Python tools for processing HCP data using MNE-Python

This code is under active, research-driven development and the API is still unstable. At a later stage this code will likely be wrapped by MNE-Python to provide a more common API. For now consider the following caveats:

• we only intend to support a subset of the files shipped with HCP. Precisely, for now it is not planned to support io and processing for any outputs of the HCP inverse pipelines.
• the code is not covered by unit tests so far as I did not have the time to create mock testing data.
• this library breaks with some of MNE conventions due to peculiarities of the HCP data shipping policy. The basic IO is based on paths, not on files.

• MNE-Python master branch
• scipy
• numpy
• matplotlib

The following data layout is expected. A folder that contains the HCP data as they are unpacked by a zip, subject wise. See command that will produce this layout.

for fname in $(ls *zip); do
    echo unpacking $fname;
    unzip -o $fname; rm $fname;
done

The code is organized by different modules. The io module includes readers for sensor space data at different processing stages and annotations for baddata.

These are (all native coordinates + names):

hcp.io.read_info_hcp  # get channel info for rest | tasks and a given run
hcp.io.read_raw_hcp  # same for raw data
hcp.io.read_epochs_hcp  # same for epochs epochs
hcp.io.read_ica_hcp  # ica solution as dict
hcp.io.read_annot_hcp  # bad channels, segments and ICA annotations

All data readers have the same API for the first two positional arguments:

params = dict(
    subject='1003007',
    data_type='task_motor')  # assuming that data are unpacked here

# all MNE objects have native names and coordinates, some MNE functions might
# break.
info = hcp.io.read_info_hcp(**params)  # MNE object
raw = hcp.io.read_raw_hcp(**params)  # ...
epochs = hcp.io.read_epochs_hcp(**params) # ...
annotations_dict = hcp.io.read_annot_hcp(**params) # dict
ica_dict = hcp.io.read_ica_hcp(**params) # ...

MNE-HCP uses custom names for values that are more mne-pythonic, the following table gives an overview

For convenience several workflows are provieded. Currently the most supported is hcp.workflows.make_mne_anatomy, a convenience function that will create MNE friendly anatomy directories and extractes the head model and coregistration MEG to MRI coregistration. Yes it maps to MRI, not to the helmet -- a peculiarity of the HCP data. It can be used as follows:

hcp.workflows.anatomy.make_mne_anatomy(
    subject='100307', hcp_path='/media/crazy_disk/HCP',
    anatomy_path='/home/crazy_user/hcp-subjects',
    recordings_path='/home/crazy_user/hcp-meg',
    mode='full') # consider "minimal" for linking and writing less 

One core element of MNE-HCP is a file mapping that allows for quick selections of files for a given subejct and data context. This is done in hcp.io.file_mapping.get_file_paths, think of it as a file name synthesizer that takes certain data description parameters as inputs and lists all corresponding files.

Example usage:

files = hcp.io.get_file_paths(
    subject='123455', data_type='meg_anatomy', output='source_model',
    processing='unprocessed', hcp_path='/media/crazy_disk/HCP', onset='stim')

print(files)
# output:
['/media/crazy_disk/HCP/123455/unprocessed/MEG/None-anatomy/4D/c,rfDC',
 '/media/crazy_disk/HCP/123455/unprocessed/MEG/None-anatomy/4D/config']

Why we are not globbing files? Because the HCP-MEG data are fixed, all file patterns are known and access via Amazon web services easier if the files to be accessed are known in advance.

• currently @dengemann is pushing frequently to master, if you plan to contribute, open issues and pull requests, or contact @dengemann directly. Discussions are welcomed.

Are in the making, however at this points you still need to download the HCP data to run them.

This project is supported by the AWS Cloud Credits for Research program. Thanks Alex Gramfort, Giorgos Michalareas, Eric Larson and Jan-Mathijs Schoffelen for discussions, inputs and help with finding the best way to map HCP data to the MNE world. Thanks Virginie van Wassenhove for supporting this project.