Setup

This wiki page documents how to set up BrainTrak

Set up the repository

1. To use BrainTrak, you will first need to set up the corticothalamic-model repository, by following these instructions

2. Next, clone the BrainTrak repository into the same directory as corticothalamic-model i.e. you should have a folder that contains corticothalamic-model and braintrak

3. To use BrainTrak, you will also need to add corticothalamic-model and braintrak to your Matlab path. As with all of the BrainDynamicsUSYD software packages, you should add the project folders to your path and work from the top-level directory that contains the repositories. For example, you might have

   • ~/romesh (home directory)
   • ~/romesh/work
   • ~/romesh/work/corticothalamic-model
   • ~/romesh/work/braintrak

   In which case you should run Matlab from (or navigate to) ~/romesh/work, add corticothalamic-model and braintrak to your path, and then remain in the same Matlab directory.

Test BrainTrak

You can perform a test fit by running the following commands in Matlab:

f = bt.fit_track(bt.model.full,'demo',1,1,'10s')
f.plot()

This should produce a plot like the one shown below

If this works, you've successfully set up BrainTrak, and you can proceed on to the theory.

Troubleshooting

If you see the error

Undefined function or variable 'bt.model.full'. 

then you have not added braintrak to your Matlab path. If you see an error like

Undefined variable "model" or class "model.params".

If you get an error like

Error using tent.compute_mex
No method 'compute_mex' with matching signature found.

then you haven't compiled the MEX files in corticothalamic-model properly.