shawnrhoads
commented
3 years ago Hi @Brainhack-Global/project-monitors: my project is ready!
Open shawnrhoads opened 3 years ago
shawnrhoads
commented
3 years ago Hi @Brainhack-Global/project-monitors: my project is ready!
SamGuay
commented
3 years ago Thanks for submitting this project. Love the idea!! I'm sure it will be useful to many! Should be on the website anytime soon! :rocket:
Project info
Title: Neuroimaging Cookbook 🧠🍳📓
Project lead: Shawn Rhoads GitHub: @shawnrhoads Twitter: @ShawnRhoads56 Mattermost: shawnrhoads
If you are reading this because of Brainhack MTL 2020ish, feel free to contact @SamGuay if you have any question! Twitter: @SamGuay_ Mattermost: SamGuay_
Project collaborators: TBD! Contributions of any kind are welcome!
Registered Brainhack Global 2020 Event: Brainhack DC
Brainhack MTL 2020ish
Project Description: Anyone ever Google how to accomplish a task for neuroimaging data more than once? For example, I’ve Googled "how to extract a mask from a parcellation scheme" or "how to output the time series from an ROI to a .csv file" hundreds of times because I can't remember the exact command/function or flags to pass (and every time I am reminded just how many times I've visited the same webpages):
There are countless software packages with widely different commands and options to perform all sorts of different functions when working with neuroimaging data. But remembering them all is nearly impossible!
The Neuroimaging Cookbook will centralize “code snippets” (or “recipes”) for different, specific, and simple tasks in neuroimaging that people can incorporate in their own analysis pipelines. And most importantly, it would be scalable so that anyone can contribute their random, useful code snippet.
The idea is inspired by 30 Seconds of Code (specifically, 30 Seconds of Python), where people can easily reference code (across software) for different neuroimaging tasks like: how to convert across different image formats (e.g., BRIK/HEAD, img/hdr, nii, etc), flatten the lower triangle of a representational similarity matrix, extract a mask from a parcellation, output the time-series from an ROI to a .csv /.txt file, etc. Not exactly tutorials, but "code snippets" that people can adapt for their own scripts, apps, or Jupyter Notebooks.
Data to use: N/A
Link to project repository/sources: https://github.com/neuroimaging-cookbook
Goals for Brainhack Global 2020: Easy:
Intermediate:
Good first issues:
Skills (at least one of these):
Tools/Software/Methods to Use:
Communication channels: https://mattermost.brainhack.org/brainhack/channels/neuroimaging-cookbook
Project labels
Type of project:
coding_methods, #data_management, #documentation,
Project development status:
0_concept_no_content
Topic of the project:
Bayesian_approaches, #causality, #connectome, #data_visualisation, #deep_learning, #diffusion, #EEG_EventRelatedResponseModelling, #Granger_causality, #ICA, #machine_learning, #neural_decoding, #neural_encoding, #neural_networks, #PCA, #reinforcement_learning, #reproducible_scientific_methods, #statistical_modelling, #tractography
Tools used in the project:
AFNI, #ANTs, #BIDS, #Brainstorm, #CPAC, #Datalad, #DIPY, #FieldTrip, #fMRIPrep, #Freesurfer, #FSL, #Jupyter, #MNE, #MRtrix, #Nipype, #NWB, #SPM
Tools skill level required to enter the project (more than one possible):
comfortable, #familiar, #no_skills_required
Programming language used in the project:
no_programming_involved, #C++, #documentation, #Java, #Julia, #Matlab,
Python, #R, #shell_scripting, #Unix_command_line, #Web
Modalities involved in the project (if any):
behavioral, #DWI, #ECOG, #EEG, #fMRI, #fNIRS, #MEG, #MRI, #PET
Git skills reuired to enter the project (more than one possible):
0_no_git_skills, #1_commit_push, #2_branches_PRs, #3_continuous_integration
[x] I added all of the labels I want an associate to my project
Project Submission
Submission checklist
Once the issue is submitted, please check items in this list as you add under ‘Additional project info’
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Contributions: All contributions will be recognized in the cookbook and follow the all-contributors specification. Contributions of any kind are welcome!