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likeajumprope / tapas

TAPAS - Translational Algorithms for Psychiatry-Advancing Science
https://translationalneuromodeling.github.io/tapas/
GNU General Public License v3.0
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Online standalone interactive tutorial (“Notebook/Browser-Demo”) using NeuroDesk and or Matlab live scripts #6

Open likeajumprope opened 2 years ago

likeajumprope commented 2 years ago
mrikasper commented 2 years ago

Idea:

Question:

mrikasper commented 2 years ago

Alternative: Video Tutorial of Standalone PhysIO in NeuroDesk

vijayiyer05 commented 1 year ago

@mrikasper

Question:

Is it possible to run live scripts with Matlab online with example data stored somewhere? e.g., Matlab Live Script Gallery

It's readily possible to use AWS data (e.g., S3 buckets) from MATLAB Online.

I wonder if using an OpenNeuro dataset would work for this tutorial(s)?

The reason I ask: these datasets are available as S3 buckets.

(There are other pathways too, but this is likely the lowest-hanging fruit.)

mrikasper commented 1 year ago

Dear Vijay @vijayiyer05,

That's an excellent idea, thank you very much! I think we will have to identify if/which of the OpenNeuro-datasets come with peripheral physiological recordings, because that's what PhysIO modeling is based on. If there are suitable ones, that would be a great example dataset indeed.

likeajumprope commented 1 year ago

Outline tutorial in matlab livescript @mrikasper

Data set to be used: https://openneuro.org/datasets/ds001168/versions/1.0.1 and https://openneuro.org/datasets/ds000113/versions/1.3.0

Step 1a: Run PhysIO toolbox on data [x] Step 1b: create github repo [x] see here

Step 2: Start preparing live script [x]

mrikasper commented 1 year ago

Idea for repository name: physio-live

Template to start from for Step one (run on data with SPM creation of F contrasts and visualization):

https://github.com/BRAIN-TO/cubric-physio

TODO @likeajumprope : Adapt inputs for openneuro dataset --> done

mrikasper commented 1 year ago

Note, for the openneuro dataset you chose, you will have to update PhysIO to support BIDS files with more than 3 columns by extending the following function with a 3rd input parameter nColumns

tapas_physio_read_columnar_textfiles(fileName, fileType, nColumns)

that can be retrieved within tapas_physio_read_physlogfiles_bids via numel(val.Columns) (in line 415)

or you find another example dataset with just 3 columns.

likeajumprope commented 1 year ago

@mrikasper, I can now run physio fully on the first subject of the forest gump data set.. Some thoughts that I have had:

likeajumprope commented 1 year ago

Update

The tutorial exists in two versions:

Both use data from the open neuro forest gump repository(sub-01).

There are a few things that need to be considered based on the experience I had with the matlab online space in particular:

likeajumprope commented 1 year ago

Update on speed of Live-script demo on Matlab online.

In order to have the demo, tapas and spm in one repository, tapas and spm were integrated as sub-modules. This solution works fine if the repository is cloned to a local machine. When opening and running the repository on Matlab online, however, pulling the sub-modules takes ~ 15min. Also, running the demo on matlab online takes significantly longer than running it on a local machine.

likeajumprope commented 1 year ago

Link to the repositories:

Git: https://github.com/likeajumprope/PhysIO-Live File exchange: https://au.mathworks.com/matlabcentral/fileexchange/128779-physio-live

mrikasper commented 11 months ago

Maybe appropriate dataset for Demo (Brainstem fMRI, native Siemens physio logfiles):

TODO: