LOCATOR MIT

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					                                                                                                                     Locator--1


LOCATOR ........................................................................................................................ 2
   STARTING UP.................................................................................................................... 2
     Open Locator. ............................................................................................................. 2
     Open the appropriate sequence file ............................................................................ 3
     Place the neck collar with the three receivers around the subject's head .................. 3
     Place the transmitter near the subject ........................................................................ 3
     Sterilize the tip of the stylus ........................................................................................ 4
     Begin the digitizing ..................................................................................................... 4
   DIGITIZE ELECTRODE/MARKER COILS .............................................................................. 4
   DIGITIZE HEAD SHAPE ..................................................................................................... 8
   FINISHING UP ................................................................................................................. 10
   TROUBLESHOOTING ....................................................................................................... 10
     Hardware/software ................................................................................................... 10
     Marker coils .............................................................................................................. 11
     Head shape................................................................................................................ 11
   MRI FROM LOCATOR DATA ........................................................................................... 12
     Open the Create MRI file dialog box ........................................................................ 12
     Load the Head Shape file .......................................................................................... 13
     Load the Marker Coil file ......................................................................................... 14
     Name and save the MRI file ...................................................................................... 14
MARKER COILS ........................................................................................................... 15
   RUNNING THE MARKER COILS ........................................................................................ 15
     Plug in and turn on the connection box. ................................................................... 15
     Close and lock the MSR ............................................................................................ 15
     Run the Marker Measurement .................................................................................. 16
       Locate the burst/coil waves ................................................................................... 16
       Locate the burst/coil waves ................................................................................... 17
     Sample Marker positions .......................................................................................... 18
       Coil 0..................................................................................................................... 18
       Coil 1..................................................................................................................... 18
       Coil 2..................................................................................................................... 18
       Coil 3..................................................................................................................... 18
       Coil 4..................................................................................................................... 18
   PROCESSING THE MARKER COILS (MEG160) ................................................................ 19
     Open the Marker Positioning dialog box (if necessary). .......................................... 19
     Load the marker.sqd file (if necessary)..................................................................... 20
     Make sure the estimation parameters are correct (if necessary) ............................. 20
     Execute the localization function (if necessary) ....................................................... 20
     Review the results of localization ............................................................................. 21
     Optional .................................................................................................................... 22
       Compare values with another marker.sqd file ...................................................... 22
       Average two or more marker.sqd files .................................................................. 22
                                                                                  Locator--2


LOCATOR
          If localization of dipoles is to be performed, the localization programs (EMSE,
Curry, Brainstorm, MEG-MUSIC) require information on the location of the sensors, the
head, and the head with respect to the sensors (N.B., if EEG recordings are going to be
used in the localization process, the positions of the electrodes too need to be digitized.).
This information is pieced together by the markerwork process. The final product is a
coregistered probe file that EMSE, Curry, and Brainstorm use to tell where the sensors
and where the head were located. Information about the location of the head comes from
the *marker.elp file that is produced by Locator during the head digitization process; this
information is in a 3-D coordinate system defined by the head/anatomical markers, and
varies from person to person. Information about the location of the MEG sensors is
produced by the markerwork process and comes initially from the*marker.sqd file that
was recorded by MEG160 prior to testing and ends up in the*meg.elp file produced by
the markerwork process; this information is in a 3-D coordinate system defined by the
center of sensor space. There are thus two different coordinate systems in play, one
head-centered (*marker.elp) and one sensor-centered (*marker.sqd/*meg.elp); EMSE
takes both of these files and creates a coregistered probe file that includes both head and
sensor information in a single coordinate system, a head-centered frame of reference. It
only needs three marker coil locations to perform this, and it disregards extra marker
coils. Additionally, EMSE simply performs a rigid transformation between the
coordinate frames. If there was a problem with any of the marker coils, either during
digitization or marker.sqd recording, it can be disregarded as long as three coils worked.
          The locator program is has been adapted to work with EMSE; however, both
Curry and MEG160 can use the data it records if converted to the proper format. There
are two outputs needed from the Locator program, head shape (.hsp files) and marker
coil/electrode placement (.elp files). NB: If for any reason one of the marker coils or
electrodes should become detached, either during digitization or during the experiment
itself, technically the electrode/marker coil and head shape data should be re-digitized: if
strict localization were going to be attempted, there would be a slight mismatch between
where a coil or electrode was when first attached, and then later reattached. For the same
reason, even if a subject has participated in many MEG studies, electrode/marker coil
placement and head shape data should be collected anew each time.

Starting up

Open Locator.
   On the desktop of the PC, there is a shortcut to
   "locator.exe;" use this to run the locator. The actual
   path of the program is C:/source signal
   imaging/Locator41. Sometimes, the computer will not
   be able to find the Fastrak; if this occurs, a message
   will come up. If this happens, turn off the Fastrak (the
   switch is in the back), wait 10 seconds, then turn it on again. When the green light on
   the front of the Fastrak becomes steady (stops blinking), try running Locator again.
                                                                               Locator--3


Open the appropriate sequence file
   The sequence file identifies the anatomical landmarks, marker coils, and/or electrodes
   for which data will be recorded. Under the "File" menu, select "Open" and choose
   the appropriate sequence file. There are at present 3 sequence files:
                                                           mark-5coils.seq" which is for
                                                           the 5 electromagnets and
                                                           fiducials
                                                           "mark-EEGonly.sqd" which is
                                                           for the 23 electrodes of the E-
                                                           cap and fiducials,
                                                           and "mark-5coils-EEG.seq"
                                                           which is for the 5
                                                           electromagnets, 23 electrodes
                                                           of the E-cap, and fiducials.


Place the neck collar with the three receivers around the subject's head
   This is easiest if you ask the subject to hold the marker coil wires that have been
   attached to his/her head, and you slide the collar underneath. Make sure the subject's
   chin goes in the chin rest; otherwise, the subject will be very uncomfortable. Velcro
   the collar shut.

Place the transmitter near the subject
   Make sure the transmitter at the right rear corner of the chair (as you face the
   chair). On the top of the transmitter are two axes in one corner, one designated "X,"
   the other "Y;" the subject's head should be within the box traced by these axes, and
   these axes should be aligned as directed on the floor. If the subject's head is not
   within a box formed by these axes, the locator program will not be able to run as
   efficiently. Note also that these X and Y coordinates are totally unrelated to the XYZ
   coordinates that are used in the EEG and MEG systems.




           x-axis

                               y-axis
                                                                                       Locator--4


Sterilize the tip of the stylus
   Use an alcohol swab; there are extra swabs located in the top left-hand drawer of the
   desk in E10-039.

Begin the digitizing
   Select, from the
   "Digitize" menu the
   "number of
   receivers on
   subject" submenu,
   and select 3 (this
   refers to the three
   located on the neck
   collar).
                                                     Select, from the "Digitize" menu, the
                                                     "electrode data" option. The locator
                                                     program will now walk you through
                                                     electrode/marker coil digitization.:




First, it asks that you confirm that the subject is wearing the collar, and that the
transmitter has been placed near the subject.




                            Press the ">>" button to advance



Digitize electrode/marker coils
        Electrode/marker coil files (.elp) record the locations of three anatomical
landmarks (fiducials) (the nasion/NZ, left preauricular point/LPA, and right preauricular
point/RPA) that are used to match up structural MRI data to MEG data, the five marker
coils (red-#0, yellow-#1, blue-#2, white-#3, ,green-#4) that are used to match up MEG
sensor placement with respect to the subject's head, and/or the 23 electrodes in the E-cap.
Note: the blue marker coil (#2) is typically placed above the NZ (the NZ is the
intersection of the vertical crease between the eyebrows and the horizontal start of the
nose cartilage), the red marker coil (#0) is typically on the LPA (the LPA is on the
subject's left; it can be found by asking the subject to move his/her jaw up and down and
left and right. The point where the jawbone goes into the skull, right by the ear, is the
                                                                               Locator--5


LPA), and the yellow marker coil (#1) is typically placed on the RPA (the RPA is
identical to the LPA, only on the subject's right).

       After selecting the
        "electrode data" option
        from the "Digitize"
        menu (see above), the
        locator program (after
        confirming set up is
        appropriate) will ask for
        the NZ. Place the tip of
        the stylus on the nasion
        (NZ) and press the stylus
        button once.
       The locator will now prompt for the LPA; place the stylus on the red marker coil
        (LPA) and press the stylus button.
       The locator will now prompt for the RPA; place the stylus on the yellow marker
        coil (RPA) and press the stylus button
       The locator will now proceed into the appropriate sensor digitization(s) (that is,
        marker coil, electrode, or both, depending on which sequence file was selected—
        see above) digitization.
       Marker Coils: The order is as follows: mark0 is the red coil (LPA); mark1 is the
        yellow coil (RPA); mark2 is the blue coil (above Nasion); mark3 is the white coil,
        on the subject's left forehead; mark4 is the black coil, on the subject's right
        forehead
                                      marker 2

                marker 4
                                                             marker 3




       RPA/marker 1
                                        +                            LPA/marker 0




                                                 Nazion
                                                                                                           Locator--6


 Electrodes/E-cap (see diagram below): The order is as follows—down the left
  hemisphere (FP1, F7, F3, T3, C3, T5, P3, O1), to the midline (FZ, Ground, CZ, PZ),
  down the right hemisphere (FP2, F8, F4, T4, C4, T6, P4, O2), to reference/auditory
  (A1, A2), to the ocular sites (EOG1, EOG2)


                                                           NZ (nasion)
                         EOG1 (left eye)                                                 EOG2 (right eye)




       LPA (left                                                                                           RPA (right
                                                FP1                           FP2
   preauricular point)                                                                                  preauricular point)



                                                               FZ
                             F7                                                                F8
                                                 F3                           F4
                                                              GND



        A1          T3                     C3                 CZ                    C4                T4          A2




                                                P3                            P4

                             T5                                                                T6
                                                               PZ




                                                      O1                 O2




Electrode placement diagram



   When you have finished, you should see a figure as below, showing the 3 fiducials
   and five markers (the labels for the markers may be turned off or on using the Labels
   radio buttons in the lower right corner.
                                                                             Locator--7




   When you have finished
    digitizing the fiducials and
    electrodes and/or markers, the
    locator will ask you if you will
    to proceed to head shape
    digitization. When done with
    electrode data, the program will
    automatically ask you if you
    wish to proceed with head shape digitization; if head shape is desired, press “yes.”
                                                                                  Locator--8



Digitize Head Shape
        Head shape files (.hsp) record the approximate shape of a subject's head by
marking a point every .5cm the stylus is moved (this is modifiable—the distance between
points can be increased or decreased). Later, during localization, these points are used to
set limits: Localization algorithms are typically “dumb” in the sense that they do not care
whether the source they find is inside the brain or in space; so, the head shape data is
used to constrain localization algorithms to preclude/exclude localizations outside the
brain. Some localization algorithms compute from the head shape data the best-fitting
sphere, and then constrain localizations to be within that sphere.
        Ideally, data points
should be collected from all
over the target area, not just
in one location—that is, the
whole of the skull enclosing
the brain, not just the top of
the head. When collecting
head shape data for MEG,



                                                       the target area is the upper portion
                                                       of the head (i.e., the portion housing
                                                       the brain; additionally, the nose may
                                                       be digitized to serve as a landmark.
                                                       The more data points collected,
                                                       ostensibly the more accurate the


localization constraint
computed; currently, we try
to get around 600 data
points, although in the past        New points
anywhere between 500 and
                                                                           Old points
1000 points have been
collected. The number of
points collected is displayed
in the lower right corner of                                        Total points
the window.
        Head shape data is
easier to digitize in a
number of small sequences
of points, rather than a
single sequence of 500 or more points. In order to digitize a head shape sequence, the
stylus should be placed so that its tip is touching the head. The button on the side of the
stylus should be pressed once to begin recording points. After a predetermined distance
                                                                                  Locator--9


has been traveled, another point is located; as long as the stylus is moving, points will be
recorded. If a zigzag path is traveled (by moving the stylus in short jags left and right),
the number of points recorded will be maximized. To finish digitizing a sequence, press
the button on the stylus a second time.
         If you accidentally remove the
stylus from the head while digitizing, or if
a sequence looks odd, you may delete it by
pressing the delete sequence button in the
lower right. Sometimes, the digitizer will
itself recognize that a series of points is
unusual, and ask you if you wish to remove
them.

        When head shape digitization has been completed, the "accept" button (bottom
    middle of the window) should be pressed. A completed head shape should give a
               reasonable approximation of the upper portion of the head.:
                                                                                 Locator--10



Finishing up
        After digitizing electrode/marker coil and head shape data, two files should be
                                              saved manually via the "File" menu. Save
                                              the head shape data by selecting an ".hsp"
                                              file type (bottom of the save window). Save
                                              the electrode/marker coil data by selecting
                                              an ".elp" file type (bottom of the save
                                              window). When exiting the locator
                                              program, it will ask again to save the data,
                                              due to a flaw in the program; it gives this
                                              prompt whether or not the data files have
already been manually saved (relax, if
you have in fact manually saved the .hsp
and .elp files, you can ignore this
message, however stressful that may be.
If you are feeling very insecure, you can
look in the data folder
(C:/fleissbackup/locator41/data/) to make
sure saved the marker.elp file was saved).
        Remove the collar from the
subject, being careful not to accidentally
                                                   rip off one of the marker coils (as with
                                                   putting the collar on, this works easily if
                                                   the subject is asked to hold up the wires
                                                   leading from the marker coils).
                                                           The PC and the digitization
                                                   hardware may be left turned on.

Troubleshooting
Hardware/software
   Monitor problems: Occasionally, the monitor of this PC freezes or is frozen; if this
    occurs, simply turn the monitor off and on again
   PC problems: Occasionally the computer itself will freeze; in this case simply restart
    the computer (note: if you restart the computer, you will have to log on again. There
    is no password to log on; when logging on, user the username <administrator> and
    leave the "password" section blank); normally, when the PC is rebooted, Locator
    requires that the Polhemus 3space digitizer be turned off and on again
   Locator program problems: Occasionally also, the locator program will tell you that it
    cannot "find" the digitization hardware; if this happens, try turning the digitization
    hardware off and on, and also make sure all the connections on the back of the
    digitization hardware and the PC are firm-- it is unclear why, but these two steps
    normally fix the problem. If both of these steps fail, try restarting the PC (see above
    note about logging on)
                                                                                    Locator--11


Marker coils
   Pressing the stylus button too soon—it is easiest to quit the program and begin again;
    while it is possible to edit the .elp file, it is much more time-consuming than simply
    starting over.
   Digitizing coils in the wrong order—see previous
   Subject movement-- Do not worry if the subject moves: the three sensors in the
    collar are designed to compensate for small movements. If you make a mistake
    digitizing the electrode placement, it is best to quit the program and begin again.

Head shape
   Stylus lifted from the head—if sufficiently deviant, the Locator program will offer a
    warning and ask if the sequence should be deleted. Even if the Locator program does
    not offer the option of deleting the sequence, in the lower right corner of the screen is
    an option for manually deleting the sequence. NB: the first sequence of points
    digitized cannot be deleted; so, if the first sequence of points is inaccurate, it is best to
    "cancel" (bottom middle of the window) out of the digitization process and begin
    anew.
   Subject movement-- As with marker coil digitization, do not worry if the subject
    moves: the three sensors in the collar are designed to compensate for movement.
                                                                                Locator--12



MRI from Locator Data
To create an "mri" file from Locator data, you need the marker.elp file, the shape.hsp file,
and MEG160.

Open the Create MRI file dialog box
Select Create MRI File from digitizer data either from the File menu or the MRI menu
                                                                         Locator--13



Load the Head Shape file




                           This data will appear in the Heasd Shape Summary




                                  This preview will appear
                             Locator--14


Load the Marker Coil file




Name and save the MRI file
                                                Locator--15


MARKER COILS

Running the marker coils

Plug in and turn on the connection box.
        The connection box is where the
marker coils are plugged in. It also provides
power to the electromagnets (via 8 AA
batteries), and feeds in the DAQ as well
(channel 104). Turn on the connection box
inside the MSR before beginning your
recoding session. Plug in the marker coils
according to the color coding.


               Power switch: turn on
               before use; TURN
               OFF AFTER USE



Close and lock the MSR
                                                     Locator--16


Run the Marker Measurement
                             This can be done simply by
                             pressing "start" under the Marker
                             Measurement section of the
                             Monitors and Acquisition dialog.
                             After 16 successful epochs have
                             been recorded, the process will
                             terminate. Consult the
                             "MEG/How to use it" manual for
                             information on the Monitors and
                             Acquisition dialog box. To view
                             the process as it occurs, see below.
                                                                                              Locator--17


LOCATE THE BURST/COIL WAVES
You should see the "burst" waves, five in a row, repeated. Each wave represents one of
the markers. Sometimes they will be smaller, depending on where the subject's head is.
If you are not sure that you see all five, examine channel 104, the marker coils reference
channel. If you do not see 5 waves there, the coil set is not working properly.
                                                                           5 magnets, on subject (note:
                                                                           NZ/coil2 is weaker than
                                                                           others, but it is still strong
                                                                           enough to localize)



 Coil 0       Coil 1        Coil 2
                                            Coil 3         Coil 4
 (LPA)        (RPA)         (NZ)




                Here, coil 3 (white/left forehead) is not working; not only is it
                not seen under the sensors (upper picture), it is also not
                present in the feeback wave on channel 104 (lower picture)
                              Locator--18



Sample Marker positions
COIL 0




                          Coil 0
                          (LPA)




COIL 1




                          Coil 1
                          (RPA)



COIL 2




                          Coil 2
                          (aboveNZ)



COIL 3




                          Coil 3



COIL 4




                          Coil 4
                                                                            Locator--19



Processing the Marker Coils (MEG160)
        After running and recording the marker coils, you should process the file.
MEG160 will prompt you for automatic processing. Otherwise, use the manual method
to invoke the Marker Positioning below. This will show where the coils are located, and
thus give you an idea of where the subject's head is located.

Open the Marker Positioning dialog box (if necessary).




                                         Open the Marker Positioning dialog box, either
                                         via the File menu, or the MRI menu
                                                                           Locator--20



Load the marker.sqd file (if necessary).




Make sure the estimation parameters are correct (if necessary)
Number of Markers should match the number of working coils.
Reference Channel is 104 for the 96-channel system, and 72 for the 64-channel system.
Averaging Count should be 16.
Trigger Threshold should be around 160.

Execute the localization function (if necessary)
                                                                              Locator--21


Review the results of localization
In particular, examine the GOF (goodness of fit) of the estimations (these should ideally
be above 99%), and the locations of the coils as displayed in the Axial (top-bottom),
Sagittal (side), and Coronal (front-back) views.
                                                                             Locator--22



Optional
COMPARE VALUES WITH ANOTHER MARKER.SQD FILE
If you have more than one marker.sqd file for the same session, you may compare values.
Press the Compare button. You will be asked to load the second file. The differences
between the localizations will be presented numerically:




and may also be presented graphically if you answer "yes" to display:

                                                                        Circles represent
                                                                        the current file,
                                                                        and crosses
                                                                        represent the
                                                                        second file.




AVERAGE TWO OR MORE MARKER.SQD FILES
If you have more than one marker.sqd file from a session, after estimating each file, you
may create a Grand Average (consult the MEG160 manual for information on this) of the
estimated files. This grand average file will also average the estimated placement of the
marker coils.

				
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