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brainhackorg / global2021

Website for Brainhack global 2021
https://brainhack.org/global2021/
MIT License
3 stars 11 forks source link

Macapype: external pipeline #131

Open davidmeunier79 opened 2 years ago

davidmeunier79 commented 2 years ago

Project info

Title: Macapype: external pipelines

Project lead and collaborators:

Description: Macapype is a python package based on nipype, wrapping the tools required for NHP MRI anatomical segmentation. Macapype provide several processing pipelines, allowing optimisation and adaptation, depending on the quality of the images (SNR), acquisition sequences and antenna types, as well as species. Today, macapype is provided as a github repo, a pip install, and a docker/singularity image. The accepted inputs have to be in BIDS format, and macapype pipelines are callable thanks to a command line interface (CLI).

Links : Macapype Github: https://github.com/Macatools/macapype Macapype Documentation: https://macatools.github.io/macapype/index.html

Goals for Brainhack Marseille Macapype is mostly oriented to PNH anatomical segmentation. However, many applications can be included starting from a good segmentation quality :

Putative schedule :

Communication channels:

Required skills :

Good first issues : Wrapping in nipype a script to reorient anatomical image to normalized orientation

Striking Image macapype_logo_manon

JuliaSprenger commented 2 years ago

@davidmeunier79 I don't think the label programming:R is correct for this project, this should be programming:python instead.

JuliaSprenger commented 2 years ago

Also for the project to be considered ready to integrate you need to add a comment Hi @Brainhack-Global/project-monitors: my project is ready! (see issue template to submit projects)

davidmeunier79 commented 2 years ago

Hi @Brainhack-Global/project-monitors: my project is ready!

davidmeunier79 commented 2 years ago

Also for the project to be considered ready to integrate you need to add a comment Hi @Brainhack-Global/project-monitors: my project is ready! (see issue template to submit projects)

Merci @JuliaSprenger !

davidmeunier79 commented 2 years ago

Also I noticed the automated labelling included: programming: R, instead of programming: python And the tag nipype could also be added!

Remi-Gau commented 2 years ago

Also I noticed the automated labelling included: programming: R, instead of programming: python And the tag nipype could also be added!

Yeah our automatic labeller is taking some interesting liberties sometimes. Will fix that

And good idea for the nipype label suggestion: will add it

Remi-Gau commented 2 years ago

@Brainhack-Global/project-monitors

actrually it is supposed to be @brainhackorg/project-monitors but the typo was in the project template so totally on us. :facepalm:

Remi-Gau commented 2 years ago

As the project was already reviewed by the local event organizers there is no need for further review on our side. Will proceed with publication on the website.

jhlegarreta commented 2 years ago

It looks like this issue was not created using the project submission template: section names are different. Same applies to virtually all BHD events... The latter have been processed by the project file generation script somehow, though. Honestly. IDK how the script succeeded.

Remi-Gau commented 2 years ago

The latter have been processed by the project file generation script somehow, though. Honestly. IDK how the script succeeded.

It works: I don't know why! It doesn't work: I don't know why!

davidmeunier79 commented 2 years ago

Many thanks to both of you @Remi-Gau and @jhlegarreta One last thing: Would it be possible to add at the end of the project page:

Communication channels: https://mattermost.brainhack.org/brainhack/channels/primedre-brainhack-2021-macapype

Thanks again for your amazing job!

Remi-Gau commented 2 years ago

@davidmeunier79

I am pretty sure that if you edit your top post (https://github.com/brainhackorg/global2021/issues/131#issue-1063332327) then the rest will be done almost entirely via github automation

davidmeunier79 commented 2 years ago

I am pretty sure that if you edit your top post (#131 (comment)) then the rest will be done almost entirely via github automation

Yes it worked; many thanks @Remi-Gau !