add BIDS reference; update others

docs/literate/HowTo/ApplyPreprocessing.jl

@@ -1 +1 @@
-# placeholder
+# # Apply MNE preprocessing

docs/literate/reference/BIDS.jl

@@ -0,0 +1,38 @@
+# # Brain Imaging Data Structure
+# If you are using UnfoldBIDS we assume you are already familiar with the BIDS format.
+# However, since the package only works if your dataset is BIDS formatted, here is a quick reminder.
+# If you want a more in-depth explanation, please refer to the official [BIDS documentation](https://bids-specification.readthedocs.io/en/stable/)
+
+# ## Folder Structure
+# Folders have to follow the following structure:
+
+#       |-BIDS-Root/
+#           |--- [required meta files]
+#           |--- sub-<label>/
+#               |--- eeg/
+#                   |--- sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_eeg.<extension>
+#                   |--- sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_eeg.json
+#                   |--- sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_events.json
+#                   |--- sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_events.tsv
+#           |--- derivatives/ <- for (pre-processed data)
+#              |--- [required meta files]
+#              |--- sub-<label>/
+#                   |--- eeg/
+#                       |--- sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_eeg.<extension>
+#                       |--- sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_eeg.json
+#                       |--- sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_events.json
+#                       |--- sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_events.tsv
+
+# ## File formats
+# By BIDS standard your files have to be in one of the following formats:
+# *EEG*
+# - edf (European Data Fromat; single file)
+# - vhdr (BrainVision format; file triplet of .vhdr, .vmrk and .eeg)
+# - set (EEGLAB saved file; .fdt file optional)
+# - fif (MNE save file; not BIDS conform, but implemented for convenience)
+#
+# *Events*
+# UnfoldBIDS.jl will automatically try to load accompanying events.tsv files. Loading events from the EEG data files is currently not supported, and not BIDS conform.
+
+# ## BIDS Transformation
+# If your dataset is not yet BIDS conform you can use [MNE-BIDS](https://mne.tools/mne-bids/v0.5/index.html) to transform your data.

docs/literate/reference/overview.jl

@@ -1 +1 @@
-# placeholder
+# # Toolbox overview

docs/literate/tutorials/quickstart.jl

@@ -6,21 +6,32 @@ using UnfoldBIDS
 
 # To load use UnfoldBIDS to find the paths to all subject specific data you can uye the bidsLayout function:
 
-path_to_bids_root = "/store/data/2023EEGManyLabs"
-layout_df = bidsLayout(path_to_bids_root, derivative=false)
-
+# ```julia
+# path_to_bids_root = "/store/data/2023EEGManyLabs"
+# layout_df = bidsLayout(path_to_bids_root, derivative=false)
+# ```
 # This will give you a DataFrame containing the paths too the eeg files of all subjects plus their accompanying event files
 
 # !!! note
 #       Since we set the derivative keyword to false here UnfoldBIDS will only look for the raw EEG files. However, by default UnfoldBIDS assumes you have preprocessed data in a derivatives folder and try to look for those.
 
 # Subsequently, you can load the data of all subjects into memory
 
-eeg_df = load_bids_eeg_data(layout_df)
-
+# ```julia
+# eeg_df = load_bids_eeg_data(layout_df)
+# ```
+#
 # !!! note
 #       The data is not actually loaded into memory, but uses MNE's lazy loading functionality.
 
 # Lastly, current functionality only supports explicit loading of the events. In the future this will be done automatically with the previous step.
 
-load_events(layoutDF)
+# ```julia
+# events_df = load_events(layoutDF)
+# ```
+
+# ## Run unfold type models
+
+# ```julia
+# resultsAll = runUnfold(eeg_df, events_df, bfDict; channels=nothing, eventcolumn="trial_type")
+# ```

docs/make.jl

@@ -36,6 +36,7 @@ makedocs(;
         ],
         "Reference" => [
             "Overview: Toolbox Functions" => "./generated/reference/overview.md",
+            "Brain Imaging Data Structure" => "./generated/reference/BIDS.md"
         ],
         "HowTo" => [
             "Apply preprocessing functions" => "./generated/HowTo/ApplyPreprocessing.md",