raamana / mrivis Goto Github PK
View Code? Open in Web Editor NEWmedical image visualization library and development toolkit
Home Page: https://raamana.github.io/mrivis/
License: MIT License
medical image visualization library and development toolkit
Home Page: https://raamana.github.io/mrivis/
License: MIT License
Hi Raamana, I was trying to do this with @lalet:
>>> from mrivis import checkerboard
>>> checkerboard('sub-01/anat/sub-01_T1w.nii.gz', 'sub-01/anat/sub-01_T1w.nii.gz', patch_size=10)
And this happened:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/glatard/.local/lib/python3.6/site-packages/mrivis/mrivis.py", line 92, in checkerboard
**mixer_params)
File "/home/glatard/.local/lib/python3.6/site-packages/mrivis/mrivis.py", line 398, in _compare
display_params, **kwargs)
TypeError: _generic_mixer() takes 3 positional arguments but 6 were given
Any hint?
deriving from Carpet, create FuncCarpet
with defaults tailored to most neuroimaging applications, such as taking tissue segmentation masks, default blurring on, etc
deriving from Carpet, create DiffusionCarpet
, similar to above with useful defaults
in_roi='seg_image.nii'
)update mrivis docs to note that all my packages assume orientation is encoded correctly
find ways not to assume it.
With cross platform support in mond
Right now, it only shows alignment-related visualizations.
Add more visualizations for all features, including
from mrivis import checkerboard
plot = checkerboard('T2w_acpc.nii.gz','T2w_acpc_centos7.nii.gz',patch_size=10)
plot.savefig("T2w_tilt.png")
These two files are output from two operating systems.
They are completely off w.r.t alignment and we tried to visualize the differences using checkerboard.
But no checkerboard is visible in the output image.
Thanks for fixing the other issue, but it would be greatly appreciated if you have any hint on this one. Please find attached the output image.
Here I will write my review for the JOSS submission: openjournals/joss-reviews#897
The purpose of the project is simple but very important and can be divided into two parts:
Alignment check between MRI images is very important in neuroimaging. Reducing the similarity between two images to a simple number (e.g. using a distance function) might be accurate but is often times not useful as it doesn't provide information about the source of the discrepancy. Using a visual approach, and in this case, providing multiple ones is a very nice solution to this problem!
The creation of MRI collages is also very important for the field of neuroimaging. A collage allows the investigation of a 3D image (with many 100 of slices in three directions). All at once with a quick glance. Even though this is important, there are only a few open source software that provides this functionality, but none does it as simple and flexible as mrivis
! The possibility of only plotting slices with a particular non-zero density or containing a given ROI is really great! A similar "one view check" can be achieved for 4D images, using the Carpet class!
My general impression of the repo is very good! The repo has an informative README.rst
file, a very detailed documentation homepage, and provides important files, such as LICENSE
AUTHORS.rst
, CODE_OF_CONDUCT.md
, CONTRIBUTING.rst
, etc.
The code is well written, uses PEP440 standard (enforced with flake8
) and is well commented.
The installation of the software is very easy. mrivis
can be installed very quickly via pip
and all required dependencies are listed in requirements.txt
.
To quickly test mrivis
and getting used to its functionality, this repo provides some example files as well as a demo notebook. This is very good, as it allows a user to quickly learn how to use mrivis
.
Concerning the review criteria under https://joss.readthedocs.io/en/latest/review_criteria.html:
I haven't reviewed the MATLAB code section in the matlab_code folder, as it contains the note: This is no longer maintained! The python version has more options and is recommended.
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.