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dpr

Diffusion profile realignment - Making your along-tract analysis reliable

https://github.com/samuelstjean/dpr

Science Score: 23.0%

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    Low similarity (11.4%) to scientific vocabulary

Keywords

along-tract diffusion-mri dpr python
Last synced: 6 months ago · JSON representation

Repository

Diffusion profile realignment - Making your along-tract analysis reliable

Basic Info
  • Host: GitHub
  • Owner: samuelstjean
  • License: mit
  • Language: Jupyter Notebook
  • Default Branch: master
  • Homepage:
  • Size: 11.4 MB
Statistics
  • Stars: 3
  • Watchers: 3
  • Forks: 0
  • Open Issues: 0
  • Releases: 7
Topics
along-tract diffusion-mri dpr python
Created about 7 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog License

README.md

Diffusion profile realignment (dpr)

An example and assorted implementation from the manuscript Reducing variability in along-tract analysis with diffusion profile realignment. Have a look at the example on how to use the package and run it on a small example dataset.

To install the package, just run ~~~ pip install dpr ~~~

The documentation is available at https://dpr.readthedocs.io.

The matlab version

There is also a shiny new version written in matlab, with an assorted example, available in the matlab folder. Feel free to check out and edit the functions as needed for your own usage.

A quick example from the command line

There is also a command line version for easy usage, here in an example for the AFD metric on the left arcuate fasciculus. The text file is already ordered in increasing order for each subject, which have the same distance between every point and are already zero padded accordingly.

We also supply the --exploredti option to remove the header column, --do_graph to save a png file with the results.

We finally resample everything to 75 points with --points 75.

The -f option overwrites the output files and the -v option prints useful informative messages throughout (and are optional).

~~~bash dpr datasets/afleftAFD.txt datasets/afleftAFDrealigned.txt --exploredti --dograph -f -v --points 75 ~~~

The output datasets/af_left_AFD_realigned.txt is a text file where each line is a subject and each column is a different point of the along tract analysis.

We also get a png file datasets/af_left_AFD_realigned.png with the before/after realignment process.

Note how the zero padding present in the original data is decreasing the metrics as less and less subjects are present. The realigned metric is instead using padding with Nans, remember to consider/keep track of it in subsequent analysis as needed.

Visualizing the results

We can also draw the p-values (computed separately) over the bundle using the script dpr_make_fancy_graph. This requires the original coordinates, the truncated version between rois and the coordinates to the representative streamline.

~~~bash dprmakefancygraph datasets/afleftpvalunaligned.txt datasets/afleftcoordinates.txt datasets/aflefttruncatedcoordinates.txt datasets/afleftaveragecoordinates.txt 0,2 pvalsunaligned.png --title 'p-values before realignment' -f dprmakefancygraph datasets/afleftpvalrealigned.txt datasets/afleftcoordinates.txt datasets/aflefttruncatedcoordinates.txt datasets/afleftaveragecoordinates.txt 0,2 pvalsrealigned.png -f ~~~

And this is the results

Datasets and reference

The main reference is

~~~ Samuel St-Jean, Maxime Chamberland, Max A. Viergever, Alexander Leemans, Reducing variability in along-tract analysis with diffusion profile realignment, NeuroImage, 2019. ISSN 1053-811 ~~~

The data is also available at https://zenodo.org/record/2483169.

The open access manuscript is also available at https://www.sciencedirect.com/science/article/pii/S1053811919305014.

To refer to a specific version of the code, everything is also archived over at https://zenodo.org/record/3248894.

Owner

  • Name: Samuel St-Jean
  • Login: samuelstjean
  • Kind: user
  • Location: Lund, Sweden
  • Company: Lund University

GitHub Events

Total
  • Release event: 1
  • Delete event: 3
  • Push event: 8
  • Pull request event: 4
  • Create event: 3
Last Year
  • Release event: 1
  • Delete event: 3
  • Push event: 8
  • Pull request event: 4
  • Create event: 3

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 76
  • Total Committers: 4
  • Avg Commits per committer: 19.0
  • Development Distribution Score (DDS): 0.553
Past Year
  • Commits: 6
  • Committers: 1
  • Avg Commits per committer: 6.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Samuel St-Jean s****l@i****l 34
Samuel St-Jean s****n@u****a 23
Samuel St-Jean s****m@g****m 10
Samuel St-Jean 3****n 9
Committer Domains (Top 20 + Academic)
usherbrooke.ca: 1 isi.uu.nl: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 0
  • Total pull requests: 18
  • Average time to close issues: N/A
  • Average time to close pull requests: 26 days
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 17
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 2
  • Average time to close issues: N/A
  • Average time to close pull requests: 8 minutes
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
Pull Request Authors
  • samuelstjean (21)
Top Labels
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Packages

  • Total packages: 1
  • Total downloads:
    • pypi 46 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 4
  • Total maintainers: 1
pypi.org: dpr

Implementation of "Reducing variability in along-tract analysis with diffusion profile realignment".

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 46 Last month
Rankings
Dependent packages count: 10.0%
Downloads: 14.9%
Average: 20.3%
Dependent repos count: 21.7%
Stargazers count: 25.0%
Forks count: 29.8%
Maintainers (1)
samuelstjean
Last synced: 6 months ago

Dependencies

docs/requirements.txt pypi
  • sphinx >=3.0
  • sphinx-autoapi *
setup.py pypi
  • matplotlib >=2.0
  • numpy >=1.10
  • scipy >=0.19
.github/workflows/python-package.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
.github/workflows/pythonpublish.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
pyproject.toml pypi
  • matplotlib >=2.0
  • numpy >=1.10
  • scipy >=0.19