DECAES

DEcomposition and Component Analysis of Exponential Signals (DECAES) - a Julia implementation of the UBC Myelin Water Imaging (MWI) toolbox for computing voxelwise T2-distributions of multi spin-echo MRI images.

https://github.com/jondeuce/decaes.jl

Science Score: 51.0%

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Low similarity (15.7%) to scientific vocabulary

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Last synced: 7 months ago · JSON representation ·

Repository

Basic Info

Host: GitHub
Owner: jondeuce
License: mit
Language: Julia
Default Branch: master
Homepage:
Size: 5.81 MB

Statistics

Stars: 34
Watchers: 3
Forks: 6
Open Issues: 2
Releases: 0

Created about 6 years ago · Last pushed about 1 year ago

Metadata Files

Readme License Citation

README.md

DEcomposition and Component Analysis of Exponential Signals (DECAES)

DECAES is a fast Julia implementation of the MATLAB toolbox from the UBC MRI Research Centre for computing voxelwise T2-distributions from multi spin-echo MRI images using the extended phase graph algorithm with stimulated echo corrections. Post-processing of these T2-distributions allows for the computation of measures such as the myelin water fraction (MWF) or the luminal water fraction (LWF).

DECAES is written in the open-source Julia programming language. Julia and command line interfaces are available through this package. The examples repository additionally provides a MATLAB interface via the MATLAB function decaes.m.

If you use DECAES in your research, please cite our work:

Doucette J, Kames C, Rauscher A. DECAES - DEcomposition and Component Analysis of Exponential Signals. Zeitschrift für Medizinische Physik 2020; 30: 271–278.

Installation

Using Julia v1.9 or later you can install DECAES as follows:

bash $ julia --project=@decaes -e 'import Pkg; Pkg.add("DECAES"); Pkg.build("DECAES")'

This will do two things:

Add DECAES.jl to a named Julia project environment separate from your global environment
Build the decaes launcher script at ~/.julia/bin for running DECAES from the command line

DECAES can then be run from the command line via decaes <COMMAND LINE ARGS>, provided ~/.julia/bin is added to your PATH. Run decaes --help for available arguments.

Quickstart

If you are new to DECAES, the best place to start is the examples repository. There, we provide:

A walk-through tutorial for using the MATLAB and command-line DECAES interfaces
Example multi spin-echo (MSE) data for demonstrating MWI processing

Documentation

Find package documentation at the above link, which includes:

The command line interface API, available command line arguments, and examples
API reference detailing how to use DECAES.jl from within Julia
Other internals and algorithmic details

Benchmarks

Due to performance optimizations enabled by Julia, DECAES is fast. As an illustration, here is a comparison between DECAES and UBC MWF MATLAB toolbox T2-distribution computation times for two multi spin-echo (MSE) datasets:

| Dataset | Matrix Size | CPU | Cores | Threads | MATLAB | **DECAES** | | :---: | :---: | :---: | :---: | :---: | :---: | :---: | | 56-echo MSE | 240 x 240 x 113 | Intel Xeon E5-2640 | 12 | 24 | 1h:25m:01s | **1m:07s** | | 48-echo MSE | 240 x 240 x 48 | Intel Xeon E5-2640 | 12 | 24 | 59m:40s | **40s** | | 56-echo MSE | 240 x 240 x 113 | AMD Ryzen 9 3950X | 16 | 32 | 22m:33s | **15.6s** | | 48-echo MSE | 240 x 240 x 48 | AMD Ryzen 9 3950X | 16 | 32 | 17m:56s | **9.3s** | | 56-echo MSE | 240 x 240 x 113 | AMD Ryzen Threadripper 3970X | 32 | 64 | -- | **7.7s** | | 48-echo MSE | 240 x 240 x 48 | AMD Ryzen Threadripper 3970X | 32 | 64 | -- | **4.3s** |

DECAES Tutorial 2022

JuliaCon 2021

Citing this work

If you use DECAES in your research, please cite our work:

tex @article{DECAES.jl-2020, title = {{{DECAES}} - {{DEcomposition}} and {{Component Analysis}} of {{Exponential Signals}}}, author = {Doucette, Jonathan and Kames, Christian and Rauscher, Alexander}, year = {2020}, month = may, issn = {1876-4436}, doi = {10.1016/j.zemedi.2020.04.001}, journal = {Zeitschrift Fur Medizinische Physik}, keywords = {Brain,Luminal Water Imaging,MRI,Myelin Water Imaging,Prostate}, language = {eng}, pmid = {32451148} }

Owner

Login: jondeuce
Kind: user

Repositories: 7
Profile: https://github.com/jondeuce

Citation (CITATION.bib)

@article{DECAES.jl-2020,
  title = {{{DECAES}} - {{DEcomposition}} and {{Component Analysis}} of {{Exponential Signals}}},
  author = {Doucette, Jonathan and Kames, Christian and Rauscher, Alexander},
  year = {2020},
  month = may,
  issn = {1876-4436},
  doi = {10.1016/j.zemedi.2020.04.001},
  journal = {Zeitschrift Fur Medizinische Physik},
  keywords = {Brain,Luminal Water Imaging,MRI,Myelin Water Imaging,Prostate},
  language = {eng},
  pmid = {32451148}
}

GitHub Events

Total

Issues event: 1
Watch event: 2
Delete event: 1
Issue comment event: 2
Push event: 6
Pull request event: 2
Fork event: 1
Create event: 1

Last Year

Issues event: 1
Watch event: 2
Delete event: 1
Issue comment event: 2
Push event: 6
Pull request event: 2
Fork event: 1
Create event: 1

Committers

Last synced: about 3 years ago

All Time

Total Commits: 236
Total Committers: 8
Avg Commits per committer: 29.5
Development Distribution Score (DDS): 0.547

Top Committers

Name	Email	Commits
Jonathan Doucette	j**e@p**a	107
Jonathan Doucette	j**e@p**a	62
github-actions[bot]	4**]@u**m	46
jondeuce	2**e@u**m	14
Jonathan Doucette	j**4@l**a	3
CompatHelper Julia	c**y@j**g	2
Jonathan Doucette	j**4@l**a	1
kamesy	5**y@u**m	1

Committer Domains (Top 20 + Academic)

login03.sockeye.arc.ubc.ca: 1 julialang.org: 1 login02.sockeye.arc.ubc.ca: 1 phas.ubc.ca: 1 physics.ubc.ca: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time

Total issues: 11
Total pull requests: 56
Average time to close issues: 14 days
Average time to close pull requests: 23 days
Total issue authors: 8
Total pull request authors: 3
Average comments per issue: 3.18
Average comments per pull request: 0.27
Merged pull requests: 49
Bot issues: 0
Bot pull requests: 49

Past Year

Issues: 2
Pull requests: 1
Average time to close issues: N/A
Average time to close pull requests: about 3 hours
Issue authors: 2
Pull request authors: 1
Average comments per issue: 2.0
Average comments per pull request: 0.0
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 1

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Top Authors

Issue Authors

ncbss (3)
orie2409 (2)
nalimilan (1)
ahsabali (1)
harrisoncbrammell (1)
emilljungberg (1)
Laura2305 (1)
JuliaTagBot (1)

Pull Request Authors

github-actions[bot] (50)
kamesy (7)
jondeuce (2)

Top Labels

Issue Labels

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Packages

Total packages: 1
Total downloads:
- julia 6 total

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 13

juliahub.com: DECAES

Documentation: https://docs.juliahub.com/General/DECAES/stable/
License: MIT
Latest release: 0.6.0
published almost 2 years ago

Versions: 13
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 6 Total

Rankings

Dependent repos count: 9.9%

Stargazers count: 24.1%

Average: 24.4%

Forks count: 24.5%

Dependent packages count: 38.9%

Last synced: 7 months ago

Dependencies

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