Artifact correction with intracranial channels - Revision history

Jaehyun at 13:23, 2 February 2021

2021-02-02T13:23:11Z

Harald at 12:03, 2 February 2021

2021-02-02T12:03:03Z

Vibhin at 11:54, 2 February 2021

2021-02-02T11:54:13Z

Vibhin at 11:41, 2 February 2021

2021-02-02T11:41:40Z

Vibhin at 11:34, 2 February 2021

2021-02-02T11:34:16Z

Vibhin at 11:32, 2 February 2021

2021-02-02T11:32:03Z

Vibhin at 11:22, 2 February 2021

2021-02-02T11:22:31Z

Vibhin at 11:17, 2 February 2021

2021-02-02T11:17:34Z

Vibhin at 11:08, 2 February 2021

2021-02-02T11:08:53Z

Vibhin at 11:07, 2 February 2021

2021-02-02T11:07:38Z

@@ Line 10: / Line 10: @@
 Intracranial channels may contain artifacts, e.g. if a stimulation is applied. These can be corrected using ICA. However, ICA is only available for scalp channels. Thus, for the purpose of artifact correction, it is necessary to re-label these channels as scalp channels.
-•	Create an *.ela file that lists the channel labels as EEG channels
+* Create an *.ela file that lists the channel labels as EEG channels
+* Create an *.sfp file with hypothetical coordinates for the EEG channels
-•	Create an *.sfp file with hypothetical coordinates for the EEG channels
+* Load these files into BESA using the channel and digitized head surface point dialog
+* Perform an ICA over a screen that shows the artifact
-•	Load these files into BESA using the channel and digitized head surface point dialog
+* Export the file without the ICA artifact components
+* Optional: Use the stimulus component to create tags via pattern search, and export the tags for later use as averaging trigger
-•	Perform an ICA over a screen that shows the artifact
+* Load the exported file, and (optionally) import the tags, average over the tags, and analyse the averaged data
-−
-•	Export the file without the ICA artifact components
-−
-•	Optional: Use the stimulus component to create tags via pattern search, and export the tags for later use as averaging trigger
-−
-•	Load the exported file, and (optionally) import the tags, average over the tags, and analyse the averaged data
 Caution: Any operation that requires coordinates (like mapping, source analysis, virtual channel montaging, source montaging, PCA-based artifact correction that models brain activity) is discouraged, as coordinates are wrong, and as the underlying assumption that the channels are on the scalp is invalid!
 == Step-by-step explanation ==
+# Create an *.ela file that lists the channel labels as EEG channels.
+#* Simply list the channel labels that should be used in the analysis in a text file like in the example below.
-	Create an *.ela file that lists the channel labels as EEG channels
+#: [[File:1.jpg]]
-Simply list the channel labels that should be used in the analysis in a text file like in the example below.
+# Create an *.sfp file with hypothetical coordinates for the EEG channels.
+#* For the channels in the *.ela file, provide fictitious coordinates. It is probably best to vary coordinates somewhat. The first 3 lines need to contain fiducials – then the channels are listed.
-[[File:1.jpg]]
+#: [[File:2_vv1.jpg]]
+# Load these files into BESA using the channel and digitized head surface point dialog.
+#* After opening the file, use CTRL-L to specify these files as shown in the example below.
-	Create an *.sfp file with hypothetical coordinates for the EEG channels
+#: [[File:3_vv.jpg|600px]]
-For the channels in the *.ela file, provide fictitious coordinates. It is probably best to vary coordinates somewhat.
+# Perform an ICA over a screen that shows the artifact.
-The first 3 lines need to contain fiducials – then the channels are listed.
+#* The ICA will disentangle the components and show the artifact. Please note that the screen needs to contain one or more artifacts – adjust time scaling and position accordingly.
+#: [[File:4_vv.jpg|600px]]
-[[File:2_vv1.jpg]]
+# Export the file without the ICA artifact components
+#* Mark the ICA components which carry the artifact by clicking on the labels (hold down the CTRL key if more than one), and right-click to select the export option for the whole file as shown below.
-	Load these files into BESA using the channel and digitized head surface point dialog
+#: [[File:5_vv.jpg|600px]]
-After opening the file, use CTRL-L to specify these files as shown in the example below.
+# Optional: Use the stimulus component to create tags via pattern search, and export the tags for later use as averaging trigger
+#* This step is optional and makes sense if you want to use the stimulus artifact as a trigger event for averaging or time-frequency analysis. Mark the pattern of interest, select the ICA component where it shows the clearest signal, and press “SAW” to find this pattern in the file, and tag with the “Pattern 1” tag.
-[[File:3_vv.jpg]]
+#* Then export the event file that contains this tag with the menu “ERP &rarr; Save Events As”.
+#: [[File:6_vv.jpg|600px]]
-	Perform an ICA over a screen that shows the artifact
+# Load the exported file, and (optionally) import the tags, average over the tags, and analyse the averaged data
-The ICA will disentangle the components and show the artifact. Please note that the screen needs to contain one or more artifacts – adjust time scaling and position accordingly.
+#* To import the tags, use the menu “ERP &rarr; Open Event File”.
+#: [[File:7_vv.jpg]]
-[[File:4_vv.jpg]]
+# To average over the events, select “Tags &rarr; Pattern 1”, “Search &rarr; Tagged Events”, and press “SAW”.
+#* You may want to adjust the default block epoch in “Edit &rarr; Default Block Epoch” before starting the average in order to adjust the width of the average buffer. The example below shows an average buffer of 2 seconds before and after the stimulus.
-	Export the file without the ICA artifact components
+#: <div><ul><li style="display: inline-block;"> [[File:8_vv.jpg|thumb|600px]] </li><li style="display: inline-block;"> [[File:9_vv.jpg|thumb|600px]] </li></ul></div>
-Mark the ICA components which carry the artifact by clicking on the labels (hold down the CTRL key if more than one), and right-click to select the export option for the whole file as shown below.
+# Note that it is also possible to perform time-frequency analysis on these data. To do this, you will need to convert the tags into triggers first using ERP &rarr; Edit Triggers. Then use the ERP &rarr; Coherence to define the condition and run time-frequency analysis.
-−
 [[File:5_vv.jpg]]
-−
-−
-	Optional: Use the stimulus component to create tags via pattern search, and export the tags for later use as averaging trigger
 This step is optional and makes sense if you want to use the stimulus artifact as a trigger event for averaging or time-frequency analysis. Mark the pattern of interest, select the ICA component where it shows the clearest signal, and press “SAW” to find this pattern in the file, and tag with the “Pattern 1” tag.
-−
-Then export the event file that contains this tag with the menu “ERP->Save Events As”.
-−
 [[File:6_vv.jpg]]
-−
-	Load the exported file, and (optionally) import the tags, average over the tags, and analyse the averaged data
-To import the tags, use the menu “ERP->Open Event File”.
-−
 [[File:7_vv.jpg]]
-−
-To average over the events, select “Tags->Pattern 1”, “Search->Tagged Events”, and press “SAW”. You may want to adjust the default block epoch in “Edit->Default Block Epoch” before starting the average in order to adjust the width of the average buffer. The example below shows an average buffer of 2 seconds before and after the stimulus.
-−
 [[File:8_vv.jpg]]
 [[File:9_vv.jpg]]
-−
-Note that it is also possible to perform time-frequency analysis on these data. To do this, you will need to convert the tags into triggers first using ERP->Edit Triggers. Then use the ERP->Coherence to define the condition and run time-frequency analysis.
 [[Category:Preprocessing]]

@@ Line 78: / Line 78: @@
 Note that it is also possible to perform time-frequency analysis on these data. To do this, you will need to convert the tags into triggers first using ERP->Edit Triggers. Then use the ERP->Coherence to define the condition and run time-frequency analysis.
-[[Category:Research Manual]]
+[[Category:Preprocessing]]
-[[Category:Methods]]
-[[Category:Mathematical]]
 {{BESAManualNav}}

@@ Line 11: / Line 11: @@
 •	Create an *.ela file that lists the channel labels as EEG channels
 •	Create an *.sfp file with hypothetical coordinates for the EEG channels
 •	Load these files into BESA using the channel and digitized head surface point dialog
 •	Perform an ICA over a screen that shows the artifact
 •	Export the file without the ICA artifact components
 •	Optional: Use the stimulus component to create tags via pattern search, and export the tags for later use as averaging trigger
 •	Load the exported file, and (optionally) import the tags, average over the tags, and analyse the averaged data

@@ Line 45: / Line 45: @@
 The ICA will disentangle the components and show the artifact. Please note that the screen needs to contain one or more artifacts – adjust time scaling and position accordingly.
-[[File:4_vv1.jpg]]
+[[File:4_vv.jpg]]
 	Export the file without the ICA artifact components

@@ Line 35: / Line 35: @@
 The first 3 lines need to contain fiducials – then the channels are listed.
-[[File:2_vv.jpg]]
+[[File:2_vv1.jpg]]
 	Load these files into BESA using the channel and digitized head surface point dialog