INCF_preclinical

Code examples for the Practical guide to overcome the reproducibility crisis in small animal neuroimaging: workflows, tools, and repositories

Practical guide to overcome the reproducibility crisis in small animal neuroimaging: workflows, tools, and repositories Chairs: Markus Aswendt, Joanes Grandjean Location: Presentation Room 1

The workshop will include interactive seminars given by selected experts in the field covering all aspects of (FAIR) small animal MRI data acquisition, analysis, and sharing. The seminars will be followed by hands-on training where participants will perform use case scenarios using software established by the organizers. This will include an introduction to the basics of using command line interfaces, Python installation, working with Docker/Singularity containers, Datalad/Git, and BIDS.

Preparation:

Questionnaire for the participants Link to Google Form

Install software

1. Software
   1.1 Anaconda
   1.2 Jupyter Notebook
   1.2.1 Bash kernel for Jupyter Notebook
   1.3 Datalad
   1.4 GIN client
   1.5 Docker

2. MRI tools
   2.1 ITK-SNAP
   2.2 Brkraw
   2.3 Clone latest AIDAmri (Docker) version from https://github.com/Aswendt-Lab/AIDAmri
   2.2 RABIES installation (Docker) pull from Docker hub https://hub.docker.com/r/gabdesgreg/rabies selecting tag number 0.4.8

Participating to the AIDAmri hands-on demo

There will be a hands-on demonstration of the AIDAmri software broadcasted during the workshop. It will be possible to follow along from your computer if you install the prerequisites. The following will be required:

• Jupyter Notebook
• Docker
• Git bash (for Windows only, in git bash type . PATH\TO\ANACONDA\Scripts\activate)
• Clone the AIDAmri GitHub repository in terminal/git bash with git clone https://github.com/Aswendt-Lab/AIDAmri.git or alternatively download and unpack the zip file. Change to the AIDAmri folder.
• Download the test dataset and unpack into the AIDAmri folder.
• Start the Jupyter Notebook "AIDAmri_workshop.ipynb" in terminal/git bash with jupyter notebook and follow the instructions in the notebook

Participating to the RABIES hands-on demo

There will be a hands-on demonstration of the RABIES software broadcasted during the workshop. It will be possible to follow along from your computer if you install the prerequisites. The following will be required:

• Jupyter Notebook (to open notebooks)
• Docker, and pulling RABIES version 0.4.8 with docker pull gabdesgreg/rabies:0.4.8 (make sure to have ~10Gb of free space)
• Download this github repository; the required notebooks and files are all include in the rabies/ folder. You can download the repo manually by clicking on "code -> download ZIP", or from a terminal using git with git clone https://github.com/grandjeanlab/INCF_preclinical.

Schedule:

Welcome: Markus/Joanes

SEMINAR 1 (20 min): Markus/Aref -- How to set up a FAIR workflow for multimodal rodent imaging data in a no-code environment of a translational stroke lab. Slides

SEMINAR 2 (25 min): Michał -- An introduction to version control, Git, DataLad. Slides: pdf, html.

SEMINAR 3 (15 min): Joanes -- Working with robust data structure (BIDS) and containers (Docker / Apptainer)

HANDS-ON 1 (1 h): Michał (Aref, Markus) -- Data Management for Neuroimaging with DataLad

HANDS-ON 2 (2 hrs): Two breakout rooms:
Breakout room (carpet) 1: Markus/Aref -- Application of image post-processing pipeline AIDAmri. Slides (Link to GitHub AIDAmri)
Breakout room (carpet) 2: Gabriel/Joanes -- Rodent functional MRI preprocessing with RABIES. (Link to GitHub RABIES)

Survey:

This workshop was hopefully only the start of a series of workshops and hackathons related to small animal MRI. Therefore we need your help and want to hear your opinion => short survey. THANKS!