GSoC 2021 Project Idea 19.3: DIPY Projects - Extend DIPY Horizon workflow for Visualization

GSoC
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#1

Description: Extend dipy_horizon workflow by adding more options for the visualization of the diffusion data. DIPY Horizon is a workflow that enables to visualize diffusion data such as dMRI, tractograms, white matter bundles, and more from the command line. This project requires student to add support for different types of file formats and visualizations in the horizon workflow.

Steps:

  • Add support to visualize orientation distribution functions (odfs) generated from diffusion data
  • Create an option in the horizon workflow to project anatomical measures such as functional anisotropy (FA), mean diffusivity (MD), etc on the white matter tracts and visualize them
  • Add region-of-interest (ROI) capacity for streamline filtering in Horizon.
  • Add Qt functionality in dipy_horizon workflow

Difficulty: Intermediate

Skills required: Python, VTK, Qt.

Mentors: Bramsh Qamar Chandio, Shreyas Fadnavis, and Jong Sung Park

Tags: DIPY, neuroimaging, Python, dMRI, VTK, Qt

1 Like
#2

Hello @bramsh , @ShreyasFadnavis , @Jong Sung Park
I am Omar Elsherif. I am studying Medical Informatics at Faculty of Computers and Artificial Intelligence Benha University in Egypt. I want to join this project and increase the visualization options of the diffusion data. I searched the messages from last year about this project and I am currently working on the DIPY tutorials. Do you recommend a another thing to do these days to gain better understanding and be ready for the project ?
I have good experience with data analysis from Udacity nanodegree and I learned a lot about machine learning from DataCamp career track. I am comfortable using using python but I am asking if I missed something or this project require more aspects so I can go ahead and prepare good for it in order to do great work during the summer.
Here is my LinkedIn for more about me, I hope to work with you soon. Omar Elsherif | LinkedIn
Thanks for your time.

#3

Hi @omarelsherif010

Take a look at the guidelines on how to contribute to DIPY. Making a small enhancement/bugfix/documentation fix/etc to DIPY already before applying for the GSoC can help you get some idea how things would work during the GSoC. The fix does not need to be related to your proposal. We have and will continue adding some beginner-friendly issues in Github. You can see some of them here.

1 Like
#4

Interested students, please send your CV to bqchandi@iu.edu

1 Like
#5

Hi @bramsh
After I went through DIPY tutorials and attended DIPY workshop 2021, I feel I have a good understanding if what we need to do with the visualization of dipy horizon but to be honest I just have a minumal experience with VTK and Qt. So I am planing to have more experience with these two after gsoc, maybe in Septamper or October. Then I will go ahead and add the support for the different types of file formats and visualizations in the horizon workflow if no other student had already did before me.
I know this will be away of gsoc but I am happy with this and want to contribute to DIPY as mush as I can because I want to work in neuroimaging in the future and will be happy if I joined DIPY team one day.
So, I will not apply for this project during gsoc but I will go the DIPY-Tract-or-Treat: DIPY DTI Post-Processing Pipeline project and will do my best to create the command line interface that combines different methods of reconstruction, tractography, bundle extraction, and tratometry.
Thanks for your help and I wish the best to the student who will work on this project. :sparkling_heart:

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