jchrispang / neural-flows Goto Github PK

If you use this toolbox, please cite:

Roberts JA, Gollo LL, Abeysuriya R, Roberts G, Mitchell PB, Woolrich MW, Breakspear M. Metastable brain waves. (2019) Available from here.

Sanz-Leon P, Gollo LL, and Roberts JA (2020) (in prep).

This is neural-flows, a library to estimate wave velocities and singularities in 3D+t in neuroimaging data.
The figure below gives you an idea of a typical workflow you can run with this toolbox:
Each link of the path is a component of the core-module namely:

• data interpolation,
• flow estimation,
• singularity detection and classification, and
• streamline tracing.

The toolbox has a number of ancillary modules, including examples with exemplary scripts to execute a full or partial workflow; external, which contains code implemented by others, the most prominent being C-NEM invoked by so-called meshless methods, and the Hungarian method used track singularities; and finally, utils which gathers small standalone functions that support the main modules.

MATLAB

• tested on R2018b & R2020a
• in principle should work on any OS that MATLAB supports; tested on Windows 10, Debian 10, Ubuntu 20.04, Ubuntu 16.l4, OpenSuse 15.1

CNEM, https://m2p.cnrs.fr/sphinxdocs/cnem/index.html

- used version (v03, 2014-05-04) available here: https://ff-m2p.cnrs.fr/frs/?group_id=14
- aka cnemlib: https://au.mathworks.com/matlabcentral/linkexchange/links/3875

input data

- `data`: a tpts-by-n 2D array with the data for unstructured datasets (i.e., soruce reconstructed MEG data) 
- `locs`: a n-by-3 2D array with the locations of nodes/rois/sources, expressed in mm or m.
- `ht`  : sampling period expressed in ms or s.

If you download the zip folder, first unzip and then ...

• Windows 10: see the instructions here.
• Linux: on the terminal change directory to neura-flows folder, then start matlab. That's it. The toolbox paths should be appended automatically.

If you clone the repo, same rules as above apply.

A bunch of things, mostly the ones described in the diagram above.

To get started follow the next steps (timestamp: Fri 31 Jul 2020 21:21:17 AEST):

0. (Optional) Inside directory neural-flows, make a new directory call scratch (by default we will store results there, you can change it later ...)
1. (Optional) Open the file rotating_wave_uah_in.json under examples/ 1a.(Optional) if you are on Windows change line 6 of that file

      "dir_tmp": "/tmp",    

to

   "dir_tmp": "C:\Users\guest\AppData\Local\Temp",    

or any other directory where some temporary files will be stored during execution.

1b. (Optional) If you are on Mac, the default value /tmp should work, otherwise change it to an appropriate temp folder.

1c. (Optional) If you re on Linux, you're good to go.

2. Run the function under examples/ at

rotating_wave('uah')

It should take about 5 minutes to run everything and pop up figures with flow mode decomposition and singularity tracking!

Coming soon, sorry <(~.~)> ...