[website] import h2mri

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• bug/error report
• feature request

What is the current behaviour?

In 2018-2020, Cass wrote a guide on open science MRI data collection and analysis best practices for PERL. There is some content which could be usefully incorporated into the Community Pages.

Action to take

Import relevant sections of https://git.fmrib.ox.ac.uk/cassag/h2mri.

To be considered:

• What "chapters" to include?
• Where should they go? Analysis? Separate pages on RDM?
• move the code from git.fmrib...cassag/h2mri to a community repository (perhaps open-science/analysis?
• flag the known issues with the code! 1) singularity container should not be in there repo (people should pull it using a stated path to the container repo); 2) conda packages should not be in the repo, people should pull them!

@mmartens What chapters should we include?

Include = [ ✓ ] Not include = [ x ]

Tools for reproducibility:

• [ ✓ ] Electronic lab-book
• [ ✓ ] WIN IT Account
• [ x ] Create OSF account

Acquire, archive and and check raw data

• [ ✓ ] Acquiring data / calpendo
• [ ✓ ] Move your data
• [ ✓ ] Check dicoms

Programming in Atom with version control

• [ ✓ ] Code version control with gitlab

• [ ✓ ] Programming in Atom

• [ ✓ ] Converting to BIDS

• [ ✓ ] Formal quality control assessment with mriqc

• [ x ] Preprocessing with fmriprep

• [ x ] Workshop VII: Event files and behvioural analysis in python

• [ x ] Workshop VIII: First level analysis for factorial designs (this is for fmriprep preprocessed data)

• [ x ] Higher level analysis for factorial designs

• [ x ] Workshop X: Covariates

• [ x ] Workshop XI: Extracting and plotting ROI data

• [ x ] Workshop XII:COBIDAS reporting (not written)

changed the description

Some of this documentation is already on the community pages. The bits missing (and should be added!) are below. I've created holding pages for these linked below, but they are not yet listed in the navigation menu. Need to think about where they should live (maybe under analysis?).

• Electronic Lab notebook
• Converting to BIDS

Suggested action:

• Please review the above pages. They were written as a guide for a specific set of researchers/projects, so they will need to be re-written to make appropriate for a more general audience.
• Add a relevant sub heading
• convert the links to proper markdown syntax
• make sure code blocks are used consistently throughout for actual code and file names
• consider whether headings should be numbered (on BIDS page particularly) to improve readability.
• review against the original google doc sections on ELN and BIDS for formatting (line breaks etc.)
• decide where each page should be published!
• @lbaxter and @mmartens have made lots of comments in the google doc ELN and BIDS sections, but these have NOT been copied into the markdown pages! Need to make sure this feedback is incorporated!

These below documentation will not include the included on the Open WIN Community pages, because they live more naturally in the WIN IT guides. The WIN IT guides are scheduled be moved in a planned re-development of the WIN Intranet, so I'll make sure we have a chance to improve that documentation with some of this material when the move happens.

• Acquiring data / calpendo
• Move your data
• Editing your bash profile (from here

Checking dicoms and some sort of qc is something which should be covered in analysis training. @mmartens , do you know if there is room to add something similar to this on the graduate or FSL training?

added Ambassadors label

marked the checklist item What "chapters" to include? as completed

Hi @bpz864, I've edited the description of this issue a little. Please ready though and let me know if the actions to take aren't clear :).