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BET VIEWER

1. Solid Cancel Figure 37 Selection of style dialog for grid and vectors Atlas settings This command in the View menu set the atlas configuration for viewing When activated a dialog is presented for setting visibility color and style for the different structures present in the atlas 46 User Manual BET Viewer Version 1 3 Description of comnands Atlas settings Structures kS medial front orbital gyrus right E middle frontal gyrus right EJ vewe insula right precentral gyrus right 7 Color lateral front orbital gyrus right HA cingulate region right medial frontal gyrus left superior frontal gyrus right Style globus pallidus right globus pallidus lett putamen left l interior frontal gyrus left C Filled f Contour angular gyrus right brain stem subthalamic nucleus right v E v w E v E v M v E v E v Mi v E v M v M v E v E v Mi v E v E putamen right parahippocampal gyrus left With the Structures list it is possible to select the structure s for changing its attributes visibility and color The commands Load and Save allow to load and save respectively visibility and color settings from to a ATS file for using them in ulterior working sessions Plot Maximum in sequence This command in the View menu works as a toggle when turned on every time a solution is loaded from the sequence see Open Solution the Orthogonal Planes sheet will visualize the solution
2. bob A A tt A Fy tt Fee MIA 4 01M E FOR oO o 4 1t 2 U87E 3 Y q 1 E a oot bt Ft Ft O t t FF t t Ft FF Ft Ft t tae t tot tee eee EE A Figure 34 Overlapping of the grid on the tomographic slices The overlapping of the grid is not carried out in the 3D View sheet and the command is disabled in that sheet The overlapping of the grid is carried out only over the slices intercepting the grid Show vectors 44 E This command appears in the View menu It works as a toggle when turned on the vectors which indicate the generators direction are superimposed on the tomographic slices visualized in the work sheets The activation of this command inactivates the command Show grid and viceversa The vectors are visualized by means of arrows that point in the corresponding direction of the current dipoles If the direction is perpendicular to the plane it will be indicated with a point or a cross if the vector is entering or leaving respectively Overlapping of the vectors is not carried out in the 3D View or in the Max Intensity Projection sheets and the command is disabled in these sheets If the type of active tomographic solution does not contain information about the direction
3. PRINTS TOMO ING SOU A ad 23 Howto visualize IN E16 CHOOSES asc aia 23 WOW anina OS a a crs tein een een ln Cetin eee ends 24 Descrip ion OF COMMMAMNGS ico od 25 New Image Contiguraton CHEN dais 25 A asea ceutonsudpagamestnoonaeg ss 25 Open Image Conme uration C O ini rin 26 OPENA IS ern r AA AOS 26 Open Eleciodes Fl A ai 26 Open SOON E 26 AS oa O aden eens 27 VESO A 27 MOE is ie 28 EXPO o a teib taeda cemeat eho edsehes T R 28 Ada Comme sais erie uso ii is 28 PPI O 29 PANCETO OW apretar a EE UNE EATE tentodees 29 Toolbar of PANE rre iWorld tas 29 P e E T O E T oseerendesest ead 30 EXT Ca n E E E E A A 31 RR 31 COPOS dada 31 MI II O A A E ihc coea tel che IN 33 LA A O A A A E MR asl artes 33 CAS MADE di 33 ZOOM IMITA Oo 34 SCS OU O id a li 35 Shan A T E E A E E E A E cid 37 LA A A a a a a a Ri ae late es 39 Cie Chale MOV A A A A a a N 40 PIA MOVI TR 40 ER eTO a EE EE A ENEE EEE EER ENEA EE EN EE EE EEE EN 41 PREVIOUS SOMO tasa 41 FE ESOO ales ene ee eee eee E E A A a a a Mere nnT Orie 41 O A a aa a n a a ON APTN POOR T ee Ot oe Pe 41 COO O O y IRON RO e A A AA enes orate namie mamnntseeentes 41 SEP IS UENO aeni A sidune ca seue a seoa uaa aadstie a daaiae 42 A A E A NC 42 TODA co e tie 42 A A IN 43 AUasantormalon Dat lts oie odas ies 43 FOU Ci Gia estes gar tati hsa oasis atau ENE EE E T atten esas cin satan eaten toate EEEE E ec eat 43 SHOW ONMOGO Tall Dari ia ados 43 Grids SUC IOS 2c Ge thot cela cada 43 NOWE OA A
4. the option for interpolating is not set the palette will be used without interpolation By means of the option list it is possible to select any one of the available palettes Once the window is closed with the Ok button the newly selected palette will become the active palette of the application If the Edit button is pressed the window is enlarged adding new controls to change the palette Change Palette Curent RAINBOW 4 cee Previews Preliminary Number of Colors 5 coler Current fi Current color view Interpolation option Button for B changing color W Interpolated Buttons for al moving colors Edite 4 Add Color Delete Color Add and Delete color buttons Cancel Figure 30 Change palette window Button for editing palette The first element that appears is a vertical bar divided by the quantity of real colors that compose the palette The colors are denoted in bottom up order from O to the number of colors 1 The number of colors is indicated in the box Colors Dragging the mouse over the cursor 4 to the right of this bar sets the active color The active color can also be selected with the edit box Current There are also 5 buttons for editing the palette E This button changes the active color When pressed opens the standard Windows dialog for selecting colors T This button moves the active color up in the palette It is disabled when the active color is the last one in th
5. 00000 Figure 42 Black amp White visualization mode 52 User Manual BET Viewer Version 1 3 Description of comnands Isocontour Mode 2 This command in the View menu View sets the Tomographic mode as the active visualization mode In this mode the tomographic solution is visualized through isocontours that are superimposed on the underlying anatomical image This command is one of several options to set the active visualization mode Tomography Mode Inverse Tomography Mode Map Mode Image Mode and Black amp White Mode lo A i f ili h i 2 08 E 3 Cursors ks 144 Ie 2 1153 E 0 00000 Figure 43 Isocontour visualization mode I The command Isocontour style controls how the isocontours cover the image User Manual BET Viewer Version 1 3 53 Description of comnands Invert Black amp White This command appears in the View menu It works as a toggle to invert the palette direction in the Black amp White visualization mode see Black amp White Mode 13 This command only is enabled if the active visualization mode is Black amp White Use Maximum This command appears in the View menu It works as a toggle when not active the action in the commands Show Maximum and Plot Maximum in sequence is inverted becoming Show Minimum and Plot Minimum in sequence The work sheet Max Intensity Projection becomes Min Intensity Projection also plotting in this
6. A A ead scenes 44 SS retentesh cc ate aaah aa Giada tomes ace easton Sa tae See a aaa 44 A O IO 45 Tic e o A A 46 ASES A A A A a bette gees 46 PiotMaximunmn TASQUES 47 OMMOR GAIN a iii 47 Inverse Tomosra pay Mode pan an iio 49 MADAMOO ini adas 50 A states eae batts E eet eed Seed cuas 51 BICK Se WV le MOOG tances ese Asst A A eae tess 52 ISOCONMIOUR MOOC ii isis 53 WAV CTE BIA CKC VV Ii EE ec sees Seca Boa acetal O 54 RISE Nei Nl IEE AT AE E A A TEE TTA 54 W EE A E 54 INnvertaiMPI Dacia 54 O A E E EE 55 Prane INAN iS A HE Oo 55 EA A eases etaeene 55 OMe is rra a A A 55 A E O 55 E at 56 DO as es Needs 56 A A E O II A E 56 A A Roe mt nga eae CEE ror 56 Show ladeni e te o dla o a 56 Figu res Figure 1 Location of the grid in the image VOIUME sise c ccccsewseseedaveveeencecesedsedecettpewsusevdessesgancecssodsedeces 2 Figure 2 sesmentaton Or inem a 3 Figure 3 Elements of ine main screen OF BET Viewer eun shied eetebnaeseacastdeubeageedsbebetectes 5 Figure 4 BET Viewer tod Dal ri ti 6 FUE BE VIE WES tatu Dado a tae 7 Figure 6 Orthogonal Planes A filed aseamsnceesdantec cocdee 9 Feur AESI EOS WORK SM 10 FIGURE Oo Le VCW WOKS NEO eea T T 11 Figure 9 Rotation sheet in 3D Parameters osuna 12 Figure Os Lights meet 13 Paranee S ache akencs hse cadens OO a 13 PISUre a lI MISGSMECE in O Parameters dt idos 14 Figure 12 Visibilibysmect m 3L Parameters ds 15 Figure lo BOCCULSMEEL 11D Paramete eia a ases 16 Figure
7. The toggle Best Fit is also shown which when turned on automatically adjusts the scale based on the extreme value of the tomographic solution This scale type explicitly visualize the peak positive and negative values inside the tomographic solution This effect is achieved by temporarily zeroing all the values in the tomogram that do not coincide with the peak values When this scale type is selected the edit box Maximum is shown to define the value that will serve as extreme value in both directions The toggle Best Fit is also shown which when turned on automatically adjusts the scale based on the extreme value of the tomographic solution With this scale type it is possible to work with the values of the tomographic solution in relative rather than real magnitudes Conceptually it is similar to the MaxMin type but the values are scaled by percent For the percent conversion the maximum value of the tomographic solution is taken as 100 converting the rest of the values in relation to the maximum When this type is selected two edit boxes are shown Minimum and Maximum for defining the values in and the toggle Best Fit which when turned on causes an automatic adjustment based on the extreme values of the tomographic solution This scale type is similar to Percent but here it is possible to determine the sign of the peak value that will be taken as the reference of 100 When this type is selected the edit box Minimum is shown to define the
8. brain processes such as cognition or abnormal brain processes such as epilepsy BET requires a solution for the inverse problem of the EEG This is the problem of estimating the intracerebral generators given voltage measurements taken from the scalp Complex calculations using the recorded electric activity the coordinates of the scalp electrodes where the EEG was recorded and tomographic anatomical information lead to an electrical tomography describing the distribution of cortical currents that generate the recorded electric activity This tomographic solution can then be represented in image form using the BET Viewer In order to visualize the solution the BET Viewer needs to be configured with the current elements in the solution the grid used to localize these intracerebral currents and the anatomical images needed for visualization The anatomical images can provide the whole brain or only parts of the brain segments The grid is built over the whole image volume although only the points that intercept with the chosen segments are used for the calculation as showed in Figure 1 This segmentation could show the complete brain or just the gray matter as illustrated in Figure 2 The anatomical image can contain several million voxels and the grid is built so that it embraces the largest number of voxels in the regions of interest for the inverse solution The resolution and accuracy of BET depends among other factors on the number of poin
9. case only the values with the minimum intensity Invert MIP back This command appears in the View menu It works as a toggle when not active the image background in the sheet Maximun Minimun Intensity Projection is plotted in black When active the background is inverted and becomes white Isocontour style This command in the View menu sets the way in which the isocontours are plotted see Isocontour Mode By means of an edit box it is possible to set the step between an isocontour and the next one When the step is small the the isocontours will cover more of the image and viceversa Isocontour style Figure 44 Dialog for Isocontour style 54 User Manual BET Viewer Version 1 3 Description of comnands Slice orientation This command in the View menu brings up a dialog window to selecting the orientation of the slices in each plane appears Slice Orientation E4 Axial i Right Left Coronal ie Right Left C Left Right i Lett Right Sagital Anterior Posterior C Posterior mnterior Figure 45 Slice orientation dialog Plane in All Slices This command in the View menu opens a dialog window to select which orthogonal plane will be shown in the All Slices work sheet see All Slices All Slices Reference This command in the View menbrings up the auxiliary reference window in the All Slices work sheet see All Slices Contents This command in the Help me
10. in the 3 planes containing the point where the tomographic solution reaches its maximum magnitude and the solution will be scaled automatically using its extreme values see Use Maximum The command is disabled if the active tomographic solution is not a sequence Tomography Mode This command in the View menu sets the active visualization mode to tomography In this mode the integration of the color of the tomographic solution with the anatomical image is carried out using the intensity of the anatomical image as the intensity coefficient for the color The voxels of the anatomical image with more intensity will have a brighter color in the tomographic solution This command is one of several options to set the active visualization mode Inverse Tomography Mode Map Mode Image Mode and Black amp White Mode User Manual BET Viewer Version 1 3 47 Description of comnands Cursors E 0 00000 Figure 38 Tomographic visualization mode 48 User Manual BET Viewer Version 1 3 Description of comnands Inverse Tomography Mode This command in the View menu sets the active visualization mode to inverse tomography In this mode the integration of the color of the tomographic solution with the anatomical image is carried out in the same way as in the Tomographic mode using the intensity of the anatomical image as intensity coefficient for the color but the inverse of the intensity of the anatomical image is used The voxels
11. is 0 0 1 meaning that the light points to the front of the head Intensity The intensity is a real value between 0 0 and 1 0 The rendering process combines this coefficient with other factors to achieve the depth effect An intensity coefficient of 0 0 ignores the incident light whereas an intensity coefficient of 1 0 ignores all other factors The default initial value is of 0 5 Reflection The reflection coefficient is an integer value between 1 and 10 that controls the amount of reflection of light from the 3D surface Higher values cause highlights and give a metallic appearance to the surface The Default button allows restoring the implicit values for each parameter In the preview of the sheet the result of applying the active values for each parameter is shown with a model human head E The default illumination parameters lead to reasonable renderings These parameters a should be changed only if some unusual illumination is wanted User Manual BET Viewer Version 1 3 13 Work sheets Misc This sheet sets two other two parameters for the 3D rendering Thresholds This parameter sets the detection thresholds in the anatomical image of the skin and the cerebral cortex These values can be changed using the edit box existent for each surface There is no need to change the default values unless the user wants to experiment Wrong values can invalidate the surface detection process The Default button allows restoring the
12. minimum value in the maximum is always 100 as well as a radio control Peak to set the sign of the peak value With this scale type only the values of the tomographic solution included in the interval defined by the parameters are visualized When this type is selected the edit boxes Minimum and Maximum are shown to define the interval used for scaling If the minimum and maximum of the solution are given as parameters then this scale type is equivalent to a MaxMin scale with Best Fit turned on Contrasting with the Maxmin scale type the values outside the interval are not plotted This scale is similar to Spot only the values of the tomographic solution included in the interval defined by the parameters are visualized When this type is selected the edit boxes Minimum and Maximum are shown to define the interval used for scaling in the positive direction The solution values outside the interval positive and negative directions are not plotted The BIPOLAR palette see Change Palette is recommended when using the following scale types Threshold Step Pos Neg Peak and Positive Peak User Manual BET Viewer Version 1 3 Description of comnands If the toggle Keep scale parameters is turned on every time a new tomographic solution is loaded it will be scaled using the last scale parameters used Otherwise the scale parameters will be adjusted automatically using the extreme values of each tomographic solution Scale Solutio
13. of the anatomical image with more intensity will have a darker color in the tomographic solution and vice versa This command is one of several options to set the active visualization mode Tomography Mode Map Mode Image Mode and Black amp White Mode 2 067E 3 Figure 39 Inverse Tomographic visualization mode E With this mode is possible to highlight the color in the gray matter and to attenuate a the color in the white matter of the brain User Manual BET Viewer Version 1 3 49 Description of comnands Map Mode f This command in the View menu sets the Map mode as the active visualization mode In this mode there is no integration of the color of the tomographic solution with the anatomical image The tomographic solution is visualized independently of the underlying anatomical image This command is one of several options to set the active visualization mode Tomography Mode Inverse Tomography Mode Image Mode and Black amp White Mode 2 067E 3 0 00000 Figure 40 Map visualization mode E With the Map mode is possible to visualize details of the tomographic solution that a might be hidden if the solution were integrated with the anatomical image 50 User Manual BET Viewer Version 1 3 Description of comnands Image Mode 2 This command in the View menu sets the Image mode is set as the active visualization mode In this mode as in the Map mode there is no integration of the color of the tomogr
14. shows at each point of the slice the maximum intensity of all slices in that plane see use Maximum The view is similar to what would be seen if the active areas were in a glass head The sheet also shows the values of the active scale and palette E In this sheet it is possible to visualize the tomography in either Map or Black amp White E modes Mas Intensity Projection 1 12916 0 00000 Figure 15 Max Intensity Projection work sheet E When moving the mouse cursor over the slices the coordinates are only fully fi reported in the status bar if the current voxels intercept the grid Otherwise only the two coordinates that intercept the plane are reported nt In this work sheet the command Show vectors is disabled The command Show grid is disabled if the projection is carried out over a template associated with the anatomical image User Manual BET Viewer Version 1 3 19 Work sheets Electrode View This work sheet shows the electrode positions on the 3 dimensional anatomical image The sheet behaves in the same way as the 3D View sheet and there is a similar auxiliary window for selecting the different parameters to use in the 3D rendering E 3D Parameters joy x Electrode View Preview 3D Parameters auxiliary window Render Eahtel Figure 16 Electrode View work sheet In the auxiliary window the Render button starts the rendering once the desired parameters have been set The Cancel bu
15. solution Scale solution A S5 R M e Scale blankini 7 ll le H H A detailed explanation of these commands will be given in the following chapters User Manual BET Viewer Version 1 3 Working screen Status bar BET Viewer has a status bar describing in several fields the current state of the active work sheet and other contextual information Image coordinates Sequence Talairach Indicator Tomography coordinates value Active Solution Active configuration l AVERAGE JCBFACE THT 5 6 120 7 34 2161 0 00025045 5 35 7 68 2 12 Figure 5 BET Viewer status bar Pressing the right button of the mouse on the fields of the bar gives further E E information Active The active image configuration is described configuration Sequence indicator This field shows which image in a sequence is presently imaged see command Go to Solution Image coordinates This field describes of the x y z coordinates BET system used by the BET Viewer for the present tomograms Talairach This provides the equivalent Talairach coordinates if the coordinates anatomical image of the active image configuration is in Talairach space E The Talairach coordinates are showed only if the anatomical image of the active i image configuration is in Talairach space User Manual BET Viewer Version 1 3 7 Work sheets Work sheets BET Viewer has 5 work sheets When a tomographic solution is loaded the Orthog
16. the anatomical image and not the tomographic solution Use the command Scale Solution for scaling the solution Zoom Image EN This command appears in the Display menu and in the local menus of all the work sheets This command makes it possible to magnify that part of the image indicated by the mouse cursor When activated a window is opened for showing with the active zoom factor the area of the image where the mouse cursor is located Pressing the left mouse button increases the zoom factor If the left button is pressed in combination with any of the Shift keys the zoom factor is decreased The zoom factor varies between 2x and 20x When this command is activated the form of the mouse cursor changes to a or a to indicate the direction of the magnification 34 User Manual BET Viewer Version 1 3 Orthogonal Planes Description of comnands All Slices 30 View Max Intensity Projection Current zoom factor Zoom window Figure 28 Zoom image window The zoom window stays open until it is explicitly closed by the user I Scale Solution Scale MaxMin 7 This command appears in the Display menu and in the local menus of all the work sheets By means of this command is possible to scale the active tomographic solution When activated a window is shown that sets the scale type and its parameters There are 8 scale types MaxMin Threshold Step Pos Neg Peak In this scale type the values mini
17. 14 Movie sheet 1m 3D ParamMeteS pd id R A 18 Figure Lo Max Intensity Projection work sheet isisi iea Uaioe Gasaliial Ui ie cuaa nasil a 19 Pietire To Electrode View Work SHEE estriado una dalla lem 20 Figure 17 Misc sheet for Electrode View work Sheet ooooooonccccccccncncnnnononnoooonnnnnnnnnnnnncnnnnanananann nono 21 Figure 19 Lormiorimase COMU dd olaa 25 Figure 19 Dialog Tor Open Solid 26 Figure 20s And CONMEN ES WII Wi A dd 28 Heurs 21 Printer sele chontal alo ida 29 Eig te 22 J PRIME Preview OO Dale nta al 29 F ure 235 PEM DLC IS WS SO 30 Fue 4 Prat nerolalo pe casa aci is 31 sure 20 COPY toDlimMap all el ea eahrude 32 Figure 26 Selection of background color dialog ooccccccccncncnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnninanoss 32 PIGUIC272 Scalea WIN O Weston as 34 Figure 20 ZOOM Mage WINdOW iaa 35 Figure 2D Cale SOMO WINDOW lit A 37 Figure 50 Change palco WIN o T ated eee 38 Figure al ePlay Movie WIN Westland 40 Foures GOO SOMO a aloe ii acacia 41 Figure oe oep ms AA cement tudpagaumeaianenntagns 42 Figure 34 Overlapping of the grid on the tomographic sliCeS ssssssssesessssesessssssssserssresresseseeses 44 Figure 35 Overlapping of the vectors on the tomographic slicCes ooooooooooouuuuooonconnnnnnnnnnnnnnnnan ono 45 Figure 36 Overlapping of the Atlas on the tomographic slices cccccnnnnnnononnoocoonnnnnnnonnnnnnnnnananano nos 46 Figure 37 Selection of style dialog for grid vectors a
18. BET Viewer dh A 4 Version 1 3 USER MANUAL WYNEURONIC s a Contents WFO OUCH E E E E A E A E EET E EE sehen ante O E E E E E E E T 1 Cone ural oeie A E E E A ansaevee eo seees 3 VOIKIN SCTE Ics Alene statuette e E E E E E E EN 5 AA o o OOO EP E E NT 6 Elements ome alt aa 6 A Serle trate bate occ cen nee Sea see taste E Sessa Sees ee anes ae cranes Sasa ie nee tes 7 WO SEC US 205256 soe ages AE area ce cS tee es Eee ee ce at eG te sees Eee ace T Eee tees 8 Oniosona llenas 8 A cite us dsiad aad oatech lett nee eatet ys edad aad cate chen ciate ted eeldend nad cates iciatataiet vdaacact one eanieees 10 EI POPE OE S a unssin Siraa oles an Slatted as 11 ROTA ONT ccstancaecsctaddetas uastacsdoiectentamscenadondeesaa lcd 12 A ES OREN E Sd er ee Sere eee etene 12 A AE EA pu as iasott 0A tunkupadecbicsnentonyadationtwaadndadt situstesecadadsagdoueeteencadtl 14 VISIOI Y vases A AA EE E 14 BOX CU poe erst AS A id IESS 15 EON AA N E E E ETE E E TEN E E A E AE 16 Max SMbensityPTOJEClON sannana i ps 19 EIECIOUE NIE OS 20 MISC aaa e r tinciee yasuaiee ened eaaeayncgsutatorebeessmebameat acta 21 Working Wit DET VS e os Alemariae 22 Crane ne tho concurat ON sieren aos 22 Loading lOMmOsrapMiG solutions sranane e A A A AA A 22 Chang ne Tae AC IVE Work SINC Teea aaa T A S 22 Changing the visualiza ONE sis 22 Woikine WINS Med a ia lo ela 22 Howto makea 3 DTrenderiNg ara di acacia Ae EE iia 23 CMAN BING th palote ti Rodo Roi 23
19. E 7 viewer segmentation Erain C Program Filess Meuronc Be T Viewer Grid C Program Files Neuronic BET Viewer Top View C Program Files Neuronic BET Viewer e Left View C Program Files Neuronic BET Viewer Index C Program Files Neuronic BET Viewer Atlas C Program Files Neuronc BE T Viewer Figure 18 Form for Image Configuration Edit Image Configuration This command in the File menu allows editing an existent configuration see Configuration When activated a dialog for selecting the configuration to be edited appears Once the configuration is loaded a form for editing the elements of the configuration appears Pressing the Ok button brings up a dialog window for saving the configuration User Manual BET Viewer Version 1 3 25 Description of comnands Open Image Configuration Ctrl O pai This command in the File menu allows loading an image configuration see Configuration When activated a dialog for selecting the desired configuration appears Once the configuration is selected the loading and reinitialization process starts E When a new configuration is loaded all the work sheets are reinitialized and the a previous contents of the work sheets are lost Open Atlas This command in the File menu loads an atlas file for viewing over the anatomical image in the active configuration see Show Atlas When activated a dialog for selecting the desired atlas file is pr
20. aches its maximum magnitude see Use Maximum This command is only enabled in the work sheet Orthogonal Planes Scale Image ai This command appears in the Display menu and in the local menus of all the work sheets By means of this command it is possible to scale the anatomical image to obtain better contrast for the image When activated a window is presented with several controls that allow carrying out the scaling Minimum This parameter sets the minimum of the scale using either the edit box or the scroll bar Maximum This parameter sets the maximum of the scale Threshold This parameter which is only enabled if the active visualization mode is Black amp White controls the threshold for the image contouring operation see Black amp White Mode Best Fit If this toggle is turned on the parameters Maximum and Minimum are adjusted automatically using the last slice on which the mouse cursor was located Preview If this toggle is turned on the window is enlarged to preview the last slice on which the mouse cursor was located using the active parameters for scaling User Manual BET Viewer Version 1 3 33 Description of comnands Scale Image pol Mimimum Minima Maximum and l O O O O O O O O O O O O O S S G Threshold values edition basinum e 3 a ew al Preta O omen Alle er MA al Threshold for Best Fit 4 Preview Cancel Figure 27 Scale image window E This command scales
21. akes it possible to see into the interior of the image volume The controls on the sheet indicate if the option is applied as well as the position and size of the cube to extract Apply Box Cut Activating option box turns on the cutting algorithm and enables the other controls Position These parameters set the position of the left inferior corner of the cube The 3 controls one for each coordinate are controlled by either an edit box or a scroll bar Size This parameter sets the size of the cube is set The 3 controls one for each coordinate are cotrolled by either an edit box or a scroll bar User Manual BET Viewer Version 1 3 15 Work sheets The preview superimposes on a model human head the position and size of the extracted cube in red relative to the cube that represents the full image volume in white The coordinates axes are indicated in blue 30 Parameters Me ES Box Cut A Bey Tl Box cut toggle Positions Size po m l j ks a ae 32 Position coordinates edition AAA A z m1 Cube size edition Preview Preliminary view Render bance Figure 13 Box cut sheet in 3D Parameters E The preview shows the position of the image volume relative to the active rotation B angles When the rotation angles are O the head is looking directly at the observer The parameters shown in the figure would extract a cube corresponding to the right posterior area of the image volume Mov
22. allowing updating of the plotting window with a new voexl whenever the cursor position is changed If the cursor position is updated by pressing the Alt key in conjunction with the left button mouse a new voxel is added to the plotting window instead of updating it Time course B 5867 Woxel 4182 Y E Fa 110 938 Hz 7 8505 The vertical bar in the plotting window is a cursor for selecting a temporal point inside the temporal course The tomographic solution corresponding to that point is updated in the working sheets whenever the cursor is updated In the dialog other elements are presented The combo box Voxel allows to select the active voxel if more than one is plotted The voxel visibilty can be set wit the check box besides the combo box as well as the color and thickness of the wave The following combo box shows the current temporal instant as well as the voxel s value in that temporal position User Manual BET Viewer Version 1 3 39 Description of comnands Generate Movie This command in the Display menu creates a temporal animation using the sequence already loaded When activatated the command shows a dialog for selecting the filename for saving the animation in AVI format Once the selection is made the animation begins starting with the first solution in the sequence and using the active parameters for working with sequences see Scale Solution and Step in Sequence E The animation generated can b
23. aphic solution with the anatomical image The anatomical image is visualized ignoring the corresponding tomographic solution This command is one of several options to set the active visualization mode Tomography Mode Inverse Tomography Mode Map Mode and Black amp White Mode Figure 41 Image visualization mode E The Image mode is very convenient for visualizing the details of the anatomical a image that could not be easily observed when integrated with the tomographic solution User Manual BET Viewer Version 1 3 51 Description of comnands Black amp White Mode x This command in the View menu sets the Black amp White mode as the active visualization mode In this mode the tomographic solution is visualized with a gray palette GRAYS and the anatomical image is reduced to contours There is no real integration of the color of the tomographic solution with the anatomical image This command is one of several options to set the active visualization mode Tomography Mode Inverse Tomography Mode Map Mode and Image Mode E To control the contouring of the anatomical image the command Scale Image should E be used to vary the Threshold parameter and its relationship with Maximum and Minimum E The Black amp White mode is very convenient for printing on printers without color E capability Since the palette is automatically change in this mode the palette should be checked when changing to another visualization mode 0
24. default values for each surface Background This parameter sets the background color of the 3D rendering The default initial value is Black 30 Parameters Al ES Misc Thresholds Background Skin 50 Background color Black selection Cortes fi 30 di C White Default Detection thresholds selection Render Thane Figure 11 Misc sheet in 3D Parameters Visibility This sheet varies the visibility of the cerebral cortex in the 3D rendering With this parameter it is possible to reduce the rendering time by inhibiting the rendering in the part of the head that does not correspond to the brain To set this parameter the following controls are used All Cortex If this toggle is turned on all the brain is visible and the other controls are disabled 14 User Manual BET Viewer Version 1 3 Work sheets Y This parameter can be directly edited or controlled with the scroll bar The brain will be visible at vertical values above the selected Y coordinate The left view of the anatomical image shows the visibility achieved if the current value of the parameter is applied 30 Parameters visibility Left image view A Y coordinate edition F All cortex Visibility toggle for cortex Render ante Figure 12 Visibility sheet in 3D Parameters Box Cut This sheet sets the parameters for cutting out a cubic box from the 3D rendering of the image Activating this parameter m
25. e mode When beginning a new working session the last used palette will be selected To change the palette the command Change Palette will be used Printing the tomographic solution BET Viewer can print the contents of the different work sheets The Print Setup command configures the printer and selects the pages to print The Print command prints the selected sheets The Add Comment command adds comments or observations to the work sheets for printing The Print Preview command previews the sheets as they will appear on paper How to visualize the electrodes To obtain a 3D rendering of the electrodes requires loading the file of electrode coordinates by means of the Open Electrodes File Inmediately after 5 renderings are generated automatically corresponding to the front back top left and right views of the head To obtain a different view the minimum steps needed to achieve it are Activate the Electrode View work sheet see Electrode View Set the rotation angles Activate the Rotation sheet of the 3D Parameters window and using the preview put the volume in the desired position see Rotation To change any of the default values for rendering the electrodes activate the Misc sheet and change the desired parameter see Misc in Electrode View User Manual BET Viewer Version 1 3 23 Working with BET Viewer e Press the Render button in the 3D Parameters window to start the rendering process This process is carried ou
26. e command Plane in All Slices in the View menu An auxiliary reference window gives a 3D rendering of the brain showing by means of a line cursor the position in the brain of the slice selected by the mouse on the work sheet This window also shows the values of the active scale and palette Dragging the line cursor in this reference window shows the corresponding slice on the work sheet The presence on screen of the auxiliary reference window can be controlled with the command All Slices Reference of the View menu In each one of the visualized slices the orientation is pointed out in the superior border where R indicates right L left A anterior and P posterior When the mouse is moved over the slices the voxel coordinates are indicated in the status bar The value for each voxel is not shown in this work sheet E When pressing the right button of the mouse over the elements of the sheet a local a menu is showed with commands available to these elements Auxiliary reference window All Slices 20 All Slices 0 00000 Figure 7 All Slices work sheet E The presence on screen of the auxiliary reference window can be controlled with the w command All Slices Reference of the View menu 10 User Manual BET Viewer Version 1 3 Work sheets 3D View This work sheet visualizes the tomography in 3 dimensions The 3D visualization requires time Depending on the volume of the image angles of rotation selected etc the render
27. e for the animation that will be generated in AVI format The chosen name will appear in the Output file box During the animation the number of frames rendered will be monitored in the Frames rendered box lt 3D Parameters JOf ES Movie Toggle for generating m movie W Generate movie Ww Starting from current parameters Toggle for using current Movie type Spins once around Y axis parameters Step 5 00 Movie type selection Output file Movie type parameters Frames rendered AVI file for storing the movie Render Cancel Figure 14 Movie sheet in 3D Parameters T The progress bar of the animation that replaces the status bar during the rendering shows the progress of each frame separately and not the progress of the whole animation process T The animation can be played with any multimedia player supporting the AVI format or with the command Play Movie nt If the Cancel button is pressed during the generation of the animation sequence the 18 user can save the frames generated until that moment User Manual BET Viewer Version 1 3 Work sheets Max Intensity Projection Like the Orthogonal Planes sheet this work sheet shows the tomography in 3 orthogonal planes All the slices of each plane are projected together onto one slice If the anatomical image has a template for this purpose this is used otherwise the projection is carried out onto the middle slice in each plane The projection
28. e names of the visible electrodes 56 User Manual BET Viewer Version 1 3
29. e palette This button allows moving the active color down in the palette It is disabled when the active color is the first one in the palette This button adds a new color in the palette When pressed opens the standard Windows dialog for selecting colors Once chosen the new color becomes the active color and is inserted after the previously Zz Add Color User Manual BET Viewer Version 1 3 Description of comnands active color It is disabled when the palette reaches the maximum of 256 allowed colors a This button erases the palette s active color The following color iii becomes the new active color This button is disabled when the palette reaches the minimum of 2 colors When pressing the Ok button a dialog for saving the recently edited palette is presented if any editing was carried out The palette files are stored as files LEV in the application s directory E The palette GRAYS cannot be altered since it is the one used by the Black amp White visualization mode The palette BIPOLAR can be edited but should keep its name Show time course This command in the Display menu shows the temporal course if a sequence is loaded of a selected voxel When activated a dialog is presented containing a plotting window showing the temporal course of the voxel indicated by the orthogonal cursors in the Orthogonal Planes sheet The dialog can be closed with the Close button at any moment staying visible for
30. e played with any multimedia player supporting the E AVI format or with the command Play Movie Movie generation can be aborted by pressing the Esc key Play Movie This command appears in the Display menu With this command it is possible to play any AVI animation created with Generate Movie with the 3D View work sheet or any other application When pressed a dialog is shown for loading the AVI file desired Once the file is loaded a window is shown with 7 buttons Play Play Stop First frame Rewind Fast forward Last frame and Close that will control the execution of the animation There is also a track bar which monitors the animation status Play Movie E APPTABET AVI Figure 31 Play movie window 40 User Manual BET Viewer Version 1 3 Description of comnands Next Solution la This command in the Display menu loads the tomographic solution following the active one in the sequence see Open Solution taking into account the defined step see Step in Sequence The command is disabled if the active tomographic solution is not a sequence or if it is the last one in the sequence Previous Solution dl This command in the Display menu loads the tomographic solution before the active one in the sequence see Open Solution taking into account the defined step see Step in Sequence The command is disabled if the active tomographic solution is not a sequence or if it is the first one in the sequence Firs
31. er that allows True Color 24 bits is recommended 4 User Manual BET Viewer Version 1 3 Working screen Working screen Once BET has been loaded and initialized the system s main screen is presented BET Viewer has 5 work sheets with a menu bar a toolbar and a status bar common to the 5 sheets although there will be elements that will be available or not depending of the active work sheet Application title including tomographic solution and active configuration BET Viewer JHOR NORM A ES superior temporal gys left Figure 3 Elements of the main screen of BET Viewer E The Atlas information bar will be enabled only if the anatomical image of the active a configuration has an associated atlas or the active configuration includes an atlas User Manual BET Viewer Version 1 3 5 Working screen Toolbar BET Viewer has a toolbar with buttons for the more frequently used commands aa 000000 AG Figure 4 BET Viewer toolbar Elements of the toolbar DE hl gt ODA ys b lb dl ib H H Open image configuration Open tomographic solution Use grid steps Show orthogonal bars Set Tomographic mode Set Inverse tomographic mode Set Map mode Set Image mode Set Black amp White mode Set Isocontour mode Show solution maximum Change palette Print Preview Print all work sheets Zoom image Show vectors Scale image Show previous solution Show next solution Show first solution Show last
32. esented Open Electrodes File This command in the File menu loads a file of electrode coordinates for later visualization on the anatomical image When activated a dialog for selecting the desired file appears and inmediately after 5 renderings are generated automatically corresponding to the front back top left and right views of the head E When a new file of electrode coordinates is loaded the work sheet Electrode View is M enabled or reinitialized thus losing its previous contents Open Solution F2 pe This command in the File menu loads a tomographic solution When activated a dialog for selecting the desired solution appears Open Solution Look irr J Img En cantor aa avedell eng 8 C125_351 eng je sa Casp eng Jih 8 Div _195 eng 8 1255612 eng a Dfw_507 eng 2 1275521 eng a shc002 eng File name Casp eng Files of type ENG files bd Cancel Solution type Help selection Figure 19 Dialog for Open Solution 26 User Manual BET Viewer Version 1 3 Description of comnands There are five possible solution types TXT ENG ORT MDL and MOD The TXT and ENG files are ASCII files the ORT and MDL files are binary files storing floating point numbers in single precision 4 bytes The TXT and ORT files include information about the orientation and magnitude of the generators The ENG and MDL files only include information about the magnitude The solution files can c
33. esponding to the anatomical image seen from above Left View Specifies the full path and name of the file 3D containing a 3D rendering of the brain corresponding to the anatomical image seen from the left Index Specifies the full path and name of the file IND containing indexes to the points of the grid used to calculate the solution Atlas Specifies the full path and name for the files VOX and HDR containing the atlas attached to the anatomical image The anatomical image which used by BET can be an individual image obtained from Magnetic Resonance Imaging or Computed Assisted Tomography an average image across many individuals or an atlas image BET Viewer can work in two different execution environments e Stand alone the system can load and visualize tomographic solutions already calculated and stored on disk e Linked to a program for calculating the inverse solution BET viewer will then be called to visualize the Brain Electrical Tomography images as they are calculated BET Viewer provides both 2D and 3D visualization of tomographic solutions sequences of these visualizations like movies and different tools to explore and measure the Brain Electrical Tomography BET Viewer is a Windows 9x Windows NT compliant 32 bit application that requires large amounts of memory At least 64 Mbytes of RAM is needed for the program to work efficiently Since the application is devoted to evaluating color images a video adapt
34. f the file appears The dialog also shows the existent files on disk Preliminary view in real size User Manual BET Viewer Version 1 3 31 Description of comnands Copy To Save Ir E t Peer eerie Preliminary view Bitmap type selection File name Save as Ippe Bitmaps bmp Figure 25 Copy to bitmap dialog E E This command is only enabled if the active work sheet has content Copy Options This command in the Edit menu sets the background color of the bitmaps saved with the commands Copy or Copy To When activated a dialog for setting the 3 possible background colors appears Copy Options Background f Current f Black Cancel C White Figure 26 Selection of background color dialog E The selection made with this command is also used for the bitmaps used in the A animations generated by the command Generate Movie 32 User Manual BET Viewer Version 1 3 Description of comnands Clear all This command in the Edit menu erases all the renderings that have been carried out in the work sheets 3D View and Electrode View E This command is only enabled when there is at least one rendering For erasing only E one of the renderings the command Clear this should be used instead of Clear all Show Maximum F8 An This command in the Display menu makes the work sheet Orthogonal Planes show the 3 planes containing the point where the tomographic solution re
35. g with this brain Save Solution This command in the File menu saves a tomographic solution When activated a dialog for editing the name for the solution to be saved appears If the active solution includes information about the orientation of the generators TXT ORT it is possible to save it without that information by selecting the ENG or MDL type in the dialog User Manual BET Viewer Version 1 3 27 Description of comnands Import This command in the File menu imports an image volume in ANALYZE format or iMagic format as a tomographic solution When activated a dialog for selecting the desired image appears If the image to be imported contains more than one volume the generated solution will be considered a sequence E Only the ANALYZE images stored in transverse orientation axial can be imported To be imported the image dimensions should match with the anatomical image dimensions or grid dimensions of the active configuration Export This command in the File menu exports a tomographic solution or a sequence of them to an image in ANALYZE format or iMagic format When activated a dialog for editing the name for the solution to be exported appears The dialog allows to select the image type to export for the ANALYZE format grid image or full image If the grid image type is selected only the solutuion values matching with the grid will be exported obtaining in this way a more compact and red
36. he application for a window where a preview shows the work sheets as they would look on paper when printed The window has a toolbar with commands for adjusting the preview Toolbar of Print Preview Previous page One page Zomm selection activation Next page Full screen Two pages activation activation Current page s indicator y Ae t e OD GS Cue Figure 22 Print preview toolbar Print all pages Close preview User Manual BET Viewer Version 1 3 29 Description of comnands ee BET Viewer JCBFACE AYERAGE mm Pages fi og E El Cloe luhen ECAPACE Cenaquraaen AFE EGE Toolbar Page header Comments added to the page Figure 23 Print preview The work sheets Orthogonal Planes and Max Intensity Projection are printed in a single page respectively but the remaining sheets can take more than a page depending on their contents The work sheets Orthogonal Planes and Max Intensity Projection are therefore numbered 1 and 2 The work sheet All Slices will start on page 3 and will use as many pages as needed The numbering will then continue with the work sheets 3D View and Electrode View nr Depending on the form of the mouse cursor a or a when pressing the left button of the mouse the magnification of the page will be increased or reduced In the page headers the following elements appear application logo center where BET Viewer is installed company or distr
37. ibutor logo active tomographic solution active configuration and page number Print Ctrl P This command in the File menu prints of the BET Viewer work sheets see Print Preview When activated a dialog is shown for setting the characteristics of the printer and the pages to print When the Ok button is pressed the printing starts 30 User Manual BET Viewer Version 1 3 Description of comnands Print Printer Mame HF DeskJet 870C Seres Properties Status Ready Type HF DeskJet 8700 Series Where LPT1 Comment Print to file Print range Copies Number of copies li CU ro Cancel All pages o Pages from li to a O Selection Figure 24 Printing dialog Exit This command in the File menu allows leaving the application after confirmation When BET Viewer is executed through a linked system special attention should be paid when closing the application because undesired effects can be caused in the linked system It is therefore recommended that the BET Viewer be closed prior to returning to the linked system Copy This command in the Edit menu copies the contents of the active work sheet to the Windows clipboard rl This command is only enabled if the active work sheet has content Copy To This command in the Edit menu allows copying the content of the active work sheet to a Windows bitmap file When activated a dialog for selecting the name o
38. ie This sheet sets the parameters for carrying out a 3D animation The resulting animation is stored in standard Windows format AVI Generate If this option is turned on a 3D animation will be generated instead of a movie single view when pressing the Render button Otherwise the remaining other will be disabled Starting from When this option is activated the animation depending on the type of current animation will begin from the active values of the 3D parameters already parameters set Rotation Light Box Cut etc Movie type Select the animation type from an option list 16 User Manual BET Viewer Version 1 3 Spins Cortex visibility User defined Sequence Work sheets This type of animation generates rotations of the image volume around one of the 3 possible axes When selected the edit box Step is enabled As many frames as needed will be generated to complete a full rotation of 360 around the selected axis using the selected step This type of animation generates views of the image volume with increasing or decreasing visibility of the cerebral cortex When selected the edit boxes Step and Limit are enabled As many frames as needed will be generated to arrive at the selected limit taking into account the selected step The step sign determines if the visibility increases or decreases see Visibility sheet This type of animation generates animations defined by the user When selected a dialog i
39. if the anatomical image of the active configuration al has an associated atlas or the active configuration includes an atlas Full Screen This command in the View menu works as a toggle when turned on the main window application is maximized and at the same time the horizontal menu the toolbar and the status bar are hidden leaving the whole available space on screen for the work sheets Use the Esc key to return to the normal mode Show orthogonal bars This command in the View menu works as a toggle when turned on bars indicating the A position of the 2 orthogonal planes to every plane are shown on it This command only is enabled in the work sheet Orthogonal Planes Grid s steps ea This command in the View menu works as a toggle when turned on the cursors of the sheet Orthogonal Planes will move only in the grid s steps and when turned off they will move from voxel to voxel The tomographic values are directly calculated for the slices intercepting with the grid and interplolated for other slices This command only is enabled in the work sheet Orthogonal Planes User Manual BET Viewer Version 1 3 43 Descript ion of comnands Show grid This command in the View menu works as a toggle when turned on the grid points are superimposed on the tomographic slices visualized in the work sheets The activation of this command inactivates the command Show vectors and vice versa a e tt
40. in Talairach space the Talairach button is enabled and by pressing it a dialog is presented for selecting cursor coordinates in Talirach s system In each one of the visualized slices the orientation is indicated in the superior border where R indicates right L left A anterior and P posterior The slice orientation can ne changed with the Slice Orientation command Aditionally orthogonal bars with the option Show orthogonal bars can be superimposed over every plane showing the position of the 2 orthogonal planes When the mouse is moved over the slices the value and voxel coordinates are indicated in the status bar E Depending of the current state of the option Grid s steps the cursors will move from M voxel to voxel inactive state or in the grid steps The tomograms are directly calculated for slices intercepting the grid or interpolated if the slices are not on the grid 8 User Manual BET Viewer Version 1 3 Work sheets Axial plane Coronal plane Orthogonal Planes Active palette and current scale values Figure 6 Orthogonal Planes work sheet E Pressing the right button of the mouse over an elements of the sheet brings up a local E menu with the commands available for the selected element User Manual BET Viewer Version 1 3 9 Work sheets All Slices This work sheet shows all the tomographic slices that intercept the grid of the selected plane The plane used in this sheet is selected through th
41. ing can take up to several minutes When first activated this sheet appears empty because it works as a container where the renderings will be stored An auxiliary window is attached to this sheet for selecting the different parameters to use in the 3D rendering E In this sheet is not possible to render the tomography in Black White and a Isocontour modes pales 3D Parameters OR ES Rotation Light Misc Visibility Box Cut Movie 1 12916 Preview 0 00000 3D parameters Render Cancel or auxiliary Figure 8 3D View work sheet The Render button in the auxiliary window called 3D Parameters starts the rendering once the desired parameters are established A progress indicator of the rendering then replaces the status bar The Cancel button interrupts the rendering at any time E The rendering process is carried out as a background task so that the user can w continue working with other components of the BET Viewer The system will notify the user if he or she tries to execute an operation that would invalidate the rendering E Pressing the right button of the mouse over an element of the work sheet brings up a a local menu with commands available to the selected element The sheets composing the 3D Parameters window are described next User Manual BET Viewer Version 1 3 11 Work sheets Rotation In this sheet the rotation angles for the 3D rendering are set Angles There are t
42. lution is visualized in each work sheet using the active visualization mode as well as the active solution and image scale To change the solution scale use the command Scale Solution and for changing the image scale the Scale Image will be used 22 User Manual BET Viewer Version 1 3 Working with BET Viewer How to make a 3D rendering To obtain a 3D rendering of the tomographic solution activate the 3D View work sheet see 3D View The minimum steps needed to achieve a rendering are Set the rotation angles Activate the Rotation sheet of the 3D Parameters window and using the preview put the volume in the desired position see Rotation Set the visibility of the brain cortex Activate the Visibility sheet of the 3D Parameters window and using the preview set the visibility of the cortex in the desired position see Visibility To see the interior of the image volume activate the Box Cut sheet of the 3D Parameters window and using the preview set the size and position of the cube to extract see Box Cut If not desired pass on to the next step Press the Render button in the 3D Parameters window to start the rendering process This process is carried out as a background task allowing the user to continue with other tasks Changing the palette BET Viewer is distributed with a set of color palettes for visualizng the tomographic solution The selected palette will be used in all the work sheets except the Black amp Whit
43. mum and maximum for scaling the tomographic solution are defined When this type is selected two edit box are shown Minimum and Maximum for editing the values The toggle Best Fit automatically adjusts the scale based on the extreme values of the tomographic solution With this scale type is possible to focus on the positive and negative values in the tomographic solution When this type is selected the edit box Threshold is shown to define the threshold that will be used as the scale limit in both directions positive and negative The toggle Best Fit automatically adjusts the scale based on the extreme value of the tomographic solution This scale type highlights the peak values inside the tomographic solution When this type is selected the edit box Step is shown for defining the scaling parameter which is a positive value Bigger values cause more highlighted peaks A value of O is equivalent to a Threshold scale with Best Fit turned on This scale type explicitly visualize the peak positive and negative values inside the tomographic solution This effect is achieved by temporarily zeroing all the values in the tomogram that do not User Manual BET Viewer Version 1 3 35 Description of comnands 36 Positive Peak Percent Peak Percent Spot Spot bipolar coincide with the peak values When this scale type is selected the edit box Maximum is shown to define the value that will serve as extreme value in both directions
44. n Scale type MaxMin Tipo de escala Minimum 5 778 Par metros del tipo de escala Best Fit Freeze scale parameters We Preview Sequence best fit Uk Cancel Figure 29 Scale solution window nt The toggle Sequence best fit only appears if the current tomographic solution is a sequence When turned on an automatic fit is done using the extreme values of the whole sequence and not only the extreme values of the current solution as the Best Fit toggle does E Notice that this command scales the tomographic solution and not the anatomical E image Use the command Scale Image for the anatomical image Change Palette Es This command appears in the Display menu and in the local menus of all the work sheets Using this command is possible to change the active palette by selecting a new one or by editing the present one When this command is activated a window is shown with several controls an option list indicating the active palette s name the active palette s preview an option for interpolating the palette and the Edit button for editing the palette The palettes in BET Viewer can use up to 256 colors If the palette does not have 256 colors as usual and the option for interpolating is set the application linearly interpolates User Manual BET Viewer Version 1 3 a7 Description of comnands 38 the present colors up to 256 to obtain the palette that is actually used in the work sheets If
45. nd Atlas cccccccnnccnnnnnnnnnnnnnnnnnnnnnnnnnnninnnos 46 Figure 38 Tomographic visualization MO iio saco cuinOESS 48 Figure 39 Inverse Tomographic visualization MOE cccccccccccccsccsssscssscccccccccscscsccsscccsscssessosess 49 Figure 10 Map visualization MOE ii ee ate eae 50 Figure 4 Image visualizaOn MOE si di 51 Figure 42 Black Se White Visualization MOOG erisccnin cicle 52 Figure 43 Isoconiour MisualizalOn MOE cios es A S 53 Fisture 34 Dialog for ISOCOMOUL ibi 54 Figure 45 Slice onentaton dias dias 55 Figure 46 Parameters report for the rendering SD dai 56 Acknowledgements To Dr Alan Evans from Montreal Neurological Institute and the International Consortium for Brain Mapping ICBM for the brain average ICBM 305 probabilistic images atlas and templates used in this product Microsoft Windows Windows 95 Windows 98 and Windows NT are registered trademarks of Microsoft Corporation Introduction Introduction i BET Viewer is a system for displaying and evaluating the results of Brain Electrical Tomography BET Brain Electrical Tomography integrates the functional information provided by the Electroencephalogram EEG or Magnetoencephalogram MEG with the anatomical information provided by Magnetic Resonance Imaging or Computer Assisted Tomography BET makes it possible to localize in the brain the sources of physiologic or pathologic actvities thereby opening new ways to study normal
46. nu opens the BET Viewer help system using the standard Windows help system T The shortcut key F1 provides help specific to some windows in the application Keyword Search This command in the Help menuopens the BET Viewer help system for keyword search using the standard Windows help system User Manual BET Viewer Version 1 3 55 Description of comnands Using Help This command in the Help menu opens the standard Windows help system explanations About This command in the Help menu shows information about the application What s This 2 This command appears in the local menus of the work sheets 3D View and Electrode View When activated a window shows the parameters used for the rendering on which the mouse cursor is located when it was carried out The window can be closed by pressing the left button mouse or the Esc key Solution 625100 TT Rotation angles 15 45 O Thresholds Light Skin 30 Position 0 O 1 Cortes 60 Intensity 0 50 Bos Cut Yes Reflection 1 Position 103 195 0 Visibility 244 Size 70 50 84 Figure 46 Parameters report for the rendering 3D Clear this This command in the local menus of the work sheets 3D View and Electrode View deletes the rendering on which the mouse cursor was located For deleting all the renderings the command Clear all should be used Show Identifiers This toggle command in the local menu of the Electrode View work sheet shows th
47. of the generators e g ENG files the command is also disabled User Manual BET Viewer Version 1 3 Description of comnands Overlapping of the vectors is carried out only over the slices intercepting the grid Figure 35 Overlapping of the vectors on the tomographic slices Show Atlas This command in the View menu works as a toggle when turned on the atlas is superimposed on the tomographic slices in the work sheets E The overlapping of the atlas is not carried out in the 3D View or in the Max Intensity a Projection sheets and the command is disabled in these sheets E This command is only enabled if the anatomical image of the active configuration M has an associated atlas or the active configuration includes an atlas User Manual BET Viewer Version 1 3 45 Description of comnands Figure 36 Overlapping of the Atlas on the tomographic slices Grid Vector style This command in the View menu brings up a window to define the style for visualizing the grid with the command Show grid and the vectors with the command Show vectors The Complement or Solid style can be selected using the radio control The style Complement uses the color complementary to the color already on screen The style Solid draws using a specified color If the Solid style is chosen the Color button is enabled and pressing it brings up the standard Windows dialog for selecting colors Gid ector style Style C Complement
48. onal Planes sheet automatically becomes the active work sheet Three other sheets are also enabled All Slices 3D View and Maximum Intensity Projection but these are nor visible unless selected The Electrode View sheet is enabled only when an electrode coordinates file is loaded The names of the sheets appear on tabs at the upper edge of every sheet just below the tool bar To move from sheet to sheet click the sheet tabs Orthogonal Planes This work sheet visualizes the tomography in 3 orthogonal planes axial coronal and sagittal The sheet also provides the values of the active scale and palette two 3D surface renderings of the brain showing the views from the top and left and a control for moving the cursors that define the planes The X coordinate defines the sagittal plane the Y defines the axial and the Z defines the coronal plane In the top view of the brain the cursors corresponding to the sagittal vertical cursor and coronal horizontal cursor plane are shown In the left view of the brain the cursors corresponding to the coronal vertical cursor and axial horizontal cursor plane are shown The slices to be visualized can be selected by changing the cursor values in the boxes on the sheet or by dragging the mouse over the 3D views to the desired slice The orthogonal slices to the slice where the operating system cursor lies can be visualized too by pressing the mouse left button If the anatomical image is aligned
49. ontain a single solution or a sequence of them There are specific commands for working with a sequence of solutions The MOD files correspond to the models obtained for the electrical tomography by the Quantitative Analysis of the EEG frequency domain Open fMRI This command in the File menu loads a fMRI file When activated a submenu appears for selecting which variant will be used for loading the fMRI file Individual or Atlas When the Individual option is selected a dialog is presented for setting the elements needed for fMRI visualization Open fMRI Ed Anatomical filename a UA MAI filename 1 Cancel Grid step E Segmentation filename 2 The anatomical images can be in VOX or ANALYZE format The fMRI files are loaded only in ANALYZE format The Segmentation file is optional if no file is set the segmentation is generated automatically by the system However is recommened to set a segmentation file as precise as possible in order to obtain better results in visualization The grid step by default is 3 and can be changed by the user in order to increase accuracy in the visualization It is user s responsibility to guarantee coregistring between the anatomical image and the fMRI file When the Atlas option is selected a dialog is presented for selecting the fMRI file to load In this option the fMRI is plotted over the ICBM brain template requiring in this case a previous normalization and coregisterin
50. s presented for loading the file that contains the animation definition These files have extension MUS Once loaded the file ss name is shown in the Input file box This type of animation generates temporal animations in 3D if the active tomographic solution is a sequence When selected two edit boxes Start and Stop are shown for setting the solutions that will be used as start and stop frames in the movie respectively This type is visible only if if the active tomographic solution is a sequence Format of the MUS files The file will have as many lines as frames in the animation Each line has the following format AX AY AZ YV AppC XPC YPC ZPC XSC YSC ZSC XL YL ZL I R where AX AY AZ YV AppcC XPC YPC ZPC XSC YSC ZSC XL YL ZL Rotation angle on the axis X Rotation angle on the axis Y Rotation angle on the axis Z Coordinate Y for visibility 1 if Box Cut is carried out O if not X coordinate for positioning the Box Cut Y coordinate for positioning the Box Cut Z coordinate for positioning the Box Cut Size in X axis of the Box Cut Size in Y axis of the Box Cut Size in Z axis of the Box Cut X coordinate for positioning the light Y coordinate for positioning the light Z coordinate for positioning the light User Manual BET Viewer Version 1 3 17 Work sheets I Intensity coefficient of the light R Reflection coefficient of the light Once the Render button is pressed a dialog window requests a filenam
51. t Solution H This command in the Display menu loads the first tomographic solution of the sequence see Open Solution The command is disabled if the active tomographic solution is not a sequence or if the active solution is the first one in the sequence Last Solution H This command in the Display menu loads the last tomographic solution of the sequence see Open Solution The command is disabled if the active tomographic solution is not a sequence or if the active solution is the last one in the sequence Go to Solution This command in the Display menu selects a particular solution inside the sequence see Open Solution The command is disabled if the active tomographic solution is not a sequence Go To Solution a Figure 32 Go to Solution dialog User Manual BET Viewer Version 1 3 41 Description of comnands Step in Sequence This command in the Display menu setts the step which will be used for moving between solutions in the sequence see Open Solution The command is disabled if the active tomographic solution is not a sequence Step in Sequence E3 Figure 33 Step in sequence dialog Set labels This command in the Display menu allows tu set labels for the current sequence loaded When activated a dialog is presented for setting the parameters needed for generating automatically the sequence labels There are 3 edit boxes Initial Value Sampling rate and Units The Initial Value field allo
52. t as a background task so that the user can continue with other tasks Working with animations 24 There are two animation movies types in BET Viewer e Temporal animation using the command Generate Movie in the Display menu or by using the the Movie sheet of the Parameters 3D in the work sheet 3D View with the movie type Sequence e 3D animation using the Movie sheet of the Parameters 3D in the work sheet 3D View The temporal animation with Generate Movie is only enabled when working with a sequence of solutions In both types the animation generated is saved in AVI format allowing it to be used with any multimedia player or with the command Play Movie in the Display menu User Manual BET Viewer Version 1 3 Description of comnands Description of comnands This section descirbes all the commands specifying for each the menu where it belongs the hot key combination if available and the toolbar button if it exists New Image Configuration Ctrl N This command in the File menu creats a new configuration see Configuration When activated a form for changing the elements of the configuration appears The elements that appear when the form is presented correspond to the active configuration Pressing the Ok button brings up a dialog window for saving the configuration Hew Image Configuration Volume Image C Program Files Heuronic BET Viewer Segmentation Solution E S Program Filess Meuronic B
53. the configuration can be handled with several commands With the commands Edit Image Configuration and New Image Configuration the user can change the configuration or create a new one The command Open Image Configuration allows the user to select and load a stored configuration Loading tomographic solutions If the application is working in stand alone mode the tomographic solutions are loaded by means of the command Open Solution If the application is executed from another module the tomographic solution is loaded automatically when giving the corresponding command in that module The loaded solution becomes the active solution and once loaded the remaining work sheets are enabled Changing the active work sheet The active work sheet is changed by clicking the sheet tab for the desired sheet The selected sheet will then become the active work sheet Changing the visualization mode BET Viewer has five visualization modes Tomographic Inverse Tomographic Image Map Black amp White and Isocontour To change the mode use the commands Tomography Mode Inverse Tomography Mode Image Mode Map Mode Black amp White Mode and Isocontour which appear in the toolbar or the View menu The selected mode will become the active visualization mode Working with the image In the sheets Orthogonal Planes All Slices and Max Intensity Projection the tomographic solution is visualized in 2D by means tomographic slices The tomographic so
54. ton allows restoring the default values for each surface Background This parameter sets the background color of the 3D rendering The default initial value is Black Electrode Color This button changes the color used for rendering the electrodes When pressed opens the Windows standard dialog for selecting colors Show Identifier If this toggle is turned on the rendering will include the electrode name and the Font button will be enabled to allow a standard Windows standard dialog to select the font 3D Parameters al ES Skin detection Misc threshold selection Threshold Skin Default Electrode color selection Electrode R Show Identifier Toggle for identifying Background Background color Black selection White Color g electrodes Font Font identifier selection Figure 17 Misc sheet for Electrode View work sheet User Manual BET Viewer Version 1 3 21 Working with BET Viewer Working with BET Viewer Once it has been loaded and initialized the BET Viewer is ready to start the working session At the beginning of the working session only the Orthogonal Planes sheet will be enabled The remaining sheets will be enabled once a tomographic solution is loaded E The loading and initializations is a slow process which depending on the power and E memory capacity of the computer can take up to several minutes Changing the configuration During the working session
55. ts in the grid although there are limits to the number of points imposed by the inverse solution The values for the image voxels that do not intercept with the grid points are obtained by interpolation User Manual BET Viewer Version 1 3 1 Introduction Figure 1 Location of the grid in the image volume User Manual BET Viewer Version 1 3 Introduction Figure 2 Segmentation of the image The configuration for BET is stored in a ASCII file with extension CFG The elements are The anatomical image which used by BET can be an individual image obtained from Magnetic Resonance Imaging or Computed Assisted Tomography an average image across many individuals or an atlas image Configuration Volume Image Specifies the full path and name for the files WOX and HDR containing the complete three dimensional anatomical image Segmentation Solution Specifies the full path and name of the files SEG and HDR containing the segmentation of the anatomical image used for constraining the tomography User Manual BET Viewer Version 1 3 3 Introduction Segmentation Brain Specifies the full path and name of the files SEG and HDR containing the segmentation of the anatomical image used to define the brain Grid Specifies the full path and name of the file XYZ containing the grid used to calculate the solution Top View Specifies the full path and name of the file 3D containing a 3D rendering of the brain corr
56. tton which is enabled when the rendering begins allows the rendering to be interrupted at any time A progress indicator replaces the status bar This progress is divided in two parts anatomical image rendering and electrode rendering E This sheet is enabled when loading a file of electrode coordinates with the command m Open Electrodes File Pressing the right button of the mouse over any element of the sheet brings up a local menu with commands available to this element E The rendering process is carried out as a background task allowingthe user to E continue working with BET Viewer The user is notified if he or she tries to execute any operation that could invalidate the rendering The 3D Parameters window which sets the parameters for the rendering has 3 sheets Rotation Light and Misc The Rotation and Light sheets have the same function as those already described in the 3D Parameters window of the work sheet 3D View The sheet Misc adds further parameters 20 User Manual BET Viewer Version 1 3 Work sheets Misc In this sheet the following parameters are set for the 3D rendering Thresholds This parameter sets the detection thresholds in the anatomical image of the skin and the cerebral cortex These values can be changed using the edit box existent for each surface There is no need to change the default values unless the user wants to experiment Wrong values can invalidate the surface detection process The Default but
57. uced in size image The full image type saves all the image values Add Comment This command in the File menu adds comments to the sheets for printing When activated a window for editing the desired text appears In the window there is an option list In Page for selecting the sheet where the comment will appear The comment added using the All option appears in all the sheets before the comment specific to the particular sheet Add Comment In Fage an All Slices 30 View Mas Intensity Projection Electrode View Page selection k Cancel Figure 20 Add comments window 13 The comments will appear on the printed page after the content of the sheet 28 User Manual BET Viewer Version 1 3 Description of comnands Print Setup This command in the File menu sets the characteristics of the printer When activated a dialog that also sets the paper size and orientation appears Print Setup El ES Printer Mame HP DeskJet 8700 Series Properties Statu Ready Type HF DeskJet 6 00 Seres Wher LPT1 Comment Orientation Portrait Landscape Cancel Paper Size Letter 8 5 x 11 in Source In Tray Figure 21 Printer selection dialog E It should be kept in mind when selecting the paper size that some sizes are not valid E for printing in BET Viewer Print Preview ch This command in the File menu replaces the main window of t
58. wo ways for setting the angles by directly editing the desired value in box existent for each angle or by means of the 6 buttons which can increase or decrease the rotation angle in steps of 5 A preview of the sheet shows the results of applying the active values of the angles for each axis using a model human head 30 Parameters Aa ES Rotation Angles edition Buttons for editing angles Preview Preliminary view Figure 9 Rotation sheet in 3D Parameters E This sheet shows the position of the image relative to the BET coordinate system a When the rotation angles are O the head looks directly at the observer Light This sheet sets the illumination parameters for the 3D rendering There are three parameters for controlling the rendering illumination position of the light light intensity and amount of reflection 12 User Manual BET Viewer Version 1 3 Work sheets 30 Parameters Light Buttons for editing position Position Position coordinates edition Intensity Intensity 0 50 coefficien Reflection fi Preview Reflection coefficient Preliminary view Figure 10 Light sheet in 3D Parameters Position The position of the light indicated through the coordinates X Y Z can be set by directly editing the values for each coordinate or by pressing the 6 buttons that increase or decrease the coordinate for each axis in steps of 5 The default initial position of the light
59. ws to set by using digits the starting value for the sequence labels Sampling rate will indicate the numeric value needed for obtaining the label for the next labels The label value in a given instant is calculated by adding the label value in the previous instant with 1 Sampling rate The Units field will indicate the units used if any The command is disabled if the active tomographic solution is not a sequence Set labels ES Initial Value lo 00 Ok Sampling rate 0 00 Cancel Units Toolbar This command in the View menu works as a toggle when turned on the toolbar is visualized under the horizontal menu of the application otherwise the toolbar is hidden leaving more space on screen for the work sheets 42 User Manual BET Viewer Version 1 3 Description of comnands Status bar This command in the View menu works as a toggle when turned on the status bar is visualized in the bottom of the main window application otherwise the status bar is hidden leaving more space on screen for the work sheets Atlas information bar This command in the View menu works as a toggle when turned on the Atlas information bar is visualized at the bottom of the main window application above the status bar otherwise the Atlas information bar is hidden leaving more space on screen for the work sheets This bar shows the name of the anatomical structure where the mouse cursor is located E This command only is enabled

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