Setup real-time source localization example - Revision history

LorenzE at 00:03, 15 February 2019

2019-02-15T00:03:25Z

LorenzE at 17:29, 23 January 2017

2017-01-23T17:29:09Z

LorenzE at 17:24, 23 January 2017

2017-01-23T17:24:03Z

LorenzE at 09:20, 27 September 2016

2016-09-27T09:20:10Z

LorenzE at 09:11, 27 September 2016

2016-09-27T09:11:20Z

LorenzE at 09:09, 27 September 2016

2016-09-27T09:09:45Z

LorenzE at 15:39, 19 September 2016

2016-09-19T15:39:23Z

LorenzE: Created page with "This tutorial will show how you can setup an acquisition and processing chain in MNE Scan, which makes use of the real-time source localization. # Make sure you downloaded an..."

2016-09-19T15:26:34Z

Created page with "This tutorial will show how you can setup an acquisition and processing chain in MNE Scan, which makes use of the real-time source localization. # Make sure you downloaded an..."

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This tutorial will show how you can setup an acquisition and processing chain in MNE Scan, which makes use of the real-time source localization.

# Make sure you downloaded and correctly extracted the MNE Sample data set. If not, check for a step by step guide [[Get the sample data set|here]].
# Start ''mne_rt_server'' in your mne-cpp/bin folder
# Start ''mne_scan'' in your mne-cpp/bin folder
# Navigate to the ''Sensor Plugins'' and ''Algorithm Plugins'' buttons in the plugin window. Select and position the following plugins onto the plugin scene:
#* Sensor Plugins - FiffSimulator
#* Algorithm Plugins - Averaging
#* Algorithm Plugins - Covariance
#* Algorithm Plugins - MNE
# Select the ''Connection'' tool in the plugin window. Connect the plugins as follows by left clicking on the start, holding and releasing above the target plugin.
[[File:Mne_scan_rtMNE_setup.PNG|center|border|600px]]
# Click on the MNE plugin and wait until the ''Start Clustering'' button is clickable again
# Start the pipeline by clicking on the green play button in the left upper corner

@@ Line 2: / Line 2: @@
 The following steps will show you how to setup the online processing pipeline in MNE Scan:
-# Make sure you downloaded and correctly extracted the MNE Sample data set. If not, check for a step by step guide [[Get the sample data set|here]].
+# Make sure you downloaded and correctly extracted the MNE Sample data set. If not, check for a step by step guide [[Get the sample data set|here]]. On MacOS please make sure that you copied the MNE Sample data set to mne_scan.app/Contents/MacOS/ as well.
 # Start ''mne_rt_server'' in your mne-cpp/bin folder. It is important that the mne_rt_server is started before the mne_scan executable.
 # Start ''mne_scan'' in your mne-cpp/bin folder.

@@ Line 3: / Line 3: @@
 The following steps will show you how to setup the online processing pipeline in MNE Scan:
 # Make sure you downloaded and correctly extracted the MNE Sample data set. If not, check for a step by step guide [[Get the sample data set|here]].
-# Start ''mne_rt_server'' in your mne-cpp/bin folder.
+# Start ''mne_rt_server'' in your mne-cpp/bin folder. It is important that the mne_rt_server is started before the mne_scan executable.
 # Start ''mne_scan'' in your mne-cpp/bin folder.
 # Navigate to the ''Sensor Plugins'' and ''Algorithm Plugins'' buttons in the plugin window. Select and position the following plugins onto the plugin scene:

@@ Line 1: / Line 1: @@
-This tutorial will show how you can setup an acquisition and processing chain in MNE Scan, which makes use of the real-time source localization.
+This tutorial will show how you can setup an acquisition and processing chain in MNE Scan, which makes use of the real-time source localization method RTC-MNE.
-The following steps will show how to setup the online processing pipeline in MNE Scan:
+The following steps will show you how to setup the online processing pipeline in MNE Scan:
 # Make sure you downloaded and correctly extracted the MNE Sample data set. If not, check for a step by step guide [[Get the sample data set|here]].
 # Start ''mne_rt_server'' in your mne-cpp/bin folder.
@@ Line 12: / Line 12: @@
 # Select the ''Connection'' tool in the plugin window. Connect the plugins as follows by left clicking on the start, holding and releasing above the target plugin. <br /> [[File:Mne_scan_rtMNE_setup.PNG|center|border|600px]]
 # Click on the MNE plugin and wait until the ''Start Clustering'' button is clickable again.
 # Start the pipeline by clicking on the green play button in the left upper corner.
-Now that you setup and running the data acquisition and processing, we can start to configuresome parameters for the online processing:
+Now that you setup and are running the data acquisition/processing pipeline, we can start to configure some parameters for the online processing:
 # Click on the ''Averaging'' plugin.
 #* Click on the ''Averaging Adjustments'' button in the toolbar.
 #* Choose the correct trigger channel. Since we are making use of the MNE-Sample-Data-Set choose STI014.
-#* Once the averages are starting to come in you can take a look at the averaging in form of a butterfly and 2D layout plot. <br /> [[File:Mne_scan_rtMNE_setup_1.PNG|center|border|600px]]
+#* Once the averages are starting to come in you can take a look at the averaged data in form of a butterfly and 2D layout plot. <br /> [[File:Mne_scan_rtMNE_setup_1.PNG|center|border|600px]]
 # Click on the ''MNE'' plugin.
 #* Select the ''3D Control'' from the toolbar.
-#* Navigate to the ''RT Source Loc Data'' item.
+#* Navigate to the ''Data'' item.
 #* Now click on the item with the description "The value to normalize the source localization result".
 #* You should be prompted with the histogram based thresholding window. Use the right, middle and left mouse button to set the thresholds.
 #* The 3D view can be rotated using the middle and translated using the right mouse button. <br /> [[File:Mne_scan_rtMNE_setup_2.PNG|center|border|600px]]

@@ Line 3: / Line 3: @@
 The following steps will show how to setup the online processing pipeline in MNE Scan:
 # Make sure you downloaded and correctly extracted the MNE Sample data set. If not, check for a step by step guide [[Get the sample data set|here]].
-# Start ''mne_rt_server'' in your mne-cpp/bin folder
+# Start ''mne_rt_server'' in your mne-cpp/bin folder.
-# Start ''mne_scan'' in your mne-cpp/bin folder
+# Start ''mne_scan'' in your mne-cpp/bin folder.
 # Navigate to the ''Sensor Plugins'' and ''Algorithm Plugins'' buttons in the plugin window. Select and position the following plugins onto the plugin scene:
 #* Sensor Plugins - FiffSimulator
@@ Line 11: / Line 11: @@
 #* Algorithm Plugins - MNE
 # Select the ''Connection'' tool in the plugin window. Connect the plugins as follows by left clicking on the start, holding and releasing above the target plugin. <br /> [[File:Mne_scan_rtMNE_setup.PNG|center|border|600px]]
-# Click on the MNE plugin and wait until the ''Start Clustering'' button is clickable again
+# Click on the MNE plugin and wait until the ''Start Clustering'' button is clickable again.
-# Start the pipeline by clicking on the green play button in the left upper corner
+# Start the pipeline by clicking on the green play button in the left upper corner.
 Now that you setup and running the data acquisition and processing, we can start to configuresome parameters for the online processing:
-# Click on the the Averaging plugin
+# Click on the ''Averaging'' plugin.
-#* Click on the ''Averaging Adjustments'' button in the toolbar
+#* Click on the ''Averaging Adjustments'' button in the toolbar.
 #* Choose the correct trigger channel. Since we are making use of the MNE-Sample-Data-Set choose STI014.
-#* Once the averages are strating to come in you can take a look at the averaging in form of a butterfly and 2D layout plot.
+#* Once the averages are starting to come in you can take a look at the averaging in form of a butterfly and 2D layout plot. <br /> [[File:Mne_scan_rtMNE_setup_1.PNG|center|border|600px]]
-[[File:Mne_scan_rtMNE_setup_1.PNG|center|border|600px]]
+# Click on the ''MNE'' plugin.
+#* Select the ''3D Control'' from the toolbar.
-# Click on the MNE plugin
+#* Navigate to the ''RT Source Loc Data'' item.

@@ Line 19: / Line 19: @@
 #* Choose the correct trigger channel. Since we are making use of the MNE-Sample-Data-Set choose STI014.
 #* Once the averages are strating to come in you can take a look at the averaging in form of a butterfly and 2D layout plot.
 # Click on the MNE plugin