Merge branch 'spm:main' into main

Y-Bezs · web-flow · commit a8cddb9fdab2 · 2024-07-19T16:17:14.000+01:00
diff --git a/docs/assets/figures/daiss/beamforming/opm_coreg.png b/docs/assets/figures/daiss/beamforming/opm_coreg.png
diff --git a/docs/assets/figures/daiss/beamforming/opm_eigenspectrum_post.png b/docs/assets/figures/daiss/beamforming/opm_eigenspectrum_post.png
diff --git a/docs/assets/figures/daiss/beamforming/opm_eigenspectrum_pre.png b/docs/assets/figures/daiss/beamforming/opm_eigenspectrum_pre.png
diff --git a/docs/courses/eeg_meg/recordings/bayesian_inference.md b/docs/courses/eeg_meg/recordings/bayesian_inference.md
@@ -0,0 +1,7 @@
+# Bayesian inference
+
+In this talk, [Dr Dimitrios Pinotsis](https://www.city.ac.uk/about/people/academics/dimitrios-pinotsis) introduces the concepts underpinning Bayesian analysis.
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/mkkAKoIIHTY?si=Pu_mcFE6w0WwoyDl" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+
+--8<-- "addons/abbreviations.md"
diff --git a/docs/courses/eeg_meg/recordings/bayesian_model_selection.md b/docs/courses/eeg_meg/recordings/bayesian_model_selection.md
@@ -0,0 +1,7 @@
+# Bayesian model selection and averaging
+
+In this talk, [Dr Peter Zeidman](https://peterzeidman.co.uk) describes Bayesian model selection and averaging.
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/O3mAnlD4ibU?si=4_S-c3n-mbXK5E3Q" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+
+--8<-- "addons/abbreviations.md"
diff --git a/docs/courses/eeg_meg/recordings/daiss.md b/docs/courses/eeg_meg/recordings/daiss.md
@@ -0,0 +1,7 @@
+# DAiSS: An SPM toolbox for alternate source imaging approaches (talk & demo)
+
+In this talk, [Dr George O'Neill](https://profiles.ucl.ac.uk/74645-george-o%27neill) introduces and demonstrates DAiSS, a toolbox for alternate source reconstruction approaches. 
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/3S_VQbewl9w?si=k0oMjDoAcRMR3dqf" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+
+--8<-- "addons/abbreviations.md"
diff --git a/docs/courses/eeg_meg/recordings/dcm_cross_spectral_desities.md b/docs/courses/eeg_meg/recordings/dcm_cross_spectral_desities.md
@@ -0,0 +1,11 @@
+# DCM for cross-spectral densities (talk & DCM demo)
+
+In this talk, [Dr Johan Medrano](https://profiles.ucl.ac.uk/91185-johan-medrano) introduces DCM for cross-spectral densities.
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/ZbeZmxERRho?si=rxKc0MKKASBc8VZB" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+
+The DCM series finishes with a practical demonstration of DCM analysis of EEG data delivered by [Julia Rodriguez Sanchez](https://profiles.ucl.ac.uk/79115-julia-rodriguez-sanchez/about).
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/oocLux1lBMI?si=-l90Z0CvFur_4eUk" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+
+--8<-- "addons/abbreviations.md"
diff --git a/docs/courses/eeg_meg/recordings/dcm_evoked_responses.md b/docs/courses/eeg_meg/recordings/dcm_evoked_responses.md
@@ -0,0 +1,7 @@
+# DCM for evoked responses
+
+In this talk, [Dr Daniel Hauke](https://profiles.ucl.ac.uk/92790-daniel-hauke) describes the application of DCM for evoked responses paradigms. 
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/c3lrMfEHTSs?si=95J9r8dI9qUFLF9_" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+
+--8<-- "addons/abbreviations.md"
diff --git a/docs/courses/eeg_meg/recordings/dcm_principles.md b/docs/courses/eeg_meg/recordings/dcm_principles.md
@@ -0,0 +1,7 @@
+# The principles of dynamic causal modelling (DCM)
+
+In this talk, [Dr Amirhossein Jafarian](https://ftd.neurology.cam.ac.uk/directory/A_Jafarian) introduces dynamic causal modelling (DCM).
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/tD9peFEq1KQ?si=Bl4srE06bW1oq8Xa" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+
+--8<-- "addons/abbreviations.md"
diff --git a/docs/courses/eeg_meg/recordings/glm_classical_inference.md b/docs/courses/eeg_meg/recordings/glm_classical_inference.md
@@ -0,0 +1,7 @@
+# General linear model (GLM) and classical inference 
+
+In this talk, [Dr Zita Patai](https://spierslab.com/zita-patai/) describes how to model EEG and MEG data using the general linear model (GLM) framework and how to make inferences from your data. 
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/ZmTQTk0n4sY?si=Nkr-v7f4DHjVQqGS" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+
+--8<-- "addons/abbreviations.md"
diff --git a/docs/courses/eeg_meg/recordings/glm_convolutional.md b/docs/courses/eeg_meg/recordings/glm_convolutional.md
@@ -0,0 +1,7 @@
+# Convolutional GLM
+
+In this talk, [Dr Ashwani Jha](https://profiles.ucl.ac.uk/4064-ashwani-jha) describes advanced applications of the GLM.
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/8CugqEilaa0?si=QlLhAQh4t7URh-PR" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+
+--8<-- "addons/abbreviations.md"
diff --git a/docs/courses/eeg_meg/recordings/group_analysis.md b/docs/courses/eeg_meg/recordings/group_analysis.md
@@ -0,0 +1,7 @@
+# Group M/EEG data analysis
+
+In this talk, [Dr Jason Taylor](https://research.manchester.ac.uk/en/persons/jason.taylor) describes how to collate individual participant EEG and MEG data to perform group-level analysis.
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/PfRLlUTrCWA?si=abLjfy1uAH4K6W86" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+
+--8<-- "addons/abbreviations.md"
diff --git a/docs/courses/eeg_meg/recordings/index.md b/docs/courses/eeg_meg/recordings/index.md
@@ -0,0 +1,23 @@
+# M/EEG course lecture recordings
+
+Our SPM courses include both lectures and interactive workshops. We make videos of the lectures freely available.
+
+## Recent recordings and slides
+- [Introduction & resources](./introduction.md)
+- [What are we measuring with M/EEG?](./what_measured.md)
+- [Data preprocessing (talk & demo)](./preprocessing.md)
+- [General linear model (GLM) and classical inference](./glm_classical_inference.md)
+- [Convolutional GLM](./glm_convolutional.md)
+- [Multiple comparisons - problems & solutions](./multiple_comparisons.md)
+- [Analysis of optically pumped magnetometer (OPM) data (talk & demo)](./opm_analysis.md)
+- [Bayesian inference](./bayesian_inference.md)
+- [M/EEG source analysis (talk & demo)](./source_analysis.md)
+- [The principles of dynamic causal modelling (DCM)](./dcm_principles.md)
+- [DCM for evoked responses](./dcm_evoked_responses.md)
+- [DCM for cross-spectral densities (talk & DCM demo)](./dcm_cross_spectral_desities.md)
+- [Bayesian model selection and averaging](./bayesian_model_selection.md)
+- [DAiSS: An SPM toolbox for alternate source imaging approaches (talk & demo)](./daiss.md)
+- [Group M/EEG data analysis](./group_analysis.md)
+
+## Older recordings
+Recordings from earlier SPM courses are available [here](https://www.fil.ion.ucl.ac.uk/spm/course/video/). These are hosted on UCL's website, and therefore may be helpful if you do not have access to Youtube.
diff --git a/docs/courses/eeg_meg/recordings/introduction.md b/docs/courses/eeg_meg/recordings/introduction.md
@@ -0,0 +1,7 @@
+# Introduction & resources
+
+In this talk, [Prof Vladimir Litvak](https://profiles.ucl.ac.uk/10801-vladimir-litvak) introduces the concepts underpinning EEG & MEG analysis in SPM.
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/jDGTJrX8W1Y?si=iKQl5DMMFDxXbpR9" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+
+--8<-- "addons/abbreviations.md"
diff --git a/docs/courses/eeg_meg/recordings/multiple_comparisons.md b/docs/courses/eeg_meg/recordings/multiple_comparisons.md
@@ -0,0 +1,7 @@
+# Multiple comparisons - problems & solutions
+
+In this talk, [Dr Tim Tierney](https://profiles.ucl.ac.uk/41354-tim-tierney) outlines the problem of multiple comparisons in imaging statistics and the potential solutions that can be used to account for it.
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/ZtRKxI-RR9k?si=Uf8w0Acq23Ji3XrN" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+
+--8<-- "addons/abbreviations.md"
diff --git a/docs/courses/eeg_meg/recordings/opm_analysis.md b/docs/courses/eeg_meg/recordings/opm_analysis.md
@@ -0,0 +1,11 @@
+# Analysis of optically pumped magnetometer (OPM) data (talk & demo)
+
+In this talk, [Dr Stephanie Mellor](https://profiles.ucl.ac.uk/63631-stephanie-mellor) describes the approaches used in the analysis of optically pumped magnetometer (OPM) data.
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/clnwtTC0ZBA?si=7Y3KIjLYh7qTtvLA" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+
+In the related companion video, [Dr Robert Seymour](https://profiles.ucl.ac.uk/74338-robert-seymour) provides a practical demonstration of OPM analysis.
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/kWK7z-SYa6Y?si=MUW2Jdz8mA2nfPSL" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+
+--8<-- "addons/abbreviations.md"
diff --git a/docs/courses/eeg_meg/recordings/preprocessing.md b/docs/courses/eeg_meg/recordings/preprocessing.md
@@ -0,0 +1,11 @@
+# Data preprocessing (talk & demo)
+
+In this talk, [Dr Nicholas Alexander](https://profiles.ucl.ac.uk/74968-nicholas-alexander) outlines the steps involved in preprocessing EEG & MEG data. 
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/eFNBAHJNRVk?si=M1PvMGdSqbpFB3bV" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+
+In the companion video below, [Andrew Levy](https://profiles.ucl.ac.uk/55429-andrew-levy) provides a practical demonstration of EEG and MEG preprocessing in SPM. 
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/zlYtJF4pzo4?si=IDDJQnykyW_mBgti" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+
+--8<-- "addons/abbreviations.md"
diff --git a/docs/courses/eeg_meg/recordings/source_analysis.md b/docs/courses/eeg_meg/recordings/source_analysis.md
@@ -0,0 +1,11 @@
+# M/EEG source analysis (talk & demo)
+
+In this talk, [Dr Mansoureh Fahimi](https://profiles.ucl.ac.uk/87018-mansoureh-fahimi-hnazaee) describes source analysis for EEG and MEG.
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/R1elEBRbwE0?si=IwQbM07cLwkIj-YV" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+
+In the companion video, [Dr Meaghan Spedden](https://scholar.google.com/citations?user=5B41AG0AAAAJ&hl=da) shows a practical demonstration of source reconstruction.
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/ssmmhfHmWA8?si=rYnlj7-PglpG9Ukv" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+
+--8<-- "addons/abbreviations.md"
diff --git a/docs/courses/eeg_meg/recordings/what_measured.md b/docs/courses/eeg_meg/recordings/what_measured.md
@@ -0,0 +1,7 @@
+# What are we measuring with M/EEG?
+
+In this talk, [Dr Catharina Zich](https://www.mrcbndu.ox.ac.uk/people/dr-catharina-zich) describes the nature of signals measured with EEG and MEG. 
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/FhjTkeDhZ58?si=kcfb6KtIg6qMnAHO" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" referrerpolicy="strict-origin-when-cross-origin" allowfullscreen></iframe>
+
+--8<-- "addons/abbreviations.md"
diff --git a/docs/courses/fmri_vbm/recordings/fmri_legacy_recordings.md b/docs/courses/fmri_vbm/recordings/fmri_legacy_recordings.md
@@ -0,0 +1,12 @@
+# Earlier SPM for MRI course recordings
+Our latest recordings are available via the menu and are hosted on Youtube. The earlier recordings, below, may be useful if you do not have access to Youtube.
+
+### Spatial Preprocessing - John Ashburner
+<div style="position:relative;padding-bottom:56%;padding-top:20px;height:0;"><iframe src="https://mediacentral.ucl.ac.uk/player?autostart=n&videoId=66cjhjCc&captions=y&chapterId=0&playerJs=n" frameborder="0" scrolling="no" style="position:absolute;top:0;left:0;width:100%;height:100%;" allowfullscreen></iframe></div>
+
+### Contrasts and Classical Inference - Christophe Phillips
+<div style="position:relative;padding-bottom:56%;padding-top:20px;height:0;"><iframe src="https://mediacentral.ucl.ac.uk/player?autostart=n&videoId=j3EBj99f&captions=y&chapterId=0&playerJs=n" frameborder="0" scrolling="no" style="position:absolute;top:0;left:0;width:100%;height:100%;" allowfullscreen></iframe></div>
+
+### Random Field Theory and Alternatives - Tom Nichols
+<div style="position:relative;padding-bottom:56%;padding-top:20px;height:0;"><iframe src="https://mediacentral.ucl.ac.uk/player?autostart=n&videoId=Cb70D2J4&captions=y&chapterId=0&playerJs=n" frameborder="0" scrolling="no" style="position:absolute;top:0;left:0;width:100%;height:100%;" allowfullscreen></iframe></div>
+
diff --git a/docs/courses/fmri_vbm/recordings/index.md b/docs/courses/fmri_vbm/recordings/index.md
@@ -0,0 +1,19 @@
+# MRI course lecture recordings
+
+Our SPM courses include both lectures and interactive workshops. We make videos of the lectures freely available.
+
+## Recent recordings and slides
+- [Spatial preprocessing](./preprocessing.md)
+- [General linear model](./glm.md)
+- [Contrasts & classical inference](./contrasts_classical_inference.md)
+- [Group analysis](./group_analysis.md)
+- [Random field theory](./random_field_theory.md)
+- [Voxel-based morphometry](./vbm.md)
+- [Experimental design](./experimental_design.md)
+- [Event-related fMRI](./event_related_fmri.md)
+- [Bayesian inference](./bayesian_inference.md)
+- [Introduction to DCM](./dcm_introduction.md)
+- [DCM: Testing hypotheses](./dcm_hypothesis_testing.md)
+
+## Older recordings
+Recordings from earlier SPM courses are available [here](./fmri_legacy_recordings.md). These are hosted on UCL's website, and therefore may be helpful if you do not have access to Youtube.
diff --git a/docs/tutorials/daiss/beamforming/opm/index.md b/docs/tutorials/daiss/beamforming/opm/index.md
diff --git a/mkdocs.yml b/mkdocs.yml
