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russellu / eegfmripy

python code for denoising eeg data from eeg-fmri experiments, and fusing with FMRI
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Stand-alone tool? #2

Closed gmierz closed 5 years ago

gmierz commented 5 years ago

Would this be something we would like? i.e. a tool we could invoke from bash/CLI that does not require MNE to be used.

If so, we could use python's setuptools tool, here's an example of what I am thinking: https://github.com/gmierz/coco-tools/blob/new_tool/setup.py

If we don't want anything like this, we can close this issue.

russellu commented 5 years ago

yes, this would definitely be useful. ideally, we would just input an EEG raw file and an FMRI raw file at the command line, and it would output things like source-space EEG-BOLD correlations, denoised EEG data, etc. we could start using it on simple cases like gradient and bcg denoising and then later extend it to the entire pipeline.

gmierz commented 5 years ago

This is setup now, we can run the following as a test:

python setup.py install
eegfmripy --list
eegfmripy examplecli
eegfmripy examplecli -c eegfmripy/clianalysis/config_examplecli.yml

See https://github.com/russellu/eegfmripy/blob/master/eegfmripy/clianalysis/examplecli.py for an example of how to create a new analysis like examplecli.

gmierz commented 5 years ago

This is fully implemented and running now for most scripts.