MEG Wiki - User contributions [en]

File:Bstorm montage editor2.png

2019-05-24T20:53:23Z

Colin:

File:Bstorm montage editor1.png

2019-05-24T20:52:53Z

Colin:

EEG re-reference with Brainstorm

2019-05-24T20:51:54Z

Colin: Created page with "This tutorial explains how to re-reference electrode channels (EEG, EOG, ECG) using Brainstorm. We will focus on the case in which EOG or ECG was recorded using unipolar elect..."

This tutorial explains how to re-reference electrode channels (EEG, EOG, ECG) using Brainstorm. We will focus on the case in which EOG or ECG was recorded using unipolar electrodes instead of bipolar electrodes.

==Background==
EEG is used to measure changes in voltage, which is the difference in electric potential energy between two points in space. For this reason, a single channel of EEG requires two electrodes. The recorded signal is the difference in electric potential between the two electrodes.

In modern EEG, two types of electrode recording configurations are commonly used: ''unipolar'' and ''bipolar''.
* In a bipolar configuration, two electrodes are placed on the head, and the resulting signal is the difference between those two electrodes.
* In a unipolar configuration, multiple (more than 3) electrodes are placed on the head, and one of those electrodes serves as a ''reference'' for all the others. The recorded signals are then the difference between the remaining electrodes and the reference electrode.

EOG and ECG are commonly recorded using bipolar electrodes, and scalp EEG is commonly recorded using unipolar electrodes.

It is important to note that configuration of how the channels are referenced (commonly called a ''montage'') can be easily changed by subtracting pairs of electrodes from each other. For example, let's say that three electrodes are used at positions F3, F4, M1. In the recording, M1 is used as the reference. This means that the recordings at electrodes F3 and F4 will be the difference in potential between each electrode and M1.

* Channel 1: F3-M1
* Channel 2: F4-M1

If we want to change the reference to F4, then we can subtract the second channel from the first and multiply the second channel by -1.

* New Channel 1: (F3-M1) - (F4-M1)
* New Channel 2: -1*(F4-M1)

This reduces to:

* New Channel 1: F3-F4
* New Channel 2: M1-F4

Unipolar electrodes can also be changed to bipolar by simply subtracting the two electrodes from each other. However, bipolar electrodes cannot commonly be changed to unipolar.

==Re-referencing using Brainstorm==
Brainstorm allows you to change to a new montage either in the display, during artifact detection, or permanently. An in-depth description of this can be found on the [http://neuroimage.usc.edu/brainstorm/Tutorials/MontageEditor Montage Editor Page].

In the following tutorial, I will focus on the specific case in which the EOG and ECG electrodes were recorded using the unipolar electrode slots instead of the bipolar electrode slots. This requires first changing the montage in the display to check whether everything looks okay and second changing the montage in the artifact detection window. Note that Brainstorm also lets you permanently save the new channels, but this is probably not necessary unless the EOG and ECG are being used for something besides artifact detection.

I will assume that HEOG are recorded on channels EEG001 and EEG002, VEOG are recorded on channels EEG003 and EEG004, and ECG are recorded on EEG005 and EEG006. Substitute different channel numbers if your configuration was different.

===Changing montage in the display===

* After reading in your raw data file, right click on ''Link to raw file'' and choose ''EEG'' -> ''Display time series''.
* Under the ''Record'' tab choose ''All'' -> 'Edit montages'. Or right click in the EEG display window and choose ''Montage'' -> ''Edit montages''. This brings up the ''Montage editor''.
* Click on the wavy lines under Montages and choose ''New custom montage''. Provide a name for the new montage (e.g., Bipolar EOG and ECG).
* Enter your new montage in the Custom montage box.
[[File:Bstorm_montage_editor1.png|border]]
* Choose ''Save''.
* The new montage should be displayed in the window and available under the Montage selections.

===Changing montage during artifact detection===
The montage syntax can be used when selecting the channel to use during artifact detection. For example...
* Choose ''Artifacts'' -> ''Detect heartbeats''.
* Under ''Channel name'' type in: EEG005,-EEG006
[[File:Bstorm_montage_editor2.png|border]]
* Brainstorm will use this montage when detecting the cardiac artifacts.

File:Maxfilter.png

2019-05-24T20:49:40Z

Colin:

Pre-Processing

2019-05-24T20:49:05Z

Colin: Created page with "==Maxfilter== Signal Space Separation (SSS) is a method that utilizes the fundamental properties of electromagnetic fields and harmonic function expansions in separating the m..."

==Maxfilter==
Signal Space Separation (SSS) is a method that utilizes the fundamental
properties of electromagnetic fields and harmonic function expansions in
separating the measured MEG data into three components:

b'in': The brain signals originating inside of the sensor array (space S'in').

b'out': External disturbances arising outside of the sensor array (space S'out').

n: Noise and artifacts generated by the sensors and sources of interference located very close to the sensors (space S'T').

[[File:Maxfilter.png|600px]]
===SSS===
The basic Maxwell filtering operation can be regarded as spatial filtering,
because separation of b'in' and b'out' is done on the basis of the spatial patterns
and is independent of time. Spatial separation can suppress only
external interference emanating from space S'out', such as electromagnetic
pollution due to power lines, radio communication, traffic, elevators etc.
External interference can also arise in the patient. For instance, normal
cardiac and muscular activation cause fields detectable by MEG sensors,
and any pieces of magnetized material in/on the body may cause very
large disturbances.

===tSSS===
Identification and suppression of the S'T'-space components require additional
knowledge of the temporal dynamics. The temporal extension of
the SSS method (tSSS) significantly widens the software shielding capability
of MaxFilter, because tSSS can suppress also internal interference
that arises in the S'T'-space or very close to it. Such disturbances can be
caused, for example, by magnetized pieces in/on the subject's head (such
as dental work, braces, or magnetized left-overs in burr-holes), or by pacemakers
or stimulators attached to the patient.

Reference: [http://imaging.mrc-cbu.cam.ac.uk/meg/Maxfilter_V2.2?action=AttachFile&do=get&target=Maxfilter_Manual_v2pt2.pdf MaxFilter Manual]

==SSP==

EOG Type : 202 ac1.info.chs.kind - Eye Blink
<br>ECG Type : 402 ac1.info.chs.kind - Heart Beat

File:MEGPortDuration.jpeg

2019-05-24T20:47:40Z

Colin:

File:SendMEGTrigger.jpeg

2019-05-24T20:46:29Z

Colin:

File:ResetMEGTrigger.jpeg

2019-05-24T20:45:16Z

Colin:

File:AddPort.jpeg

2019-05-24T20:44:14Z

Colin:

EPrime

2019-05-24T20:43:36Z

Colin: Created page with "==Using E-Prime== Using E-Prime on one of the machines in the Lab can be tricky. When you are designing your experiment, you will probably have to check to see if the compute..."

==Using E-Prime==

Using E-Prime on one of the machines in the Lab can be tricky. When you are designing your experiment, you will probably have to check to see if the computer you are using for Stimuli presentation is running the same E-Prime version that you are testing/building your experiment in.
===MEG Machine===
The MEG presentation computer has the E-Prime version 1 installed. When you are building your experiment in the Lab area, you can contact Travis Williams to setup the Virtual Machine(VirtualBox) to link to the WindowsXP machine on your work station. You can then create, test and edit your experiment at your own office space! It is very convenient.

==Designing your experiment==

===Reference Guide===
There are some E-Prime Reference guides in the Lab. Contact [[Contacts|Candida Jane Maria Ustine]] if you would like to have a look at them. They are very useful if you are new to E-Prime. Trust me!!

==Common Problems and Solutions==

There is an online web support page for common problems and their solutions. Please follow the link [http://www.pstnet.com/support/kb.asp?TopicID=3000 HERE]

Some additional problems that can be encountered are listed below with instructions on how to solve them.

'''1) It says, "sound device is set not to open"'''

*Double-click on the Experiment Object Icon in the Structure Window and a properties window should pop up
*Then click on the Devices tab near the top
*There should be a Sound Option - Make sure that it is checked (If it is not there, select Add and add the Sound Device).
*Now, click on the Sound Option to highlight it and click Edit (option at the bottom of the screen)
*An "Edit SoundDeviceObject Properties" Window should now pop up...make sure the following values are there:
*Channels: 2
*Samples: 44100
*Bits Per Sample: 16

NOTE: Check your wave file to see if you can generate a specific tone with a desired frequency. See [[Scripts|Stimuli Presentation Scripts]] for the generate_tones.m script that can create mono tones with the desired sampling frequency.

==Triggering in E-Prime==
When using Eprime to present your stimuli in the MEG you will have to do the following:
<br>1) Add the Port to the Experiment Devices
<br>2) Insert specific Inline object codes telling the script when to send triggers to the Machine.

===PST WIKI PAGE===
Read [http://www.pstnet.com/support/kb.asp?TopicID=1318 here] about the '''three ways to send triggers''' to the MEG.

===STEP1: Add Port Device===
*Go to Edit --> Experiment --> Devices Tab
*Click on the Add device button and select Port device.
*Select the Port device you have added and click on the Edit button
[[File:AddPort.jpeg]]
*Choose the settings you see in the picture above.
**Collection Mode: Presses Only
**Address: &H379
**Size: 8
**Invert: No
**Mask: -1
**Emulate Device: None (Unless you are testing this on your computer then choose keyboard or Mouse)

===STEP2: InLine Code===
This set of script lines are inserted wherever you would like to send triggers to the MEG machine.
====Initialising MEG communication====
Before you start sending triggers to the machine ie., before you start the actual experiment you will have to initialise the MEG communication.
[[File:ResetMEGTrigger.jpeg]]

Insert a similar code to the beginning of your experiment. The WritePort command will send the port address the value of 0, in other words resets the port.

====Sending MEG Triggers====
This is the part when you send the MEG triggers to the MEG machine when an event happens. For example: Stimulus Onset or Key Response.
[[File:SendMEGTrigger.jpeg|Sending MEG Triggers]]

Note that in this experiment the triggers that the Experiment must send the MEG machine is coded along with the trials. And so they are easily referenced in the in line code.

====Encoding Responses====
When you have a task that requires the subject to press a button in the MEG then you will have to edit the properties of the Stimulus object so that the exact triggers are sent to the MEG system when the subject presses a button. You will also have to edit the Properties of your Stimulus object and add the Port as a device of response. You will also have to include another column in your trial list specifying the correct answers codes for the response pads in the MEG system.
[[File:MEGPortDuration.jpeg]]

You can have E-Prime code the button presses with an additional trigger which also gets stamped into the MEG output file. In this case, you will ne alerting E-Prime that you’d like all button presses to be referenced as a specific trigger number. Look at the Properties window for SoundOut1. Here you can let E-Prime know that it should look for responses from the Port device, and that the responses it should be looking for are numbered 7 and 8 (see ‘Allowable’). 7 is the left button and 8 is the right button.
<br>Your triggers from the response will always be 7 and 8 because these are the channels used for button responses by the MEG Trigger Box.

=====Encoding Responses: Inline code=====
If you would like to send a trigger when the subject has pressed a button then you can use the following inline object script.
Syntax: WritePort address value
Example: WritePort &H378,SoundOut1.RESP

==Links to more Info on Triggers and Ports==
See [http://www.pstnet.com/eprimelegFAQ.cfm#12 Pstnet FAQ] page for more information.

See [http://www.pstnet.com/support/kb.asp?TopicID=1318 Pstnet Parallel Port Info] for information on parallel port i/o.

File:StimToMSR.jpg

2019-05-24T20:41:46Z

Colin:

File:TriggerCabinet.jpg

2019-05-24T20:40:42Z

Colin:

File:TriggerBox.jpg

2019-05-24T20:40:05Z

Colin:

File:MEG-headphones.jpg

2019-05-24T20:39:23Z

Colin:

File:ProjectorMainPanel.JPG

2019-05-24T20:38:43Z

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File:SubjectInScanner Task.JPG

2019-05-24T20:37:47Z

Colin:

File:MEGRoom1.JPG

2019-05-24T20:36:49Z

Colin:

Designing your Experiment

2019-05-24T20:36:23Z

Colin: Created page with "Please read this wiki page if you would like to run an MEG experiment at MCW. Here you will find information about the various stimulus presentation software available and inf..."

Please read this wiki page if you would like to run an MEG experiment at MCW. Here you will find information about the various stimulus presentation software available and information on setting up triggers for your experiment.

<br>
=MEG Lab Components=
#Stimulus presentation computer: Windows XP 2002.
#Analysis Computer: Windows 7
#MEG Neuromag Vectorview Acquisition System
#Optical response pad (Elekta Finger pad)
#Stimulus Trigger BNC Interface Units
#Polhemus Head Digitisation Unit

[[File:MEGRoom1.JPG| 650px]]
<br>

=Scripting your Experiment=

Your study experiment can be programmed using Presentation, Matlab, [[EPrime]] or [[Psychopy]]. Eprime, Matlab scripts can be written and executed using the Stimulus presentation computer kept at the MEG facility. Please call ahead, if you would like to schedule a time to use the stim computer to program your experiment.

==Software==
#'''Matlab''' R2007b Version 7.5
# [http://www.pstnet.com/eprime.cfm '''Eprime'''] EStudio Version 1 See [[EPrime]] for more information.
# Eprime 2 - Standard Version
# [http://compumedicsneuroscan.com/stim2-stim%C2%ADu%C2%ADlus-presen%C2%ADta%C2%ADtion-and-exper%C2%ADi%C2%ADmen%C2%ADtal-design-system/ '''Stim2'''] from Neuroscan
#Presentation 11.3 (Please check with staff before programming)
#[[Psychopy]]

<br>

==Stimulus Presentation==

There are different ways of presenting the stimuli to your subjects, we will elaborate the systems we have at the facility here.

[[File:SubjectInScanner_Task.JPG|450px]]

===Visual===
=====Projector and Screen=====
Visual stimuli are projected on to the screen inside the MSR using a Panasonic DLP Projector Model PT-D7700UK [http://www.projectorcentral.com/pdf/projector_manual_3149.pdf Manual] projector that is housed outside the MSR inside the Helium tank room. The signal is projecting though a periscope into the MSR onto a back-projection screen that is placed in front of the chair. The optimal positions for the screen is marked by tape on the floor for correct focus. Please make sure to place the screen at these locations before your experiment and be sure to move it towards the wall after your finish. There is a small note on the screen showing which side should face the subject.

=====Delays=====
Photodiode test:
<br>Using a light diode we measured a jitter of about 35.9 ± 0.4 ms between the trigger codes sent from the stimulus PC to the MEG acquisition computer and the visual output in the projector screen inside the MSR that the subject sees. These results were acquired for a specific setting and therefore the researchers are encouraged to conduct their own personalized tests. They are advised to simulate the same settings as their experiment and collect the data. The photodiode and related equipment to conduct the test will be provided.

=====Instructions for Projector=====
#Turn on the projector by using the switch on the left side of the projector and press the ON button in the main panel.
#Wait for a few seconds for the red light to turn Green.

======Adjustments======
*If the focusing, zooming or positioning of the image projected on the screen is not successful, even though the projector is properly positioned against the screen, you can adjust the focus, the zoom, or the vertical or horizontal position of the image.
*Click on the LENS button on the main panel or in the remote control and use the navigation buttons to adjust the focus, zoom and shift aspects.

[[File:ProjectorMainPanel.JPG|350px | Projector Main Panel]]

===Auditory===
For delivering auditory input to the subjects in the MSR, we use a pair of MEG compatible Tubal Insert head Phones (TIP 300 - Nicolet). The use of Nicolet TlPs maximizes interaural stimulus isolation, prevents ear canal collapse, and reduces stimulus artifact. TlPs are easy-to-use, lightweight, durable and comfortable for the patient.

Use a new set of foam ear-tips for every subject. Attach the yellow foam tip to the tubes and hand it over to the subject. After use, throw away the yellow foam ear-tips, but make sure you do not dispose off the white plastic piece attached to the end of the tubes.

[[File:MEG-headphones.jpg|350px]]

=Triggers=
During an MEG scan, stimuli from the presentation computer are presented to the subject seated inside the MSR (Magnetically Shielded Room) and the MEG signal is recorded on the acquisition computer simultaneously. As the stimuli are presented to the subject, a trigger pulse (digital pulse) is recorded along with the MEG signal in a separate channel and serves as a temporal marker. This is the STIM channel that contains information about the events/triggers such as start of the event, duration of the event and the event ID. These triggers are useful for time locking analysis of your MEG data such as evoked analysis etc.,

===Stimulus Trigger Interface===

'''STI102'''

[[File:TriggerBox.jpg|450px]]

<br>
'''STI101 Inside the Triggers/Electronics Cabinet'''

[[File:TriggerCabinet.jpg|450px]]

The digital triggers are sent from the stimulus computer through the parallel port to the Trigger Box - STI102 (Shown above) that is placed on the Stimulus presentation table. Any visual stimulus input from the Presentation computer is directly sent to the MSR via a relay device shown below.

[[File:StimToMSR.jpg|350px]]

The triggers sent by the computer are sent to STI102 that are directly fed to the Neuromag MEG Acquisition computer to be recorded along with the MEG signal collected from the subject seated inside the MSR.

===Response Triggers===

The responses collected from the subject using the Elekta optical response pads. These responses are encoded in the trigger box (STI101) via BNC cables, that is housed inside the Trigger Cabinet shown above and are recorded in the ST101 channel along with the stim triggers (STI102) and MEG signal data.

===Trigger Settings===
As we mentioned before there are two trigger units - STI101 (inside cabinet) and STI102 (stimulus computer table).

'''OPTION 1:'''

When the STI101 is not selected in the Acquisition settings, then the two trigger units operate in Parallel, or in 'Mirror' mode. So when STI102 receives a input in any of the IN pins, it is seen in the corresponding OUT pins of both STI102 and STI101 and in addition to this the signal is also sent to the STIM channel(STI102) to be recorded with MEG data.

'''OPTION 2:'''

When both STI102 and STI101 are connected - they act independently. But NOTE that any responses sent to the Trigger Unit STI101(inside cabinet) do not get sent to the stim computer.

=Supplies=
#4 EEG 60 channel caps in 4 different sizes
#1 set of Ambu Neuroline cup electrodes
#Ten20 conductive gel (electrode paste)
#Nuprep (skin preparatory gel)
#Cotton tips, tapes, gauze
#Electrode gel syringe (BD Diagnostics 5m)
#Blunt syringe tips (needles)
#Hand-Held Degausser (Geneva PF 215)

File:Tsss dental artifact.png

2019-05-24T20:31:33Z

Colin:

File:Orig dental artifact.png

2019-05-24T20:30:35Z

Colin:

File:Ecg artifact.png

2019-05-24T20:29:41Z

Colin:

File:Eog artifact.png

2019-05-24T20:28:51Z

Colin:

Artifacts in MEG data

2019-05-24T20:27:26Z

Colin: Created page with "=Artifact Handling= ==What is an artifact?== Artifacts are unwanted interference in your data that may or maynot mask your desired signal. It is good practice to remove these..."

=Artifact Handling=

==What is an artifact?==
Artifacts are unwanted interference in your data that may or maynot mask your desired signal. It is good practice to remove these artifacts from your data before you begin analysis. There are a lot of MEG analysis software modules in the market that help you remove the artifacts. General procedure followed by most methods is first to identify them and then to remove them. Artifacts can be physiological or environmental in nature.

Some of the common artifacts are as follows:

====Physiological Level====
# Eye blinks (EOG) Electroocculogram
# Heart Beats (ECG) Electrocardiogram
# Head movements
# Muscle artifacts
# Dental artifacts

====Environmental and System Level====
# Power line noise:
# Squid Jumps

==Common Examples of Artifacts==

===EOG===
This is the most common artifact seen mostly in the "Frontal" MEG channels.
[[File:Eog_artifact.png|800px]]

===ECG===
The heart beats are more visible in the temporal channels that are closer to the chest.
[[File:Ecg_artifact.png|800px]]

===Dental Noise===
Some participants may have metal fillings, braces that will cause huge artifact in the data. It is not in any way harmful to the participants, but degrades the data quality by a huge extent. We discourage the researchers who are recruiting participants from taking in subjects who have metal fillings, braces, permanent retainers etc., Although we understand this may be unavoidable in certain cases. We have a degausser in the lab that can be used in such cases where we 'demagnetise' the subject before we put them in the scanner.

Below is an example of one such dataset collected from a participant who had a permanent retainer. In the case of a permanent retainer, even the degausser did not help.

'''tSSS''' is an cleaning procedure that we run on the data after acquisition. The tSSS procedure takes care of dental noise and cleans the data.
=====Dental noise from a permanent retainer=====
[[File: Orig_dental_artifact.png|800px|Dental Artifact Before]]
=====tSSS cleaned data=====
[[File: Tsss_dental_artifact.png|800px|Dental Artifact After tSSS]]

File:Putty config2 tunnel.PNG

2019-05-24T20:25:22Z

Colin:

File:Putty config1.PNG

2019-05-24T20:23:12Z

Colin:

SQUIGGLES Computer Login

2019-05-24T20:21:51Z

Colin: Created page with "Squiggles is general purpose analysis and storage computer for MEG/Neurophysiology/Epilepsy data Configuration: For Windows For Mac/Linux To Login from Windows Computer: Do..."

Squiggles is general purpose analysis and storage computer for MEG/Neurophysiology/Epilepsy data

Configuration:
For Windows
For Mac/Linux

To Login from Windows Computer:

Download Putty:
https://www.chiark.greenend.org.uk/~sgtatham/putty/

[[File:Putty config1.PNG]]

!

[[File:Putty config2 tunnel.PNG]]

MEG Physics

2019-05-24T20:19:16Z

Colin: Created page with " IN PROGRESS See http://www.mcw.edu/MEG/AboutMEG/MEGPrinciples/MEGandEEGinstrumentation/MEG.htm Here NEEDS TO BE UPDATED!!!"

IN PROGRESS

See [[http://www.mcw.edu/MEG/AboutMEG/MEGPrinciples/MEGandEEGinstrumentation/MEG.htm Here]]
NEEDS TO BE UPDATED!!!

Source Level

2019-05-24T20:17:41Z

Colin: Created page with "==Placement of HPI coils== Usually when you are doing MEG study (no EEG) it would be convenient to place the HPI coils on the skin - Two on the subject's forehead just above..."

==Placement of HPI coils==
Usually when you are doing MEG study (no EEG) it would be convenient to place the HPI coils on the skin - Two on the subject's forehead just above the place where you place the Vertical EOG coil and two behind your subject' ears (below the refs).

Scripts

2019-05-24T20:17:14Z

Colin: Created page with " =Stimuli Preparation= In Progress... ==E-Prime== TO BE COMPLETED <br>1) AudioStim_v6 <br>2)VisualStim_v1 ==Psychopy== 1) audiostimuli_v2.py: /home/custine/Desktop/Experimen..."

=Stimuli Preparation=
In Progress...

==E-Prime==
TO BE COMPLETED
<br>1) AudioStim_v6
<br>2)VisualStim_v1

==Psychopy==
1) audiostimuli_v2.py: /home/custine/Desktop/Experiments/Scripts/Psychopy
<br>2) visual.py /home/custine/Desktop/Experiments/Scripts/Psychopy

=MEG Scripts=

==Pre-Processing==

1) preProc_setup.sh subjID
<br> Example: ./preProc_setup sh ac1
<br>2) preProc_project.sh subjID tag nmag ngrad neeg
<br>Example: ./preProc-project.sh ac1 ecg 1 1 0
<br>4)python makeAveFiles.py subjID projon
<br>Example: python makeAveFiles.py ac1 projon
<br>5)python preProc_avg.py subjID expName
<br>Example: python preProc_avg.py ac1 Left

==Sensor Level==
* python sensor_grandAverage.py exp paradigm
* Example: python sensor_grandAverage.py msabri Left

==Source Level ==

Using GitLab

2019-05-24T20:16:18Z

Colin: Created page with "==Introduction== In this page you will find information on how to use gitlab in general and for our Epilepsy project in particular. Gitlab is a web based Git repository that..."

==Introduction==

In this page you will find information on how to use gitlab in general and for our Epilepsy project in particular. Gitlab is a web based Git repository that provides an opportinty to develop a streamlined project workflow. It is a cloud based sharing center where users working on the same code can compare, develop, pull and push code to the master repository.

== Git Useful Links ==
# [https://www.git-tower.com/blog/git-cheat-sheet/ Cheat sheet]
# [http://longair.net/blog/2009/04/16/git-fetch-and-merge/ Git Fetch & Merge]

==Steps to create a gitlab repo==

Go to the git lab login page and create a project. If you already have files you can push them using command line instructions below. Otherwise you can start with adding a README, a LICENSE, or a .gitignore to this project. You will need to be owner or have the master permission level for the initial push, as the master branch is automatically protected.

===Command line instructions===

====Git global setup====

git config --global user.name "C Ustine"
git config --global user.email "custine@mcw.edu"

====Create a new repository====

git clone git@gitlab.com:candidaustine/Name_Of_Project.git
cd Name_Of_Project
touch README.md
git add README.md
git commit -m "add README"
git push -u origin master

====Existing folder====

cd existing_folder
git init
git remote add origin git@gitlab.com:candidaustine/Name_Of_Project.git
git add .
git commit -m "Initial commit"
git push -u origin master

====Existing Git repository====

cd existing_repo
git remote add origin git@gitlab.com:candidaustine/Name_Of_Project.git
git push -u origin --all
git push -u origin --tags

==Basic GitLab commands==
Go to the master branch to pull the latest changes from there

git checkout master

Download the latest changes in the project. This is for you to work on an up-to-date copy (it is important to do every time you work on a project), while you setup tracking branches.

git pull REMOTE NAME-OF-BRANCH -u
(Ex: git pull origin develop-v1)
(REMOTE: origin) (NAME-OF-BRANCH: could be "master" or an existing branch)

Create a branch. Spaces won't be recognized, so you need to use a hyphen or underscore.

git checkout -b NAME-OF-BRANCH

Work on a branch that has already been created

git checkout NAME-OF-BRANCH

To List the name of the branch that you are working on
git branch

To List the name of the remote
git remote

View the changes you've made. It's important to be aware of what's happening and what's the status of your changes.

git status

Add changes to commit. You'll see your changes in red when you type "git status".

git add CHANGES IN RED
git commit -m "DESCRIBE THE INTENTION OF THE COMMIT"

Send changes to gitlab.com

git push REMOTE NAME-OF-BRANCH

Delete all changes in the Git repository, but leave unstaged things
git checkout .

Delete all changes in the Git repository, including untracked files
git clean -f

Merge created branch with master branch. You need to be in the created branch.

git checkout NAME-OF-BRANCH
git merge master

===Git ECP===
We have created a repository of the connectome scripts written and managed for the ECP project. The ECP project is a private repository managed by the ECP MEG team at MCW.

We have currently created two branches of the existing code obtained from the HCP megconnectome database. The "master" branch is our main branch and will only be accessed when we would like to make permanent edits to our code. The developers in the project wil be working on the branch called "develop-v1" which will be our workspace where we store temporary code during trial & development stages. Developers, please pull a copy of the code from the "develop-v1" branch to your workstation to work on the most updated version of the code.
==== Pull from ECP Repository====
git clone git@gitlab.com:candidaustine/epilepsy_megconnectome.git OutputDir

Sending/Receiving triggers through parallel port interface

2019-05-24T20:15:34Z

Colin: Created page with " =Parallel Port= The Stim computer and the Data Acquisition computer are connected via a parallel port. This is how the triggers are sent from the stim computer to the STI ch..."

=Parallel Port=

The Stim computer and the Data Acquisition computer are connected via a parallel port. This is how the triggers are sent from the stim computer to the STI channels. You can use any experimental program - Eprime, Psychopy in order to send triggers to the MEG system. The codes are completely your choice. In MEG, one would want to tag every event in the data for further analyses. So you can specify the event codes in the script you are using to tag the event stim.

==Sending Triggers==
You can bring your own laptop or use the stim computer we have setup in the MEG lab. In order to send triggers to the MEG acq Trigger system, you will need a parallel port available in your device. The parallel port will connect your laptop to the BNC trigger box that sends the triggers to the MEG_ACQ computer.

The MEG acquisition software accepts stimulus codes as binary triggers. The system supports a 8 bit code, which means you can send pulses between 0 and 255. While your scripts are coded with event numbers (0 to 255), you will actually be seeing binary trigger combinations light up on the BNC trigger box (STI 102) that is located on the stim computer table.

==Reading Button Responses VIA Parallel Port==
You can use the fibre optic response pads to record your responses in the MEG data acquisition computer along with your raw signal data. If you would like to design a task that is adaptive to the participant's response or if you would simply like to have the responses recorded both in the MEG raw signal and in the stim computer side, you will need to have the participant responses fed into the stim computer via the parallel port.

TO DO: Connect your response cables to any of the BNC "IN" pins 12 to 16 in the trigger box STI101, and have it mirrored to STI102 so it can be read through the interfaced parallel port.

REASON: The cable from the 37 pin output on the trigger box is connected to the 25 pin input to the computer. Basically, only 5 of the output channels (12-16) are being fed to the computer. These channels appear on pins 11-15 on the 25 pin end of the cable, which are the status channels, not the data channels. So in order to read the responses on the stim computer end, one must connect the response cables to channels in the 12-16 range of the trigger box.

1) To write to the trigger box, use address 0x378.
2) To read from the box, use address 0x379.
3) The button box and any TTL input should be plugged into lines 12-16 on the trigger box.

Psychopy

2019-05-24T20:14:29Z

Colin: Created page with "=Why PsychoPy?= PsychoPy is an open-source, python-based stimulus presentation software package that can be used as an alternative to PsychToolBox (PTB). It does not have a..."

=Why PsychoPy?=

PsychoPy is an open-source, python-based stimulus presentation software package that can be used as an alternative to PsychToolBox (PTB). It does not have a reliance on Matlab as PTB does, and it has the flexibility to control stimulus presentation by frames based on the screen refresh rate, reducing variability in timing making it much better suited to experiments that rely on timing accuracy (e.g. EEG).

=Ease of Use=

In Psychopy you can either use the [http://www.psychopy.org/builder/builder.html#builder Builder] or the [http://www.psychopy.org/coder/coder.html#coder Coder] Interface to write your stim presentation scripts.
===Builder Interface===
As their name suggests the Builder Interface is for the user who does not like to write scripts from scratch. It is completely GUI driven and very user friendly. Builder makes it easy to visualize the structure of your experiment, create trial loops, integrate code components, add keyboard responses, present visual stimuli, etc. You can compile the code from Builder (a .psyexp file) and use Coder to view and edit it (.py file).
===Coder Interface===
This is for the user who loves to write hiss/her own scripts. Coder view is far more powerful since you can use various python modules (such as NumPy, a mathematical module comparable to Matlab) to customize your code and go beyond the limitations of the Builder.

'''NOTE:''' When you are satisfied with the experiment you have built in the Builder you can view its script or code in the coder and make changes there and fine tune your experiment. However YOU CANNOT GO BACK to the Builder view from a code view... :( That is the only drawback! I think!

'''RECOMMENDATION:''' It is recommended to always build your experiment in the Builder and then "compile", so you have a foundation to work on or tweak in the coder interface.

=Tips=

==Auditory Stimuli==

Import the sound package from psychopy before beginning. If possible build your basic Experiment using the Psychopy Builder, compile it as a script and then work from there.

You can set a Frequency of a sound/tone you want to play or provide a link to the sound you want to play.

sound_1 = sound.SoundPygame(value = u'/home/custine/Desktop/Experiments/tones/tone_400Hz.wav')

or
highA = sound.Sound('A',octave=3, sampleRate=44100, secs=0.8, bits=8)
highA.setVolume(0.8)
tick = sound.Sound(800,secs=0.01,sampleRate=44100, bits=8)#sample rate ignored because already set
tick.play()

or
ding = sound.Sound('ding')
ding.play()

==Visual Stimuli==
===Using Images as Stimuli===

Always save your images as .bmp. JPEGs and PNGs also work though.

==Writing trial by trial info into a text file==

You may not find the output that psychopy automatically outputs that helpful (with version 1.73, aside from the log file, the other output files were only written when the experiment concluded. If you quit in the middle of a running experiment, you would not have any saved data.) You can instruct Psychopy to write a text output file for your data after each trial shown, so that when you quit midway you have data saved up to that point.

To open a new text file and write header at the beginning:

datFile=open('Data'+os.path.sep+'%s_part%s_subj%s_dat_%s.txt'%(expInfo['expName'],expInfo['session'],expInfo['participant'],expInfo['date']),'w') #customize your output filename
datFile.write('participant\tTrialNumber\tdescrip\tIAPS\n') #this is your customizable, tab-delimited header row

Then, at the end of the loop containing your repeating trial (don't forget any indents)!!

#push to dat File
datFile.write('%s\t%s\t%s\t%s \n'%(expInfo['participant'],trials.thisTrialN+1,thisTrial.descrip,thisTrial.IAPS))

=Useful Links=
* [http://sapir.psych.wisc.edu/wiki/index.php/Psychopy Sample Scripts]
* [https://groups.google.com/forum/#!forum/psychopy-users Psychopy-Users Google Group]

MRI Acquisition

2019-05-24T20:13:49Z

Colin: Created page with "==Introduction== In order to run a source analysis on the MEG data it is necessary to have an accurate head model describing the shape of the scalp, skull, and cortical surfac..."

==Introduction==
In order to run a source analysis on the MEG data it is necessary to have an accurate head model describing the shape of the scalp, skull, and cortical surface. The best way to calculate a subject-specific head model is to use a high resolution anatomical MRI scan of the subject. Information about collecting MRI, such as scheduling and fees, can be found at the [http://www.mcw.edu/CIR.htm CIR Website].

==Recommended MRI Protocols==
The MRI protocol will depend on how much time you have available for data collection. At the very least, a T1-weighted scan, such as an SPGR or MPRAGE, is necessary. In addition, we currently recommend collecting a T2-weighted scan with the same resolution as the T1 scan. If there is additional time available then the protocol could include: additional T1 scans, a resting state fMRI scan, a proton density (PD) scan, or a diffusion (DTI) scan. It is VERY important that the scan covers the entire scalp surface including the ears. If some of the head is cut off than this will decrease the accuracy of the head model.

===T1-weighted (required)===
The T1 scan is used to identify the gray matter cortical surface, as well as the boundary of the scalp, skull, and dura. Several T1 scans can be collected and averaged together; however, because of alignment error, averaging may not provide much benefit unless there are at least three scans.

===T2-weighted (recommended)===

===FLAIR (optional)===

===Proton Density (optional)===

===Resting State (optional)===

===DTI (optional)===

==MRI Safety==
If the subject has metal implants, check the nanufacturer name and see if it is listed as safe in this website.
http://www.mrisafety.com/TheList_search.asp

FAQs

2019-05-24T20:13:16Z

Colin: Created page with "==General Scanning Inquiries== In this section you will find answers to some common questions that most MEG scanners will have when they begin scanning with us. *What is the..."

==General Scanning Inquiries==
In this section you will find answers to some common questions that most MEG scanners will have when they begin scanning with us.

*What is the fee for using the MEG facility?
The research fee is $400/hour

*What is the size of the data that gets generated?
If your sampling rate is 2000Hz, the data size would be about 10G for 1 hour of scanning. (MEG channels only).

*Does the MEG suite have the new Eprime version installed?
Yes, we have Eprime 2 Standard version at the MEG suite.

*Can I bring my own laptop for stimulus presentatioon?
Yes. Make sure you schedule a test run with us to test the scripts, trigger signalling etc., before you begin scanning.

==IRB Related questions==
*Does IRB consider MEG a device? where is it located?
The MEG is an FDA approved measurement device just like the MRI and the EEG. And it is located at Froedtert Hosipital.

Getting Access

2019-05-24T20:12:56Z

Colin: Created page with "Being an MCW employee you cannot get access to the MEG Room and the facility with your MCW ID card, as they are physically located in the Froedtert Hospital premises. The alte..."

Being an MCW employee you cannot get access to the MEG Room and the facility with your MCW ID card, as they are physically located in the Froedtert Hospital premises. The alternate option is to alert the MEG technical manager [[Contacts]] that you would be scanning on certain day so they can let you in.

==Getting an Froedtert ID Card==
The first step is to speak with the MCW Neurology Administrator. Once you let her know that you need access you will have to go to the Froedtert Hospital Security Control Room and get an ID card there.
<br> NOTE: You will need to pay $5.00 for the Froedtert ID card... (You will get it back once you give surrender the card to them)

Froedtert Security Office is located close to the Information Desk of Froedtert Hospital.
Contact: 414-805-7050

==MEG Calendar==

The MEG calendar is maintained by MCW and Froedtert and will show the MEG facility availability for research purposes. Please contact [[Contacts|Robert Rohloff]] with a desired date and time and he can schedule it for your group. If the requested time is unavailable, you will be contacted with alternate dates and times.

===Cancellations/No-Show===
'''Use it or lose it:'''
Frequent non-use of scheduled scan time indicates a problem that should be discussed before additional time slots are allocated, and may result in a reduction of a user’s assigned time in the schedule.

Please be aware that the MEG Facility is used for both clinical and research purposes and act responsibly in reporting any unused scan time as soon as you can.

MEG Acquisition

2019-05-24T20:12:35Z

Colin: Created page with "=Preparation= Always make sure you have tested the entire experiment for triggers, button responses etc., once before scan subjects and collect data. When you are ready with y..."

=Preparation=
Always make sure you have tested the entire experiment for triggers, button responses etc., once before scan subjects and collect data. When you are ready with your experiment, you can start data acquisition. Please contact the [[Contacts|Candida Ustine]] the MEG Engineer to schedule a time for your data acquisition. Make sure that either the Engineer or an MEG experienced researcher is present at the MEG suite when you are scanning. There must be atleast one person from your research group who is familiar with the MEG scanning procedure, present for the entire scan time that is scheduled for you. You will be helped by the MEG engineer or the Technical Manager if you need assistance. Make sure to have additional help if you are doing an simultaneous EEG acquisition for help with the cap setup. See the section on Training if you like to be MEG trained.

=Starting the Acquisition Program=
In the Neuromag folder, open the Acquisition program. Load your project and settings; details on how to use the program are below in the [[MEG_Acquisition#Data_Acquisition|Data Acquisition]] These settings should have been previously created and saved so that time is not wasted while the subject is present. Once the necessary settings are loaded and double-checked, you are ready to register the subject.

=Subject Registration=
With the HIPAA regulations we have made several changes in how to register subjects, so be sure to follow these steps in order to be compliant!
Press the “Change” button next to Subject:
Enter name, birth date, sex, and handedness (height/weight can be skipped)

=Digitization=

Once registration is complete, you are ready to digitize the subject. Turn on the Polhemus system, which is used for digitization, and is located on the table in the patient prep area. Instructions for using the system are as follows:
* Move the wooden chair away from the Polhemus system.
* Have the subject sit in the wooden chair
* Move all rolling chairs and other objects with large metal components away from the chair and Polhemus
* Position the goggles on the subject’s head, being careful not to cover up any electrodes or HPIs. It is critical that the goggles are tight and do not move once digitization has begun.
* In the Acquisition program on megacq1, press the “Change” button next to HPI. At this point you will be prompted to digitize cardinal landmarks, HPI coils, electrodes, and extra head points. At the top of the screen, hit the “Coordinate frame alignment” button; you are now ready to begin digitization
* Digitize the three cardinal landmarks (left pre-auricular point, nasion, right pre-auricular point, see below) by pointing to each and simultaneously clicking the button on the stylus.
* It is a good idea to check that the two ear points are within a maximum (absolute value) distance of 5mm.
* After the third point has been digitized, you will hear two beeps instead of one—this is simply to indicate that you are done digitizing a section. If at any point during the digitization of the different sections you hear two beeps (before the last point), you have accidentally pushed the stylus button twice and should start over.
* Instructions on how to do this are [[MEG_Acquisition#Data_Acquisition| Data Acquisition]] further below.
* To move on to the next section (HPI coils), there is no need to click anything else; you will simply be prompted to begin digitizing HPI.
* Digitize the four HPI coils in any order. Be very careful when digitizing these points, as they can come back to haunt you later if not done properly the first time!
* Next, if using the EEG cap, digitize the electrodes in order, starting with the reference electrode. A map of electrode locations can be found on the bullaten board next to the Polhemus.
* If not using the cap, you will not be prompted to digitize any electrodes (unless you failed to rename any of your facial electrodes as EOG rather than EEG).
* Finally, you will be asked to digitize additional head points. It is a good idea to make a straight line down the forehead and nose, as the nose is easily identifiable in the subject’s MRI. An extra 50 or more points from the head should be taken so to cover the head; these will also be used in conjunction with the MRI.
* When finished, hold the stylus about a meter away from the subject and press the button.
* If at any point you should make a mistake, you can hold the stylus away, press the stylus button, and then click on the button at the top of the section you would like to do again. This will clear any points taken in a given field, allowing you to start over. (It will not clear points in previous fields).

=Connecting HPI, EEG Electrodes to Vectorview=
The plug for the HPI coils is inserted into the "subject’s" right side of Vectorview. The plug has a small notch on it; this should be placed downwards, and the whole plug should be positioned so that extra spaces are on the right. The earphones are also plugged in on the subject’s right into the slot labeled “auditory stim out.”

All electrodes are plugged in on the subject’s left. For EOG and other bipolar electrodes, be sure to pair them together correctly (e.g., vertical with vertical and not vertical with horizontal), although which goes in (+) and which goes in (-) is unimportant. Ground and reference are plugged into the same location labeled ground and reference, respectively. If using the EEG cap, the cap’s connectors should be plugged into the slots with corresponding numbers.

If doing an auditory study, be sure to place the earphones in the subject’s ears before raising the subject up into the helmet. The foam insulation for the earphones can be found in the cabinet above the analysis workstation. To adjust volume, use the audio adjustment in the stimulus PC.

If any of the supplies are running low please contact [[Contacts|Candida Ustine]] about it. It is a Froedtert Facility.

=Placing Subject in the Helmet=
The pump for the chair is located on the [subject’s] right; the longer lever pushes the chair up; the shorter one lowers it. Subjects should be pushed up far enough so that they can feel pressure on the top and back of their head. It is important to have the subject first slouch down and get comfortable so that they do not do so later and slip down in the helmet. If using the bed, lock the wheels and move only the upper portion of the bed. This way subjects can position themselves comfortably, and you can easily slide them into the helmet until their head touches the back.

=Subject Instructions=
Before exiting the MSR, be sure to remind the patient of both the general MEG instructions as well as any instructions specific to your task. General instructions include:
*For auditory studies, focus on a point on the wall or a fixation cross displayed on the screen; for visual studies, focus on the fixation cross.
* For any kind of stimulus, try not to blink while stimuli are being presented or while responding.
* Do not move once the measurement has begun.
* To communicate with the experimenter, simply speak aloud; there is a microphone built into the machine. However, you should avoid speaking during a measurement, unless it is an emergency.
* Be aware that there is a camera in the room and that we can see you from outside.

=Data Acquisition=

See [[Scanning_Specifics]] Page for information on setting your scanning parameters and for info on troubleshooting.
For a detailed description of the acquisition software and how to create your acquisition settings, see the Vectorview manual, section five (this manual can be found online as well as in the MEG lab. [[Getting_Started#Helpful_References.2FManuals |Neuromag Manuals page]]

==Entering Task and Subject Info==

* Log into the MEG Acqusition System. Contact the [[Contacts|MEG Engineer]] for Login Information.
* Select Neuromag Folder --> Acquisition
* The Settings Dialog Box opens
** Change: Project
** Change: Subject
** Change: Acquisition
** Change: Stimulus Generation
** Change: Online averaging
** Change: HPI
* Select a Project from the list
* Go to File --> Load Settings. (You will find a list of saved projects/studies in your user directory. Select the appropriate study and all the settings will be automatically loaded) (NOTE: If you are setting your experiment for the first time then visit the [[Scanning_Specifics#Preparing_an_experiment | Scanning Specifics]] page to read information/suggestions on choosing scanning parameters.
* Subject Registration: You should never enter patient identifying information here(NAME)!! See [[MEG_Acquisition#Subject_Registration| Subject Registration]] above for more information.

==Beginning a Measurement==

Below the six “Settings” buttons is a series of buttons marked “Acquisition Controls,” which read from left to right: GO, Stimulate, Average, Record Raw, Restart, and Stop.
Hitting GO will start acquisition. (It may be up to ~10 seconds before you see any channel activity, so be patient!) Once the channels come up, it will take several more seconds for them to settle; you can shorten this process by going to “Tools” and “Reset Channels.”

===Initial Check===
Before beginning stimulation and recording any data, briefly browse through all channels to make sure that none are showing artifact. To do this, click “Selection” at the bottom of the raw display window (which automatically popped up on the right monitor when you started the Acquisition program). You will then see a list of channels, grouped both by location or number; either is suitable for looking at the channels. Go through each section to check the channels one by one.

===Troubleshooting===
If you do find any sensor showing some artifact, you can usually perform a quick fix by heating the sensors. See my page on [[Scanning_Specifics#Troubleshooting | Sensor Troubleshooting]] and follow the directions.

===Measuring HPI===

Once all channels look fine, you are ready to measure the subject’s head position. A window prompting you to do this will have automatically popped up after hitting GO. In this window hit the “Measure” button, and wait several seconds until a new window with the HPI results pops up.

If everything went well, the suggestion at the bottom of the window will say “Accept.” After accepting, you are ready to begin recording.

====When HPI is not OK====
Occasionally you will find that '''one out of the four HPIs is not OK''', yet the suggestion is still “Accept.” This is true because the system only requires three functioning HPIs; however, having all four function properly is preferred in the event that one fails, in which case you will still receive the “Accept” suggestion and be able to move ahead.

'''If less than three HPIs are OK''', the suggestion will be to “Redo HPI.” In the event that you receive the Redo message, re-measure the HPI and see if things improve. If not, scan through all channels and tune/reheat any that are noisy. A noisy channel can compromise the HPI measurement. Ask also the subject to help his breath for a few seconds while HPI measurement is running (breathing artifacts w/ VNS may impede measures). Try measuring again.

If the suggestion is still “Redo HPI”, you may need to remove the subject from the MSR and see if one or more of the HPIs have come loose. If yes, redigitize subject and start over.

==Data Recording==

At this point you should have your stimuli ready to present to the subject. Before beginning presentation, however, be sure to hit the '''“Record Raw”''' button first for all recordings and then the “Average” button for evoked recordings; this will ensure that all trials are included in data collection.

As stimuli are presented and the subject responds, you will see a list of trials (or “epochs”) collected for each different category designated in the online-averaging setup. If a trial is excluded from the average, a message indicating why is displayed at the top of the Acquisition window. Most often trials are rejected due to eye blinks, which would show as EOG 61 or 62. If an MEG channel is frequently causing rejections, attempt to heat or fix otherwise before beginning the next run. (However, never heat a channel while actually recording data).

If you feel that the subject is blinking too much and you want to restart the run, de-select the Average and Record Raw buttons, and hit '''“Restart.”''' This will clear all data collected and allow you to speak with the subject, re-measure HPI, and begin recording again.

When the run is over, hit '''STOP''' and save your data (details on saving are below). Most likely you will be collecting several runs, so after saving your data, simply hit '''GO''' again and follow the above steps.

==Saving your RAW Data==
Saving Data
At the end of a measurement, hitting “Stop” in the acquisition window will automatically bring up a window prompting you to save your data—first evoked and then raw data (if both were collected). Data is saved directly to a raid rather than the local disk.

Simply name your file with the extension '''"_raw.fif"''' and hit save.

==Subject Exclusion Criteria==

Subjects who are ready to be run on the MEG machine must satisfy the following criteria
* HEAD SIZE
* Weight
* Height

=After Data Acquisition=
After you have collected data the raw data is saved in the MEG suite computer . You will have to transfer the data to your own workstation that might probably not be in Froedtert. In this case please contact the MEG Engineer [[Contacts|Candida Ustine]] in order to transfer yoru raw data.
Please see [[Data_Transfer|Data Transfer]] for more information.

Scanning Specifics

2019-05-24T20:12:07Z

Colin: Created page with "==Getting Started== When you are ready with your experiment and would like to test it on the MEG machine before running subjects, contact Rob Rohloff to set aside..."

==Getting Started==
When you are ready with your experiment and would like to test it on the MEG machine before running subjects, contact [[Contacts|Rob Rohloff]] to set aside a time during the week when you can test your triggers on the Machine. See [[Getting_Started|Getting Started]] for information on how to access the current MEG scanner schedule at Froedtert Hospital.
==Preparing an experiment==
===Recording Parameters===
Come down to the MEG lab when there is some free time in the schedule and ask the lab technician to be present so there is help. Please make sure that you speak with [[Contacts | Rob]] and notify him that you will be in the MEG suite during that time. Click on the 'change Project' tab and select 'new'. Fill in the basic info there and save under the project name you've selected.
* Although some people use their PI as a project name, this is a bit risky since recording parameters could change across studies. It could be better to create a study-specific project every time you start a new study.

* But '''NOTE''' that a single 'Project' can be associated with a bunch of different 'Settings'. So to be safe you should make sure to explicitly load your 'Settings' every time, after you load the Project.

Now save this and click the button to change the acquisition settings. Several options here:
* You need to make sure you've selected all the MEG channels and possibly a subset of EEG channels. Confusingly, 61-64 are reserved for the bipolar channels, even if your cap has more than 60 channels...they pick up again at 65. So if you plan to record HEOG, VEOG, and/or ECG (heartbeat), make sure these are selected.
So after you have selected 61, 62, and 64, right click on each sequentially and choose either 'EOG' or 'ECG' as appropriate. '''If you leave them coded as EEG type instead of EOG type, the EEG digitization will be incorrectly mapped''' and it will be a big pain to reconstruct post-processing.
* Decide on online high-pass and low-pass filters. Convention in EEG literature is highpass of .01 Hz. Low-pass cutoff usually doesn't matter as long as it's >= 100 Hz.
* Decide on a sampling rate. The maximum allowed sampling rate depends on the data acquisition hardware and the slider automatically reflects the limitation imposed by the hardware. (Make sure it is atleast twice your low pass frequency according to the Nyquist Criterion)

==Troubleshooting==
===Restarting Acquisition===
Sometimes the Acquisition computer freezes, this can most often be fixed by rebooting the Acquisition machine. Go to Maintenance --> RestartAcquisitionPrograms. This just takes a few seconds. It can be really noisy after you do this so you should go to Tune and load vv-now.
<br>NOTE: Always alert [[Contacts|Candida Ustine]] the MEG Engineer before doing this!

===Noisy Channels===
Sometimes some MEG channels may look noisy, either with sporadic electronic spikes or be flat, in those cases you will have to Tune the channels.
Please do not tune the channels by yourself, please make sure to ask the MEG Engineer for further assistance.

MEG Lab Etiquette

2019-05-24T20:11:39Z

Colin: Created page with "=Laboratory Safety= No matter how important the study, safety always comes first. The usual rules of any lab apply to the MEG, but some additional points unique to using MEG..."

=Laboratory Safety=

No matter how important the study, safety always comes first. The usual rules of any lab apply to the MEG, but some additional points unique to using MEG are worth stressing. No measurements should be made prior to reading the following section!

===Before entering the MSR===
Subjects may not enter the magnetically shielded room (MSR) without signing a '''consent form'''. Anyone entering the MSR must first “de-metal” (empty pockets; remove jewelry, watches, wallets, cell phones, beepers, hairclips; leave pens, clipboards etc. outside).
<br>Don’t use paper clips or other small metal objects (staples, etc.) around the MSR; they tend to land on the floor and find their way inside the room.

=Dos and Don'ts for MEG=

==Experimenter==
There are a few important things one will need top know before you begin using the MEG machine.

* '''Do not open the door to the MEG chamber''', the MSR (Magnetically Shielded Room) when MEG acquisition is in session. Opening the MSR during acquisition during session will overload the sensitive SQUIDs and damage the system beyond repair.

* The MEG machine uses '''LIQUID HELIUM'''. It is extremely cold, 4K (-269°C, -452°F). If the helium tank leaks, the liquid helium will immediately boil off. This can cause rapid suffocation and severe frostbite. Handle with care.

* If you notice anything strange while doing an experiment (i.e., you suspect a helium leak), open the MSR and '''release the subject''' immediately. Do not leave the room with a subject in the MSR! Someone must be available for help if the subject suddenly has an attack of illness, or if something unexpected happens.

* '''Do not bring ANY magnetic things''' (This includes belts, keys, watches, coins, bras, hair barrettes and pins, eyeglasses and pieces of clothing with magnetic parts. Objects such as cell phones, pagers, cameras, flashlights, or any other electrical equipment are strictly forbidden.) into the MSR. Strong magnetic fields may cause damage to the MEG sensors.

* Always check the subjects for any Magnetic material before taking them into the MEG chamber.

* Subjects who may arrive unprepared will be issued non-magnetic clothing supplied by the hospital.

* '''No food or beverage''' is allowed inside the MSR!! You may bring food/beverage into the lab, but do NOT bring them into the MSR.

==Subject==
===Subject Preparation and Experimental Setup===
Before beginning any measurement, several steps must be taken to prepare the subject and the acquisition system. An overview of these steps is as follows:
====Consenting the Subject====
You MUST receive the subject’s consent before he or she can begin the study. Please make two copies of each of this document: one for the subject and one for the MEG lab.
====De-metalling====
Have the subject empty pockets, remove all jewelry, glasses, wire-bras, etc and take off shoes (see above). All subjects are required to wear hospital-issued pants, and if necessary (due to non-removable metal on shirts), subjects can be provided with tops and robes. Those subjects requiring glasses will be given special non-magnetic frames and lenses. Experimenters should also de-metal to the extent of removing items from pockets, jewelry, ID tags, etc, and most importantly anything electronic. (It is not necessary to remove glasses so long as you do not bring your face especially close to the sensors).

Getting Started

2019-05-24T20:11:10Z

Colin: Created page with "=Getting Started in the MEG Lab= Welcome to the MCW - Froedtert's MEG facility! If you would like to tour the facilities please contact our MEG Lab Manager Contacts|Dr. Jef..."

=Getting Started in the MEG Lab=

Welcome to the MCW - Froedtert's MEG facility! If you would like to tour the facilities please contact our MEG Lab Manager [[Contacts|Dr. Jeff Stout]] or our MEG Engineer [[Contacts|Candida Jane Maria Ustine]]. If you would like to speak with someone about incorporating the MEG technique into your research work, please contact our Research Director, [[Contacts|Dr. Colin Humphries]].

=Getting Trained=
Before new researchers can start using the MEG facility at Froedtert, they will have to be trained on how to use the system and also informed about the dos and donts in the lab. Please contact [[Contacts|Candida Ustine]] to arrange for a training session.

Please read the page on [[MEG_Lab_Etiquette |MEG Lab Etiquette]] before you begin.

=Reserving Measurement and Analysis Time=
Once you ready with your experiment and would like to start testing you will have to reserve the MEG machine for your study.

All time requests for the MEG should be submitted directly to Robert Rohloff, rrohloff@mcw.edu

===Tech Support===

'''Possible tech-supported measurement times for Research purposes are: Weekdays from 1pm-5pm'''

Weekend scanning can be arranged upon prior request and approval.

Tuesdays are reserved for the helium fill. All Mornings are reserved for Clinical studies.

=== MEG Calendar===

See [[Getting_Access|MEG Calendar]] for more info.

=Helpful References/Manuals=
Paper copies of the Elekta Neuromag manuals can be found in the cabinets located above the acquisition desk. Various stimulus system manuals can also be found in the lab. Tech support will be available to all new users, but please '''familiarize yourself with the stimulus and Elekta Neuromag manuals''' (in addition to this introductory manual) before beginning any recordings.

'''List of References:'''
<br>
# [http://www.unicog.org/pm/uploads/MEG/NM23065A%20Dacq-4.0_Users_Manual.pdf Elekta Neuromag Manual]
# [http://www.megwiki.org/images/a/aa/MaxFilter-2.0.pdf Maxfilter]

Freesurfer

2019-05-24T20:10:32Z

Colin: Created page with "== Introduction == Freesurfer is a software package developed at the [http://www.nmr.mgh.harvard.edu/ Martinos Center for Biomedical Imaging] for performing surface-based ana..."

== Introduction ==

Freesurfer is a software package developed at the [http://www.nmr.mgh.harvard.edu/ Martinos Center for Biomedical Imaging] for performing surface-based analyses of brain imaging data.

== Documentation ==

A comprehensive description of using the various tools in Freesurfer can be found at the [http://surfer.nmr.mgh.harvard.edu/fswiki Freesurfer Wiki].

== Usage ==

[[Creating a surface in Freesurfer]]

Brainstorm

2019-05-24T20:09:55Z

Colin: Created page with "=Introduction= Brainstorm is a very user friendly software for MEEG data analysis, that is predominantly GUI driven. This page will give you information on how to use Brainsto..."

=Introduction=
Brainstorm is a very user friendly software for MEEG data analysis, that is predominantly GUI driven. This page will give you information on how to use Brainstorm to analyse your neuromag MEEG data collected at the MCW-Froedtert facility.

=Download=
The software can be downloaded from the [http://neuroimage.usc.edu/bst/download.php Brainstorm Download] page. Instructions on how to install are also found there. NOTE that you will need to have MATLAB installed on your machine, but stand-alone versions of the software can also be installed.

=Using Brainstorm with Neuromag=
TO BE COMPLETED

=Creating your own pipleine=
TO BE COMPLETED

FieldTrip

2019-05-24T20:09:28Z

Colin: Created page with "=Introduction= FieldTrip is a Free and Open Source MATLAB based toolbox for MEEG analysis. It is developed by the Donders Institute for Brain, Cognition and Behaviour. Field..."

=Introduction=

FieldTrip is a Free and Open Source MATLAB based toolbox for MEEG analysis. It is developed by the Donders Institute for Brain, Cognition and Behaviour. FieldTrip can read and work with all commercial MEG data formats. It can do all parts of analyses, preprocessing, artifact removal, averaging, source analyses and much more.

=Importing Neuromag(*.fif) in FieldTrip=

Fieldtrip can import neuromag data but there is a special way to do this. Follow the following commands to read and import your Neuromag306 data in fieldtrip and work on it as a matlab data structure.

*hdr = ft_read_header('cu1_AudioRun1_raw.fif')
*dat = ft_read_data('cu1_AudioRun1_raw.fif')
*Fevents = ft_read_event('cu1_AudioRun1_raw.fif')
*cfg.headerfile = 'cu1_AudioRun1_raw.fif'
*cfg.inputfile = 'cu1_AudioRun1_raw.fif'
*cfg.dataset = 'cu1_AudioRun1_raw.fif'
*cfg = ft_definetrial(cfg)
*To define the trials
**F = []
**[len, ~] = size(Fevents);
**for i = 1:len
** %disp(Fevents(i).sample);
** F = [F, Fevents(i).sample];
**end
**F = F';
**endS = F(:,1);
**begS = F(:,1);
**endS = endS(2:len);
**begS = begS(1:len-1);
**offset = zeros(1,len-1)';
**samples = horzcat(begS, endS, offset)
*cfg.trl = samples

=Artifact Removal=
==ICA Artifact Removal==
See the [http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_ecg_artifacts ICA for ECG] page for information on how to apply ICA projection on your raw data to remove ECG - heart beat artifact.
<br> Useful mailists answers: http://mailman.science.ru.nl/pipermail/fieldtrip/2012-April/005011.html

=Converting FieldTrip to Neuromag Raw FIFF=
Once you are satisfied with the necessary data processing steps in the FieldTrip environment in MATLAB, you can write the raw data back to the Neuromag FIFF structure that can be read by mne.

== Steps to Follow ==
* Open Matlab
* Have the data struct ready after you are done with FT processing(eg: ft_preprocessing, ft_resampledata etc.,)
* ft_defaults
* fifffile = [pathstr filesep name '.fif'];
* data = ft_checkdata(data, 'datatype', {'raw', 'timelock'}, 'feedback', 'yes');
* info = data.hdr.orig;
* [outfid, cals] = fiff_start_writing_raw(fifffile, info);
* fiff_write_raw_buffer(outfid, data.trial, cals);
**NOTE that the channel data structures must match the buffer and the calibration struc obtained from the data.hdr struct
**Make sure you are writing all the trials into the raw fiff file. For this purpose, you can set one sample to hold the entire time period.
* fiff_finish_writing_raw(outfid);

=Time Lock analysis =
When you have pre-processed your data and have run the ICA analysis to clean the data you are now ready to proceed to the sensor level analysis. This is done by calling the ft_timelockanalysis and ft_timelockgrandaverage commands in FieldTrip. Follow the commands below for computing the average across runs within a subject and for computing the average of a run for a specified trial condition.

===Within Subject Average ===
# cfg = []
# cfg.channel = meg
# cfg.vartrllength = 1 % Accept variable length trials
# tl_run1 = ft_timelockanalysis(cfg, run1.data_clean)
# tl_run2 = ft_timelockanalysis(cfg, run2.data_clean)
# cfg = []
# cfg.keepindividual = 'no'
# cfg.channel = meg
# cfg.method = 'within'
# cfg.parameter = 'avg'
# [tl_all] = ft_timelockgrandaverage(cfg, tl_run1, tl_run2)

===Plotting Averages ===
# cfg = []
# cfg.showoutline = 'yes'
# cfg.layout = 'neuromag306mag.lay'
# cfg.xlim = [0.0 0.5] You can edit the time window here
# ft_multiplotER(cfg, tl_all)

=Source Analyses=
==Preparing Anatomical and Spatial Information==
# ft_defaults
# [mri] = ft_read_mri('MPRAGE.nii')

=Common Issues=
===1) ICA on Neuromag MEG: runica error===
Problem: surf, X, Y, Z, S cant be complex
<br>Solution: Do not include the Reference channel in the cfg or the other option is to specify the components to be 1 less than the number of channels you would like in the component analysis. Read the links below for more detailed info and for commands to included in your script.
<br>http://mailman.science.ru.nl/pipermail/fieldtrip/2013-October/007067.html
<br>http://fieldtrip.fcdonders.nl/faq/why_does_my_ica_output_contain_complex_numbers

===2) fiff_start_file: Permission denied===
See here: http://mailman.science.ru.nl/pipermail/fieldtrip/2014-March/007748.html

MNE

2019-05-24T20:08:58Z

Colin: Created page with "Link to Page: [http://martinos.org/mne/stable/index.html MNE Python Homepage]"

Link to Page:

[http://martinos.org/mne/stable/index.html MNE Python Homepage]

Anaconda

2019-05-24T20:08:29Z

Colin: Created page with " ==Install anaconda== https://docs.continuum.io/anaconda/install Open your .cshrc file and add the following lines depending on the version you downloaded set path = (/ho..."

==Install anaconda==

https://docs.continuum.io/anaconda/install

Open your .cshrc file and add the following lines depending on the version you downloaded

set path = (/home/custine/anaconda2/bin $path)

To use a specific version of python say for example Python version 2.7: (In Linux)

conda create -n py27 python=2.7 anaconda

Useful Webpages:
* https://docs.continuum.io/anaconda/faq#does-anaconda-include-python-2-or-python-3

==Installing MNE python dependencies==

conda install scipy matplotlib scikit-learn mayavi ipython-notebook

Data Transfer

2019-05-24T20:07:29Z

Colin: Created page with "=Transfer of Data from the MEG Suite= When you are done collecting data you will have to transfer the raw.fif datasets over to your own workstation outside of Froedtert. The..."

=Transfer of Data from the MEG Suite=

When you are done collecting data you will have to transfer the raw.fif datasets over to your own workstation outside of Froedtert. The data data acquired at the MEG facility at Froedtert must be processed with SSS as the Suite has Active Shielding.

The raw data is convereted into SSS raw data and then handed over to the Researcher. Please contact the [[Contacts|MEG engineer Candida Ustine]] for this purpose. As soon as you are done collecting data, the Engineer will do the initial processing and have the _raw.fif and _raw_sss.fif data ready for you. You will then have to transfer the data(sftp) over to your machine.

==fileZilla==

For the purpose of secure data transfer, the raw.fifs will be hosted in the Froedtert server for '''only 7 days'''. PLEASE be mindful that data will be refreshed every 7 days and any old data will be deleted. It is your responsibility to copy files over from the Froedtert server over to your local machine.

As soon as you finish data collection, the raw.fif are converted to sss_raw.fif and saved under a folder hosted by the Froedtert server.The name of the folder will be the name of your institution. You will have to connect to this server from your local machine via the fileZilla client and then use the password assigned to your institution and copy the data over from the server over to your machine.

Please contact [[Contacts|Candida Jane Maria Ustine]] for your secure Institutional password.

Contacts

2019-05-24T20:06:36Z

Colin: Created page with "__NOTOC__ The MEG Lab and its Personnel are spread across the Medical College of Wisconsin and the Froedtert Hospital. Here are a list of Personnel who are involved in the ME..."

__NOTOC__

The MEG Lab and its Personnel are spread across the Medical College of Wisconsin and the Froedtert Hospital. Here are a list of Personnel who are involved in the MEG Program.

'''MCW PEOPLE DIRECTORY:''' If you are looking for someone not in this list, go to the [http://infoscope.mcw.edu/mcwephonebook.htm? MCW Directory] website.

=At MCW=
<table style="background: inherit;" border="0" width="100%" cellpadding="20%">
<tr valign="top">
<td style="border: 1px solid gray" width="33%">

===Manoj Raghavan, MD, PhD===
Medical Director
<br>mraghavan@mcw.edu

===Colin Humphries, PhD===
Research Director
<br>chumphri@mcw.edu
<br>(414)-456-4660

===Jeff Stout, PhD===
MEG Technical Manager
<br>jstout@mcw.edu
<br>(414)-805-1174

===Candida Jane Maria Ustine, M.Eng===
MEG Engineer
<br>custine@mcw.edu
<br> (414) 955-7376

</td>

</table>

Equipment

2019-05-24T20:05:39Z

Colin: Created page with "<DIV align="right">Go back to: Main Page</DIV> =MEG= == Elekta Vectorview Scanner == Our Program is equipped with state-of-the-art MEG instrumentation. * 306 MEG channe..."

<DIV align="right">Go back to: [[Main Page]]</DIV>

=MEG=
== Elekta Vectorview Scanner ==

Our Program is equipped with state-of-the-art MEG instrumentation.

* 306 MEG channels (204 planar gradiometers and 102 magnetometers)
* 60 simultaneous EEG channels
* Sampling up to 5 KHz
* Simultaneous ECG, EOG recordings
* Simultaneous recording of 8 analog channels (for e.g. audio, respiration, skin conductance, etc.)
* Magnetic shielding provided by a 7-tons magnetically-shielded room with active flux compensation (MaxShield™ technology, Elekta)
* Online head-movement monitoring and offline correction provided by MaxMove™ technology (Elekta)
* MEG measurements can be done in supine and seated position.

=EEG=
64 channels
TO BE COMPLETED

MEG at the Medical College of Wisconsin

2019-05-24T20:04:00Z

Colin: Created page with "= About MEG = Magnetoencephalography (MEG) is a non-invasive diagnostic tool that can help neurologists and neurosurgeons evaluate and map brain activity before surgery. MEG..."

= About MEG =

Magnetoencephalography (MEG) is a non-invasive diagnostic tool that can help neurologists and neurosurgeons evaluate and map brain activity before surgery. MEG offers a way to localize brain activity with a high spatial and temporal resolution, and represents a significant advance in the care of patients with brain tumors or severe epilepsy. A MEG scan is performed as an outpatient procedure.

See the [http://www.mcw.edu/MEG/AboutMEG.htm MCW MEG Program] website for more detailed information on the MEG system, its physical significance and application.

=MEG system=
Froedtert & the Medical College of Wisconsin are the first in Wisconsin to offer MEG in a clinical (patient care) setting. In addition to clinical uses for neurosurgical planning, Froedtert & the Medical College conduct research studies using MEG to further develop this technology.

See [[Equipment]] for further information on the Instrumentation in the Building.
TO BE COMPLETED.

=Location and Contact Info=

The MEG lab is located in Froedtert Hospital at the Milwaukee Regional Medical campus. Our address is:

MEG Laboratory
Froedtert Hospital
9200 W. Wisconsin Ave
Milwaukee, WI, 63226
Phone: +1 414 805 1106
Fax: +1 414 805 1103

For directions by car: [http://www.froedtert.com/locations/froedtert-directions See here]

We are located on the lower level in the connector tunnel between Froedtert and Children’s Hospitals. Patients and clinical subjects are scheduled through the Neurophysiology Lab: EEG, EMG, EVP and should check into that department before coming to the MEG lab for a scan.

Main Page

2019-05-24T20:02:28Z

Colin:

__NOTOC__
{| cellspacing="5" cellpadding="20" width="100%" style="border: 1px solid blue"
|-
|<DIV align="left" style="color: blue; FONT-size: 200%">Welcome to the MCW MEG wiki!</DIV>
These pages would give you an overview about MEG, its physics and how to record and analyse your datasets acquired here at MCW. Please feel free to [[Contacts|contact us]] with any updates or information you would like to share on this wiki page. Thanks and hope you would find this useful!
|}
<table style="background: inherit;" border="0" width="100%" cellpadding="20%">
<tr valign="top">
<td width=50%>
== SiteMap ==

* [[MEG at the Medical College of Wisconsin]]
* [[Equipment|MEG/EEG Instrumentation]]
* [[MEG Physics]]

==People==
*[[Contacts]]

==Computing==
*[[Data Transfer]]
*[[SQUIGGLES COMPUTER]]

==Useful Websites==
* Official Medical College of Wisconsin MEG Website: [http://www.mcw.edu/MEG/AboutMEG.htm MEG Program at MCW]
* MEG Principles and Neuronal Basics: [http://www.mcw.edu/MEG/AboutMEG/MEGPrinciples/Physiologicalsourcesofelectromagneticfields.htm MEG Basics]
* MCW People Directory: [http://infoscope.mcw.edu/mcwephonebook.htm? Phone Book]

<br>
==MEG Lab News==
*[[News and Updates]]
*[[MEG Talks]]

==Software==
*[[Anaconda]]
*[[MNE]]
*[[FieldTrip]]
*[[Brainstorm]]
*[[Freesurfer]]

<td>

==Information for New MEG studies==
<table>
<tr><td valign="top" width=50%>
'''Running MEG Studies at MCW'''
*[[Getting Started]]
*[[MEG Lab Etiquette]]
*[[Scanning Specifics]]
*[[MEG Acquisition]]
*[[Getting Access]]
*[[FAQs]]
*[[MRI Acquisition]]
</td>

<td valign="top" width=50%>
'''Experimental Presentation and Trigger Information'''

*[[Designing your Experiment | Experimental Setup]]
*[[Psychopy]]
*[[EPrime]]
*[[Sending/Receiving triggers through parallel port interface]]

'''Data Quality'''
*[[Artifacts in MEG data]]

</td>

</tr> </table>

==Epilepsy Connectome Project==
<table>
<tr><td valign="top" width=50%>
'''MEG - Epilepsy Connectome at MCW'''
*[[Using GitLab]]
*[[Data Acquisition Protocol]]
*[[ECP Analysis Pipelines]]
*[[FAQs]]

</td>
</tr> </table>

== MEG Analyses ==
<table>
<tr><td valign="top" width=50%>
'''Pipeline'''
*[[Scripts]]
*[[Pre-Processing]]
*[[MEG Artifact Correction]]
*[[Sensor Level]]
*[[Source Level]]

</td>

<td valign="top" width="50%">
'''Software'''
*[[MNE]]
*[[FieldTrip]]
*[[Brainstorm]]
*[[Freesurfer]]
</td></tr></table>

== MEG Tutorials ==
*[[EEG re-reference with Brainstorm]]