Tools and scripts for visualization and comparison of 3d MRI scans (T1, T2 etc)
Tools for comparison of registration and spatial similarity of 3d MRI scans (T1, T2, PET etc) using checkerboard plots.
pip install -U mrivis
Note: this package is in ACTIVE development.
Expect minor bugs, along frequent fixes/changes.
from mrivis import checkerboard, voxelwise_diff, color_mix
path1 = '/Users/Reddy/Desktop/image.nii'
path2 = '/Users/Reddy/Desktop/another.nii'
checkerboard(path1, path2, patch_size=5) # square patches
checkerboard(path1, path2, rescale_method=(0, 256) )
checkerboard(path1, path2, patch_size=10,
num_rows=1, num_cols=3) # 1 row per dimension, with 3 columns
checkerboard(path1, path2, patch_size=[10, 20], # rectangular patches
num_rows=2, # 2 rows per dimension (6 rows in total)
num_cols=5) # 5 panels per row
voxelwise_diff(path1, path2, abs_value=False)
color_mix(path1, path2, alpha_channels=(1, 1))
color_mix(path1, path2, alpha_channels=(0.7, 1))
## Various options available
Download this image to get a better look at the differences:
## Comparing two BOLD images
## Sample outputs for checkerboard plots
When the two scans are mismatched:
When the mismatch is low (here a smoothed image is comapred to its original),
you can see the differences in intensity (due to smoothing),
but you can also see that they are both spatially aligned accurately:
With really low patch-sizes (e.g. 1, which is voxel-wise alternation), you can see the alignment even better:
When there is mismatch, you can clearly see it (patch size 15 voxels square):
Let's make the patches a bit bigger (patch size 25 voxels square):
Let's make the patches a even bigger (50 voxels square):
Let's use a **rectangular** patch (10 voxels high and 30 voxels wide):
If they were identical (no mismatch at all), you won't see any edges or borders:
Full layout with 6x6 pangels can be seen in [this folder](docs/comprehensive).
## More example outputs
Many more example outputs, for different combinations of parameters, can be seen in this [example outputs folder in docs](docs/example_outputs).
* First release on PyPI.
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
|Filename, size & hash SHA256 hash help||File type||Python version||Upload date|
|mrivis-0.2.8-py2.py3-none-any.whl (15.4 kB) Copy SHA256 hash SHA256||Wheel||py2.py3||Apr 12, 2018|
|mrivis-0.2.8.tar.gz (12.9 MB) Copy SHA256 hash SHA256||Source||None||Apr 12, 2018|