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learn-neuroimaging / hitchhackers_guide_brain

A list of tutorials and other resources useful to learn open science and neuroimaging, EEG and MEG
https://learn-neuroimaging.github.io/hitchhackers_guide_brain/
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Structure webpages as steps through a neuro{-science/-imaging} pipeline #63

Closed roopa-pai closed 4 years ago

roopa-pai commented 4 years ago

It could be helpful for people new to the field (or to this website) to navigate it if the website were structured along the lines of a pipeline, e.g.:

  1. Introduction / General neuroscience introductory resources
  2. Getting data
  3. Processing 3.1 modality 3.1.1 software 3.1.2 tutorial
  4. QC
  5. Analysis 5.1 Statistics/ML

I suggest we create a mindmap / storyboard to have a rough sketch of what we'd want the organization to look like, using something like miro: www.miro.com ‎ Let me know what you think!

Remi-Gau commented 4 years ago

OK I am copying below part of the table of content of my own list of resources. https://github.com/Remi-Gau/online_neuroimaging_resources/blob/master/Main.md

So we can compare.

My stuff is VERY fMRI focused though.

Starting from your structure @roopa-pai I think we need to some stuff about planning a study before your getting data step.

I totally love the idea of dividing each section according to modality.

I totally agree that quality control should be an entire section.

I think we should have something about:

[BEFORE YOU START]
    [Reproducibility]
    [Ethics and consent forms]
    [Code and data management]
        [Code management]
            [Version control]
            [Coding style]
            [Avoid selective debugging: unit tests, positive and negative control]
        [Data management]
            [BIDS]
            [Datalad]
        [Documentation]
[PLANNING YOUR STUDY]
    [Reusing data]
    [Defining your terms and your task]
    [Ontologies]
    [Piloting]
    [Pre-registration]
    [Optimizing your design]
    [Design efficiency]
    [Power]
    [For MVPA: same analysis approach]
    [Defining your region of interest]
    [Using previous results]
    [Localizers]
    [Atlases]
    [Non-standard templates]
Getting data
        Stimuli presentation softwares
            psychopy
            expyriment
            psychtoolbox
    Existing protocols
[ONCE YOU HAVE DATA]
    [quality control]
    [preprocessing]
        [Pipelines]
        [Artefact/Noise removal]
    [Analysis]
        [general linear model]
        [Model selection]
        [Multivariate analysis]
        [Resting state]
        [Diffusion weighted imaging]
        [Statistical inferences and multiple comparison correction]
        [Encoding models]
    [Robustness checks]
    [Computational neuroscience]
    [Laminar and high-resolution MRI]
    [Meta analysis]
REPORTING METHODS AND RESULTS (also useful for reviewing papers)
    A checklist: COBIDAS report
    Percent signal change
    Making figures
    Tools to check results/statistics
    Peer review
YOU ARE NOT DONE YET: sharing your code, data and your results
    Sharing code
    NeuroImaging Data Model (NIDM)
    Sharing your data
    Meta-analysis databases
Metalist
Online courses
Video series
Blogs
Where to ask for help
Image formats
UNIX command line
Matlab and SPM specific resources
The python ecosystem ( ??? )
R
Web apps ( ??? )
EEG and MEG Softwares
Remi-Gau commented 4 years ago

So to make a concrete proposal I would structure it this way.

roopa-pai commented 4 years ago

This is wonderful!! I love it. What do you think regarding next steps? I can suggest:

I create new docs for the top-level pages, and if these are okay then we (slowly) migrate resources to the right place.

However, I also think it would be best if we agree on templates / website syntax first though. Maybe I can think about that and make some suggestions, and once we have a working set of rules we pick this up again.

What do you think?

Remi-Gau commented 4 years ago

I create new docs for the top-level pages, and if these are okay then we (slowly) migrate resources to the right place. Let's see what the other say (@alexandreroutier @dr-xenia) but if we think this is a good enough structure then you could open a Pull request that sets this basic hierarchy of pages.

Remi-Gau commented 4 years ago

However, I also think it would be best if we agree on templates / website syntax first though. Maybe I can think about that and make some suggestions, and once we have a working set of rules we pick this up again.

Yes before migrating anything I think we should agree on the templates. But you can still open a PR for the overall structure.

alexandreroutier commented 4 years ago

I create new docs for the top-level pages, and if these are okay then we (slowly) migrate resources to the right place. Let's see what the other say (@alexandreroutier @dr-xenia) but if we think this is a good enough structure then you could open a Pull request that sets this basic hierarchy of pages.

The plan seems great! I have a few comments:

Remi-Gau commented 4 years ago 
* I would prefer putting "General neuroscience introductory resources" into some kind of appendix section. It contains too many information to digest for a newcomer. I would be better to refer to the relevant part at the beginning of each section (e.g. "Getting Data" or "Analysis")

yes I was wondering about this when I wrote this down. Should we just move it at the end?

Remi-Gau commented 4 years ago 
* I feel like that QC will be part of "Processing" and "Analysis" in the end. But let's keep it that way.

I will ping @raamana on this. Given that QC is his jam, he might be able to give us some informed opinion whether QC should be independent or should be sprinkled through the whole processing and analysis chapters.

Remi-Gau commented 4 years ago 
* The wording for Processing: I would change to something like Pre(processing) and features extraction

pre-processing could do but feature extraction might be too obscure for quite a few people.

raamana commented 4 years ago 
* I feel like that QC will be part of "Processing" and "Analysis" in the end. But let's keep it that way.

I will ping @raamana on this. Given that QC is his jam, he might be able to give us some informed opinion whether QC should be independent or should be sprinkled through the whole processing and analysis chapters.

I think it needs to be BOTH. A dedicated section saves time for those focusing on or learning QC, and regularly linking to the QC tools/resources under various processing streams would help folks discover them, as well as helps them realize and learn most processing requires QC.

also, 1) there isn't a perfect organization, so get something done reasonable.. adapt it based on user feedback 2) I hope this becomes THE list of learning resources, so over time, everyone can add to it. In other words, we must work with OHBM, INCF etc to try discourage multiple lists all over the web, and consolidate them here.

Remi-Gau commented 4 years ago

I think it needs to be BOTH. A dedicated section saves time for those focusing on or learning QC, and regularly linking to the QC tools/resources under various processing streams would help folks discover them, as well as helps them realize and learn most processing requires QC.

Hum... I had not considered that. I am not a big fan of duplication so what I would suggest is keeping QC its own section but adding very clear internal links to it from other other parts of the doc.

Remi-Gau commented 4 years ago
  • there isn't a perfect organization, so get something done reasonable.. adapt it based on user feedback

OK I will tell my inner perfectionist. But I doubt he will listen. Joke aside: thanks that is a very good reminder. It will have to be good enough.

  • I hope this becomes THE list of learning resources, so over time, everyone can add to it. In other words, we must work with OHBM, INCF etc to try discourage multiple lists all over the web, and consolidate them here.

I will tell my inner impostor. I have not even started to think about contacting OHBM or INCF... Baby steps first.

roopa-pai commented 4 years ago

I think it needs to be BOTH. A dedicated section saves time for those focusing on or learning QC, and regularly linking to the QC tools/resources under various processing streams would help folks discover them, as well as helps them realize and learn most processing requires QC.

I agree! I wanted to put it at the end of each "processing" section, but also wanted a way to find it easily.

Hum... I had not considered that. I am not a big fan of duplication so what I would suggest is keeping QC its own section but adding very clear internal links to it from other other parts of the doc.

This is perfect

roopa-pai commented 4 years ago

2. I hope this becomes THE list of learning resources, so over time, everyone can add to it. In other words, we must work with OHBM, INCF etc to try discourage multiple lists all over the web, and consolidate them here.

This would be so cool!