From 36e4850df18da0ba2208ec25d2f1323c68476e7e Mon Sep 17 00:00:00 2001 From: Deepa Gupta Date: Sat, 1 Jul 2023 22:10:36 -0700 Subject: [PATCH 1/2] Update EEG_sources.md DIPFIT plugin hyperlinked, Heading edited from EEG to EEG or ERP, added fieldtrip-lite plugin installation requirement, added "Background" and "Implementation", tutorial appendix added in the the relevant section --- tutorials/09_source/EEG_sources.md | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/tutorials/09_source/EEG_sources.md b/tutorials/09_source/EEG_sources.md index ac4d27cf..6dc59dad 100644 --- a/tutorials/09_source/EEG_sources.md +++ b/tutorials/09_source/EEG_sources.md @@ -5,7 +5,7 @@ long_title: c. EEG source model parent: 9. Source analysis grand_parent: Tutorials --- -Equivalent dipole source localization of EEG data +Equivalent dipole source localization of EEG or ERP data ======================================== {: .no_toc } @@ -21,9 +21,9 @@ Equivalent dipole source localization of EEG data Using DIPFIT to fit one dipole to EEG or ERP scalp maps -------- -Though the implementation of the DIPFIT plugin has not been expressly -designed to fit dipoles to raw ERP or EEG scalp maps, EEGLAB provides a -command-line function allowing DIPFIT to do so. Fitting may only be +EEGLAB provides a command-line implementation of the [DIPFIT plugin](https://github.com/sccn/dipfit) to fit +dipoles to raw ERP or EEG scalp maps that has otherwise not been +expressly designed anywhere else. Fitting may only be performed at selected time points, not throughout a time window. First, you must specify the DIPFIT settings on the selected dataset. Then, to fit a time point at 100 ms in an average ERP waveform (for example) from the @@ -67,7 +67,7 @@ Its graphical output is the same as the script shown in the next section. Advanced source reconstruction using DIPFIT/Fieldtrip -------- -DIPFIT relies on Fieldtrip, though in fact, DIPFIT was also an ancestor +Background: DIPFIT relies on Fieldtrip, though in fact, DIPFIT was also an ancestor of Fieldtrip: when Robert Oostenveld, the first Fieldtrip developer, decided to release source imaging functions he had developed during his dissertation work, he first packaged them in EEGLAB as DIPFIT. A few @@ -78,7 +78,7 @@ maintained for use in Fieldtrip. Below is a short tutorial on how to perform source modeling using Fieldtrip applied to data in an EEGLAB dataset. -First, use DIPFIT to align the electrode +Implementation: First, use DIPFIT to align the electrode locations with a head model of choice (menu item Tools → Locate dipoles using DIPFIT → Head model and settings). The resulting DIPFIT information may then be used to perform source localization in @@ -108,7 +108,8 @@ EEG = pop_dipfit_settings( EEG, 'hdmfile',fullfile(bemPath, 'standard_vol.mat'), Then calculate a volumetric leadfield matrix using Fieldtrip function *ft_prepare_leadfield*. Note that the head model is also used to -assess whether a given voxel is within or outside the brain. +assess whether a given voxel is within or outside the brain. (Note: Please ensure that the Fieldtrip-lite plugin is installed. If not, please go to File → Manage EEGLAB extensions to install the Fieldtrip-lite plugin in EEGLAB.) + ``` matlab %% Leadfield Matrix calculation @@ -308,6 +309,7 @@ Relevant Fieldtrip tutorials - [Minimum norm estimates](http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate/) for MEG, but can be adapted for EEG +- [Previous tutorial version of DIPFIT](https://sccn.ucsd.edu/eeglab/dipfittut/dipfit.htmlold) This section was written by Arnaud Delorme with contributions and feedback from Robert Oostenveld and Scott Makeig. From f18165a80a6e403a7fbd6f6a9389b41eaed64ea1 Mon Sep 17 00:00:00 2001 From: Arnaud Delorme Date: Mon, 10 Jul 2023 09:16:07 -1000 Subject: [PATCH 2/2] Update EEG_sources.md --- tutorials/09_source/EEG_sources.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tutorials/09_source/EEG_sources.md b/tutorials/09_source/EEG_sources.md index 6dc59dad..d5d9f9fe 100644 --- a/tutorials/09_source/EEG_sources.md +++ b/tutorials/09_source/EEG_sources.md @@ -108,7 +108,7 @@ EEG = pop_dipfit_settings( EEG, 'hdmfile',fullfile(bemPath, 'standard_vol.mat'), Then calculate a volumetric leadfield matrix using Fieldtrip function *ft_prepare_leadfield*. Note that the head model is also used to -assess whether a given voxel is within or outside the brain. (Note: Please ensure that the Fieldtrip-lite plugin is installed. If not, please go to File → Manage EEGLAB extensions to install the Fieldtrip-lite plugin in EEGLAB.) +assess whether a given voxel is within or outside the brain. ``` matlab