From a6795432838117a76d1b84f40b9cbaa0ef9f63d5 Mon Sep 17 00:00:00 2001 From: Daniel McCloy Date: Tue, 2 Jul 2019 18:30:11 -0800 Subject: [PATCH 1/3] DOC: add list of side-packages --- doc/install/pre_install.rst | 34 ++++++++++++++++++++++++++++++---- 1 file changed, 30 insertions(+), 4 deletions(-) diff --git a/doc/install/pre_install.rst b/doc/install/pre_install.rst index f21cadab628..ad3cb0b15dd 100644 --- a/doc/install/pre_install.rst +++ b/doc/install/pre_install.rst @@ -28,10 +28,23 @@ Overview of the MNE tools suite - :doc:`MNE-CPP <../mne_cpp>` provides core MNE functionality implemented in C++ and is primarily intended for embedded and real-time applications. -There are also Python tools for easily importing MEG data from the Human -Connectome Project for use with MNE-Python (`MNE-HCP`_), and tools for -managing MNE projects so that they comply with the -`Brain Imaging Data Structure`_ specification (`MNE-BIDS`_). +There is also a growing ecosystem of other Python packages that work alongside +MNE-Python, including packages for: + +- easily importing MEG data from the Human Connectome Project for + use with MNE-Python (`MNE-HCP`_) +- managing MNE projects so that they comply with the `Brain + Imaging Data Structure`_ specification (`MNE-BIDS`_) +- automatic bad channel detection and interpolation (`autoreject`_) +- sparse dictionary learning (`alphaCSC`_) +- preconditioned ICA for real data (`PICARD`_) +- phase-amplitude coupling (`pactools`_) +- representational similarity analysis (`rsa`_) +- microstate analysis (`microstate`_) +- connectivity analysis using dynamic imaging of coherent sources (`conpy`_) +- general-purpose statistical analysis of M/EEG data (`eelbrain`_) +- post-hoc modification of linear models (`posthoc`_) + What should I install? ^^^^^^^^^^^^^^^^^^^^^^ @@ -69,3 +82,16 @@ simplify your example script to only the elements necessary to replicate the bug. **Next:** :doc:`mne_python` + + +.. LINKS: + +.. _autoreject: https://autoreject.github.io/ +.. _alphaCSC: https://alphacsc.github.io/ +.. _picard: https://pierreablin.github.io/picard/ +.. _pactools: https://pactools.github.io/ +.. _rsa: https://github.com/wmvanvliet/rsa +.. _microstate: https://github.com/wmvanvliet/mne_microstates +.. _conpy: https://aaltoimaginglanguage.github.io/conpy/ +.. _eelbrain: https://eelbrain.readthedocs.io/en/stable/index.html +.. _posthoc: https://users.aalto.fi/~vanvlm1/posthoc/python/ From 9e5d07df0d4532332868b4307d4ffbf835afd615 Mon Sep 17 00:00:00 2001 From: Daniel McCloy Date: Wed, 3 Jul 2019 10:27:15 -0800 Subject: [PATCH 2/3] Apply suggestions from code review Co-Authored-By: Alexandre Gramfort --- doc/install/pre_install.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/install/pre_install.rst b/doc/install/pre_install.rst index ad3cb0b15dd..71c12aa3b85 100644 --- a/doc/install/pre_install.rst +++ b/doc/install/pre_install.rst @@ -36,12 +36,12 @@ MNE-Python, including packages for: - managing MNE projects so that they comply with the `Brain Imaging Data Structure`_ specification (`MNE-BIDS`_) - automatic bad channel detection and interpolation (`autoreject`_) -- sparse dictionary learning (`alphaCSC`_) -- preconditioned ICA for real data (`PICARD`_) +- convolutional sparse dictionary learning and waveform shape estimation (`alphaCSC`_) +- independent component analysis (ICA) with good performance on real data (`PICARD`_) - phase-amplitude coupling (`pactools`_) - representational similarity analysis (`rsa`_) - microstate analysis (`microstate`_) -- connectivity analysis using dynamic imaging of coherent sources (`conpy`_) +- connectivity analysis using dynamic imaging of coherent sources (DICS) (`conpy`_) - general-purpose statistical analysis of M/EEG data (`eelbrain`_) - post-hoc modification of linear models (`posthoc`_) From 475e411b67ffb695934d234b981a37c4990cbaea Mon Sep 17 00:00:00 2001 From: Daniel McCloy Date: Wed, 3 Jul 2019 10:30:29 -0800 Subject: [PATCH 3/3] add MNELAB; fix long lines --- doc/install/pre_install.rst | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/doc/install/pre_install.rst b/doc/install/pre_install.rst index 71c12aa3b85..4a5953062f4 100644 --- a/doc/install/pre_install.rst +++ b/doc/install/pre_install.rst @@ -31,17 +31,21 @@ Overview of the MNE tools suite There is also a growing ecosystem of other Python packages that work alongside MNE-Python, including packages for: +- a graphical user interface for MNE-Python (`MNELAB`_) - easily importing MEG data from the Human Connectome Project for use with MNE-Python (`MNE-HCP`_) - managing MNE projects so that they comply with the `Brain Imaging Data Structure`_ specification (`MNE-BIDS`_) - automatic bad channel detection and interpolation (`autoreject`_) -- convolutional sparse dictionary learning and waveform shape estimation (`alphaCSC`_) -- independent component analysis (ICA) with good performance on real data (`PICARD`_) +- convolutional sparse dictionary learning and waveform shape estimation + (`alphaCSC`_) +- independent component analysis (ICA) with good performance on real data + (`PICARD`_) - phase-amplitude coupling (`pactools`_) - representational similarity analysis (`rsa`_) - microstate analysis (`microstate`_) -- connectivity analysis using dynamic imaging of coherent sources (DICS) (`conpy`_) +- connectivity analysis using dynamic imaging of coherent sources (DICS) + (`conpy`_) - general-purpose statistical analysis of M/EEG data (`eelbrain`_) - post-hoc modification of linear models (`posthoc`_) @@ -86,6 +90,7 @@ bug. .. LINKS: +.. _MNELAB: https://github.com/cbrnr/mnelab .. _autoreject: https://autoreject.github.io/ .. _alphaCSC: https://alphacsc.github.io/ .. _picard: https://pierreablin.github.io/picard/