Examples update (#297)

* Only include generic examples. * Two different CTF examples. * Added message/link for oxford-ohba examples. * Updated readme.
OHBA-analysis · May 27, 2024 · 252e3e7 · 252e3e7
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diff --git a/examples/README.md b/examples/README.md
@@ -1,6 +1,6 @@
 Example Scripts
 ---------------
 
-- See the `oxford` directory for scripts for preprocessing/source reconstructing data collected at OHBA.
-- See the `parallelisation` directory for how to parallelise a script in OSL.
-- The other directories are scripts for preprocessing/source reconstructing public M/EEG dataset.
+This directory contains generic scripts for preprocessing/source reconstructing MEG data collected with different scanners.
+
+For example scripts for various public M/EEG datasets, see https://github.com/OHBA-analysis/OHBA-Examples.
diff --git a/examples/camcan/1_preprocess.py b/examples/camcan/1_preprocess.py
diff --git a/examples/camcan/2_coregister.py b/examples/camcan/2_coregister.py
diff --git a/examples/camcan/3_source_reconstruct.py b/examples/camcan/3_source_reconstruct.py
diff --git a/examples/camcan/4_sign_flip.py b/examples/camcan/4_sign_flip.py
diff --git a/examples/camcan/5_save_npy.py b/examples/camcan/5_save_npy.py
diff --git a/examples/camcan/README.md b/examples/camcan/README.md
diff --git a/examples/ctf/ctf_with_headshape_pos/1_preprocess.py b/examples/ctf/ctf_with_headshape_pos/1_preprocess.py
@@ -0,0 +1,36 @@
+"""Preprocess CTF data.
+
+"""
+
+# Authors: Chetan Gohil <chetan.gohil@psych.ox.ac.uk>
+
+from osl import preprocessing
+
+# Settings
+config = """
+    preproc:
+    - filter: {l_freq: 1, h_freq: 125, method: iir, iir_params: {order: 5, ftype: butter}}
+    - notch_filter: {freqs: 50 100}
+    - resample: {sfreq: 250}
+    - bad_segments: {segment_len: 500, picks: mag}
+    - bad_segments: {segment_len: 500, picks: mag, mode: diff}
+    - bad_channels: {picks: mag}
+    - interpolate_bads: {}
+"""
+
+# Create a list of paths to files to preprocess
+inputs = [
+    "data/raw/Nottingham/sub-not001/meg/sub-not001_task-resteyesopen_meg.ds",
+    "data/raw/Nottingham/sub-not002/meg/sub-not002_task-resteyesopen_meg.ds",
+]
+
+# Directory to save output to
+outdir = "data/preproc"
+
+# Do preprocessing
+preprocessing.run_proc_batch(
+    config,
+    inputs,
+    outdir=outdir,
+    overwrite=True,
+)