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Update online-lfp.rst (#152)
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Replaces (out-of-date) instructions for how to create weights file with a link to the BlueRecording repository.
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joseph-tharayil authored and atemerev committed May 24, 2024
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Expand Up @@ -16,17 +16,7 @@ More information about this file can be found in the `SONATA Simulation Specific
Generating the Electrodes File
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The electrodes file can be generated using specific steps and considerations. Follow the instructions below to generate the file:

1. Produce a compartment report from a target including the cells that will be used for the LFP calculation.

2. Run the file getPositions.py, using the bash script GetPositions.sh. This will create a folder containing pickle files listing the (x,y,z) position of each segment in each cell in the target.

3. Run the file writeH5_MPI_prelim.py, using the bash script WriteH5Prelim.sh. This will create the weights file, populating all coefficients with 1s. The script writeH5_MPI_prelim.py will have to be modified depending on the desired electrode array; it currently creates the weights file for a Neuropixels probe.

4. Run the file writeH5_MPI.py, using the bash script WriteH5.sh. This populates the weights file with the correct coefficients. This step requires the use of a version of h5py built with MPI support. This two-step procedure is used because the calculation of the LFP coefficients is not feasible without parallelization, but MPI cannot be used when H5 files are created.

The files mentioned can be found `here <https://github.com/joseph-tharayil/create_lfp_weights_for_neurodamus>`_
The electrodes file can be generated using specific steps and considerations. Code and instructions to generate these files can be found `here <https://github.com/BlueBrain/BlueRecording>`_

Generating the LFP report
--------------------------
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