1, 1, 1, 1] pixdim [-1.0, 0.199074, 0.198795, 0.5, 0.0, 0.0, 0.0, 0.0] phase_dim 0 PAM50_200um_EquivDiameter.nii.gz dim [3, 108, 83, 205, 1, 1, 1, 1] pixdim [-1.0, 0.199074, 0.198795, 0.5, 0.0, 0.0, 0.0, 0.0] phase_dim 0 PAM50_200um_EquivDiameter14.nii.gz dim [3, 108, 83, 205, 1, 1, 1, 1] pixdim [-1.0, 0.199074, 0.198795, 0.5, 0.0, 0.0, 0.0, 0.0] phase_dim 0 PAM50_200um_EquivDiameter48.nii.gz dim [3, 108, 83, 205, 1, 1, 1, 1] pixdim [-1.0, 0.199074, 0.198795, 0.5, 0.0, 0.0, 0.0, 0.0] phase_dim 0 PAM50_200um_MVF.nii.gz dim [3, 108, 83, 205, 1, 1, 1, 1] pixdim [-1.0, 0.199074, 0.198795, 0.5, 0.0, 0.0, 0.0, 0.0] phase_dim 0 PAM50_200um_Naxons.nii.gz dim [3, 108, 83, 205, 1, 1, 1, 1] pixdim [-1.0, 0.199074, 0.198795, 0.5, 0.0, 0.0, 0.0, 0.0] phase_dim 0
Note that a modified version of resampling.py was used to set img.header["pixdim"][4:] = 0; context here.
resampling.py
img.header["pixdim"][4:] = 0
The size is 31M, which is under the 50M threshold proposed by Julien in #7.
valosek@macbook-pro:~/code/PAM50/histology$ du -h 31M .
Fixes #7 Fixes https://github.com/spinalcordtoolbox/PAM50/issues/8
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: https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/4077
Resulting
dim
andpixdim
for all histological images:Note that a modified version of
resampling.py
was used to setimg.header["pixdim"][4:] = 0
; context here.The size is 31M, which is under the 50M threshold proposed by Julien in #7.
Related issues/PRs
Fixes #7 Fixes https://github.com/spinalcordtoolbox/PAM50/issues/8