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README.md
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run_tvb_nipype.py
setup.sh
sim_instructions.txt
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tvb_environment.yml
tvb_interface.py
tvb_nipype_connectivity.py
tvb_nipype_demo.py
tvb_nipype_interface.ipynb
tvb_nipype_interface_presentation.ipynb
tvb_nipype_spec.json
tvb_nipype_template.py
tvb_nipype_testrun.py
tvb_nipype_widgets.ipynb
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README.md

TVB simulations in nipype

SETUP

git clone https://github.com/amandakeasson/tvb_nipype
cd tvb_nipype
conda env create --name tvbenv --file tvb_environment.yml
source activate tvbenv

If you are using a Mac, also run this command:

echo "backend: TkAgg" > ~/.matplotlib/matplotlibrc

RUNNING TVB_NIPYPE

Put all structural connectivity data in the input folder. Each file is a .mat file which contains sc_weights and tract_lengths for a subject.

From within your tvb_nipype directory modify the template file called tvb_nipype_spec.json. The iterables field specifies the parameters for which you would like to test multiple values; the inputs field specifies parameters for which you would like to fix at a single value.

Then, simply run

python run_tvb_nipype.py pse_name nproc 

where pse_name is the name for your set of simualtions and nproc is the number of processes to launch in parallel.

LICENCE

This is released under the MIT licence, but please make sure that you are following the licences of our dependencies, for example tvb-library is released under the GPL licence.