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This is POLGUI Ver 1.0, a Matlab Interface for Polhemus DigitizerAuthor Nitin B Bangera POLGUI is distributed under the terms of the GNU General Public License,with an exception to allow for easier linking with external meshgenerators. See LICENSE.txt for more information.Type help polgui_ver1_r14 on the MATLAB command prompt or read below :-------------------------------------------------------------------------                  -- POLGUI Ver 1.0 for Matlab R14 -- -------------------------------------------------------------------------Matlab Interface for Polhemus Digitizer( Only with one stylus pen )Author Nitin B Bangera NOTE : Set Screen Resolution to "1280 by 1024" or higher for GUI to bedisplayed correctly Usage :        ------ polgui_ver1_r14, by itself, creates a new POLGUI_VER1_R14 with     default settings of 1 receivers (stylus pen)     ------ modify line 235 to change EEG Montage      ------ modify line 271 and 273 to set Baud rate euivalent to that on     Polhemus (default set to 57600)     Baud Rate Settings on switch on back of Polhemus ( 1= UP, 0=Down)      Baud rate    SW 1  SW 2   SW 3        1200        0      0      0        2400        1      0      0        4800        0      1      0        9600        1      1      0        19200       0      0      1        38400       1      0      1        57600       0      1      1        115200      1      1      1Important Variables Saved: in file collected_data.mat-------------------------------------------------------------------------data_orig --> Original Data including the 3 consecutive points collected for each location for averaging and pen movement error detectiondata -> Averaged datadata_transf -> Data transformed to head co-ordinate framelocation -> Names of locations digitizedcount -> Total number of digitized pointsM -> Rotation matrix for transformationT -> Translation matrix-------------------------------------------------------------------------Description of global variables and counters in the code needed_loc LOC DATA DATA_ORIG DATA_TRANSF COUNTER COUNTER1 special_case strmatch_index redigitize additional T M   needed_loc  -> chararcter array with the CARDINAL POINT locationsand EEG montage locationsLOC-> Set of digitized  locationsDATA_ORIG -> Original Data before averagingDATA -> Data after averaging 3 successive digitizations for each pointDATA_TRANSF -> Data after co-ordinate transformationCOUNTER -> Main CounterCOUNTER1-> Counter which includes count for 3 successive digitization for each pointTag for 4 cases for remove button : special_caseCase 0-> Initial Condition  , Case 1-> counter <=4Case 2-> Counter between 4 and length of needed montage Case 3-> Additional Pointsstrmatch_index ->  matches current Vaue in the listbox with needed_loc matrix and returns index redigitize -> Tag to check if redigitization is needed Values: 0 or 1additional -> Tag to check if digitization of additional points is needed Values: 0 or 1T -> Translation MatrixM -> Rotation Matrtix--------------------------------------------------------------------------Steps for head digitization using POLGUI1.Before starting GUI, edit EEG_MONTAGE variable (on line 215 in this m-file) to set requiredmontage to be acquired. 2. Start GUI by typing name of this m-file in MATLAB command line (GUImode) e.g. polgui_ver4_r14 Follow these steps in GUI by clicking on respective buttons in sequentialordera. Initialise Device: Serial Object created with specific Baud rate. Change this call back tochange serial port propertiesTo digitize position the tip of the Isotrack Stylus at the desired pointand click on the dialog box within the GUI. The co-ordinatesdisplayed are the averages of three sequential readings taken from thedigitizer. If they differ from each other by more than 2 mm, you are askedto digitize the point again.b. Get Test Point:Secure one test pointc. Get Cardinal Points in order LA(left Auricular), RA(Right Auricular)and Nasion.d. Align Frame from device coordinates to head co-ordinate axes determined by the cardinal pointsHead Coordinate system:The head coordinate system is defined as folloew: The x axis passes through the preauricular points with positive values on the right, the y-axis will beperpendicular to x axis, passing through the nasion and the positive axis pointing towards the nose, and the z axis will be pointed up, perpendicular to xy plane.The auricular points are known as anatomical landmarks or cardinal points.Principle: When Align Frame is press, the coordinates of the cardinal locations will change to head frame. Notice the z coordinates of all three points arezero. The y coordinates of the auricular points are zero with a positive xcoordinate on the right and a negative on the left auricular point,respectively. The nasion has  a zero x coordinate and its y coordinate ispositive. The auricular points will be almost symmetrically located: their x coordinates are opposite and about of equal magnitude -Procedure for alignment-------------------------------------------------a1. Calculate the new origin coordinates oDefine three vectors a(nasion-la), b1(ra-la) and b2(la-ra)Drop projection of a on b1 and b2 to calculatet1 and t2 respectively.find ratio in which projection from b1 (point o) divides vector b1o=la+t*b1   o=(Ox,Oy,Oz)b1. Define the three new coordinate axes ox(normalised ra-o),oy(normalisednasion-o),oz(cross(ox,oy))c1. First translate orgin by -oDefine Translation matrix T as follows:    | 1   0   0    0|    | 0   1   0    0|T = | 0   0   1    0|    |-Ox -Oy -Oz   0|d1. Then Rotate .Define Rotation Matrix M as folows:R=[ox;oy;oz]R1=inverse(R) or transpose(R)   |"  "  "|   |"  R1 "|M= |"  "  "|   |0  0  0|e1. Transform points to new co-ordinate axes with center at o and threeaxes ox,oy and oz[xnew ynew znew ]=[xold yold zold 1]*T*M;-------------------------------------------------------------------------e. Get EEG montage points.f. Get additional pointsFot additional points , click the stylus pen for digitization.g. Press stop to close the serial device and delete objects from memory.------------------------------------------------------------------------- 

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