Saturn User Manual
Contents
1. 127 IMAGES 2D DTI Scalar magnitudes vite rp T pd a o y Ras Basic E E El Selected viewer FA RA MD Color Advanced Figure 8 Scalar view selection Additionally the scalar data can be also shown in an independent window as the one shown in figure 7b To show that select the scalar data to visualize and click in View Out button Each 2D viewer has also a set of options accessible from the keyboard The key feature correspondence is outlined in the table 1 Some of the features are also available from the preferences panel shown in figure 9 This panel is accessible from the menu item Saturn gt Preferences or from the P button of each viewer From this panel some features can be controlled as for instance flip the image in any direction transpose the image zoom in and out display the cursor cross the cursor value and the image details A set of controls present of this panel are designed to control an important feature available in the viewers which are the image modes The image can be shown in two different image modes grayscale image mode and color image mode The Image mode box changes the different color maps available in the grayscale image mode which are VAL intensity INV inverse intensity LOG logarithmic scale DX derivate respect to x DY derivate respect to x DZ derivate respect to z BLEND mix with the with the previous and following slice2. culation The num counter controls the number of surfaces created for the model within the selected range The Opacity slider controls the transparency of the model selected in the model data browser The Apply button finally creates the isosurfaces with the selected parameters 14 3D ISOSURFACES Do model center 6 Coronal O Sagital O Axial Color AP pacity a A mo Uh Gray RT S zoom Parameters select input output Input 1 Output y new y Hum lal 1 gt i Full Model 50 Range min Plan Model opacity 1 0 F Apply F4 a b Figure 14 Scalar isosurfaces panel a and Scalar isosurfaces viewer b 6 Tractography In figure 15 the features and parameters related to tractography are available The panel is divided into four sections Color Parameters ROIs and Execution In the following all these sections are explained in detail The upper buttons marked as Auto and Measures allows to access quickly to the Automatic fiber Clustering and the Measures sections 3D FIBERS DTI Tractograph Tract Auto Measures MFA Size RGB I Distance l Major Eig Set fiber color I skin I bone I blue sea Parameters 0 30 Radius 0 98 Step Length 0 15 FA threshold 90 Curv Thresh ROIs load radius class opacity show clear 5 H Cease 4 1 Hoo J Execution Tract Logic Tractography Brute force Tract
3. Logic T Ex all Roii 1 ror2 1 nor gt Figure 15 Tractography control panel 6 1 Color options The first section of the panel controls the color code used for the fibers to be computed There are six possibilities 6 2 ROls Edition 15 1 FA Color by FA red colors are assigned to points with low FA blue to points with large FA and green to points with intermediate FA values By default the color range is assigned from 0 to 0 8 2 Size Color by fiber size red colors are assigned to short fibers blue to large fibers and green to intermediate size fibers The scale is done independently for each fiber tract computation 3 RGB The fiber is colored depending on the seed label or class 4 Distance Color by distance of the points to the nearest seed in each fiber 5 Major Eig Color by the major eigenvalue red colors are assigned to points with low first eigenvalue blue to points with large first eigenvalue and green to points with intermediate first eigenvalue By default the color range is assigned from 0 to 0 8 6 Predefined color The fibers will be colored with one of the predefined colors skin bone gray red green blue and sea 6 2 ROIs Edition First it it is necessary in all the tractography modes to draw or select a region of interest ROI This is done in the 2D viewers by left click with the mouse over it The user can add a ROI with a predefined radius and label that can be changed in the R
4. ambient specular and specular power of the selected model 3D FIBERS DTI Fibers Properties Drar artio c l L Hm blue sea SELI POLL J set range opacity P oise OO LP Ambient OL Specular 03 Specular Power FUI Figure 21 Fibers properties control panel 23 11 Glyphs Glyph visualization allows the user to visualize tensors of the DTI data using glyphs A glyph is an icon or geometric figure which represents the tensors values on a voxel The main features of the glyph color size shape orientation displays the tensor properties It is a helpful technique to show details of information in a small area This section explains the different ways of interactuate with them The panel for Glyph Visualization is shown in figure 22 It is divided on three sections from top to bottom Color Filter and Parameters 1 Color The glyphs are colored in function of common DTI indexes Gray colors are assigned to points with low values red to points with large values and green to points with intermediate values These in dexes are Fractional Anisotropy FA Relative Anisotropy RA Geometric Coefficients linear C planar C and spherical C Apparent Diffusion Coefficient or Mean Diffusivity ADC tensor components D x D and D and finally Color by Orientation The latter uses a different color scheme red for RL direction green for AP direction and blue for IS direction 2 Filter Th
5. and MIP projection of all the values The Color mode box box changes the different color maps available for the color image mode which are FA ROIs Heat and Discrete 3 1 2D Windows 9 Diminishes increases the top limit of the window in intensity alternates the values of the top limit windows in intensity between clipping and setting to black Diminishes increases the lower limit of the window in intensity alternates the values of the lower limit windows in intensity between imik See axis labels P posterior L left S superior Change the the screen data showing way Ways change cyclically in the following views Intensity Inverse Log Derivative respect to x y and z mix with the with the previous and following slice and MIP z E zra oas MEN ES Table 1 Available options in the 2D viewers Finally the sliders of this panel controls the intensity in the grayscale image mode gray sliders and the color range in the color image mode green sliders 3 2 3D Window 10 IMAGES 2D Preferences Display image Properties Zoom l Display values Zoom Left rata Display cross Center Down Display Color Image Mode IMG VAL w Color Mode FA v Transpose Flip X Flip Y pz Flip Z Image Info min Gray1 II A 0 max Gray A 0 793722 min Colort fo max Color 1 AAA Figure 9 Preferences panel to control the 2D viewers 3 2 3D Window The 3D viewer for the
6. 0 000839 Tot 13 783497 Dxx Mean 0 001413 Max 0 002976 Fiber Measures Max 0 474588 Min 0 306689 Tot 3508 087402 Max 0 080377 Min 0 072372 Tot 658 573486 Eig Eig3 136 RA MD Length Mean 0 399340 Mean 0 075368 Size Mean 124 88143 Max 210 989883 Min 59 553829 4 gt cl c Mean 0 001410 Max 0 002754 Min 0 000737 Tot 11 693645 Dx Mean 0 000044 Max 0 000289 Mean 0 001296 Max 0 002281 Min 0 000594 Tot 10 739841 Dxz Mean 0 000036 Max 0 000268 Mean 0 002522 Max 0 008740 Min 0 000729 Tot 20 526873 Mean 0 001493 Max 0 003003 Mean 0 001118 Max 0 005866 Min 0 000106 Tot 9 389588 Mean 0 000046 Max 0 000195 Mean 0 012893 Max 0 021144 Min 0 006542 Tot 106 083466 Mean 0 001460 Max 0 002449 Min 0 000645 Min 0 000265 Min 0 000550 Min 0 000732 Min 0 000215 Min 0 000757 Tot 0 072621 Tot 0 003712 Tot 0 012430 Tot 0 075972 Tot 0 009763 Tot 0 107534 Close Mi Figure 19 DTI measures computed along the fibers 21 9 Fiber Edition In figure 20 the control panel for fiber edition procedures is shown The operations permitted in the first section are e Resize from seeds In the selected fiber tract reduce the fibers larger than a factor of the average length to that value All the fibers larger than the value factor L are reduced to that value removing points in order of distance to the seeds defin
7. Scale slider controls the size of the glyphs and the Resolution slider controls the number of polygons used to create the glyphs the downsample of the displayed tensors allows faster rendering The Max Scale counter controls the maximum size of the glyphs represented on screen The scale of each glyph is defined by the eigenvalues and weighted by the Fractional Anisotropy of the tensor its orientation is defined by the main diffusion direction of the tensor At the bottom of the panel there are two buttons the Do Glyphs button and the Update button The former creates a new glyph class from the tensor data selected in the tensor data browser The latter button update the glyphs according to the changes on the panel from the glyph model data selected in the model data browser 3D GLYPHS DTI Glyphs Color MFA RA Cl Cp DADC Dxx C Cs l Dyy Dzz Orient Filter by a plane m by Tensor Invariants v Axial o JJ FA C Coronal o J os Value threshold C sagital o JJ 0 50 Parameters Cone Shape lal 2 H Max scale fof is Scale 4 Resolution Do glyphs Update glyphs Figure 22 The Glyph Viewer module window Coronal Sagital Axial Color ser m Tdi a az 1 4 Gray zoom Figure 23 3D viewer showing fibers and glyphs
8. called Sat urn at user level The general features of this application are Object Oriented Multi platform Efficiency Easy to handle for non expert users e Wide Input Output file format support e Documentation On line availability The general view of the Saturn graphic user interface GUI appears in figure 1 This GUI is divided in two main panels the control panel on the left side of the main window and the visualization panel on the right side The control panel is divided in two panels the data panels where the data loaded and or created will be listed and the options panel where the parameters and procedures can be accessed There exist also a menu bar at the top of the main window that give access to the major part of the features included Finally a status bar is placed below the visualization panel that indicates the percentage of time taken for some processes a Saturn 1 x Saturn File View DTI DWI Help Type of Data on Tract Scalar Data vw Scalar Auto Stats Gon Scalar Data modelo vtik_FA TENSOR modelo ME Cl TTT View Rename Delete 4 7 view out Do model 20 TE Bay T TA IMAGES 2D DTI Scalar magnitudes SE e DIARAH R Color Figure 1 General view of the Saturn GUI Three direct access buttons are also available in the top right part of the main window 3D 3 1 and 4x2D to choose be
9. the Load ROI button can be used to skip the normalization process The Select Tract button is used to obtain the tracts once the normalization and the brute force tractography have been performed The Tract Logic button does the same operation than the Auto Select button but including logic operations The Do Connect button executes the same functions than the Do Tract button for the pyramidal tract and writes the adapted ROIs Load ROI Normalize Select all Do Tract Auto Select Select Tract Do Connect Tract Logic ROI14 1 H Roza 1 Aroa o H Figure 16 Automatic fiber clustering control panel 18 The Select all button select and deselect all the fiber tracts check buttons and the main button returns to the Tractography panel 15 19 8 Measures The control panel to perform measures Measures panel is shown in figure 17 This panel is available from DTI gt measures menu item and from the Stats button in the model data browser 6 The upper buttons marked as Tract and Auto allows to access quickly to the Tractography menu and the Automatic fiber Clustering menu Two different measure types can be performed here ROIs measures and Fibers measures 3D FIBERS DTI Statistical Measures Tract Auto MFA RA MD Eigenvalues Geometric Coefficients 1Dxx gt Dxy FiDxz Dyy Dyz Dzz 7 Coherence Compute Show Save file VFA RA MD WM Length Eigenvalues Geometric Coeff
10. visualization of scenes is shown in figure 10 This viewer can be shown using the 3D button at the top right of the main window The features supported by the 3D viewer are Center Center the scene in the viewer Orthogonal planes view using the coronal sagittal and axial check buttons The data shown in these planes will be the scalar data selected in the scalar data browser 2 Planes slide using the coronal sagittal and axial sliders or using the middle button of the mouse and dragging The cursor should be at the zone of the 2D outside the blue lines interior zone of the plane Oblique planes view using the middle button of the mouse and dragging The mouse must be located in the zone of the plane marked by the blue lines see figure lla Color image mode Change the to image mode in the planes to RGB mode with the Color button Gray image mode Change the to image mode in the planes to grayscale mode with the Gray button Planes intensity change Using the right button of the mouse and dragging Planes value view Left clicking with the mouse a red cross in the plane appears as well as the position value and the value see figure 11b Plane Opacity Change the opacity shown in the 2D planes using the Opacity slider Zoom in and out it can be using the and buttons and also by right clicking and moving the mouse Rotate scene Using the mouse left button and dragging Translate the scene Pressing the SHIFT butto
11. will be computed and visualized in the first 2D viewer and stored in the scalar data browser 2 Image Information Tensor Data Mpt DT OO Image file name Explore File Format Choose format x Ok Cancel E gt G5 a b Figure 4 Input tensor data dialog window a and tensor data browser b 2 3 DWI Data To load a set of Diffusion Weighted Images DWI use the menu item File gt Open DWI The data format supported in this case is DICOM series The DWI input dialog window as the one shown in figure 5 will appear Input DWI Image Input DWI Image file name Explore Open Open and process Cancel Figure 5 Input DWI data dialog window Use the explore button to go to the directory where the DWI series is stored and select one of the images Once the series is selected two different operations are supported Open it just open the volume and store it 2 4 Model Data 6 internally in a DWI object data The Open and Process where the DWI files are filtered masked the tensor is estimated and stored in the tensor data browser 4b and the FA is computed shown in the first viewer and stored in the scalar data browser 2 Notice that these set of procedures are computationally expensive taking from 1 to 10 minutes depending on the machine processor load of the system and operating system used 2 4 Model Data To load model data fiber tracts use the menu item File gt Open Model The
12. 2D viewer and no scalar magnitude is stored The color codes in this images by convention is red for RL direction green for AP direction and blue for IS direction A screenshot with some scalar magnitudes computed and visualized is the shown in figure 13 13 IMAGES 2D DTI Scalar magnitudes pun Advanced 18 i AD e z 285 A gt xz 141 x a8 i vite P T od a ro g Rast vitle Pi Ti i aaj RAS PITA pd ja lr o g RAS vi tip Ti Figure 13 Scalar magnitudes FA MD C and color by orientation 5 Scalar isosurfaces The scalar magnitudes of a DTI data can also be visualized by tridimensional surfaces This surfaces repre sents points of a constant scalar value within the scene The user must define the limits and values that wants to display The control panel for isosurfaces is shown in figure 14 user can access on this panel pressing the Do Model button placed under the scalar data browser The input data is taken from the scalar data selected in the scalar data browser and shown in the Inputl selector the name of the resultant output is shown in the Output selector The Full Model slider controls the accuracy of the model a one hundred percent value will display a full model while a zero percent value will display a simpler one the Range min and Range Max sliders control the range of scalar values of the data that will be used for surface cal
13. 7069 98205 58289 14521 93621 00902 19971 51452 07241 98490 30230 13871 55898 OOOPRrRONOONNEereNOO 33162 28663 98893 90348 5976l 16334 19236 01068 02997 39944 10973 89822 35452 10774 53774 20 at fiber points will be interpolated using Nearest Neighbor interpolation A new measure is included here the length If active it will show statistics about the fiber tract length To perform fiber measures select a fiber tract from the model data browser 6 and use the compute button Similarly to the ROIs measures section a window with the measure values will show up as the one in figure 19 The information presented in this window is e The total number of fibers computed in the tract e The mean maximum minimum and total amount of measure contained in the fiber tract for each measure e The integrity FA value last value in the FA box The computation of these measures is optimized and 1s computationally less expensive than ROIs measures computation in normal size tracts By default only FA values will be computed To select and deselect all the check buttons use the Select All button Again the Show and Save file buttons are used to show up the measures window and to save the obtained measures in a text file Number of Fibers FA Mean 0 439688 Max 0 506132 Min 0 353220 Tot 3857 864502 28 366652 4 gt Eig Mean 0 001666 Max 0 003306 Min
14. OIs section of the Tractography panel By dragging the mouse while left clicking it is possible to draw ROIs in any of the orientations axial sagittal or coronal and in any slice To remove all the ROIs drawn use the clear or to erase part of the ROIs choose class O and draw using the mouse It is also possible to change the opacity of the ROIs using the opacity slider To load ROIs from a file use the File gt Load ROIs menu item It is also possible to save the ROIs using the File gt Save ROIs menu item 6 3 Normal Tractography The most simple tractography procedure can be done using the Tractography button The result will be the set of fibers that start from the ROIs drawn There exist two stopping criteria for the algorithm the mini mum FA the fiber path computation is stopped if the FA is lower that a given threshold and a maximum angle the fiber path computation is stopped if the curvature angle is higher that a given threshold Those thresholds can be set by the user using the FA threshold and Curv Threshold sliders Additionally the step length an internal parameter that controls the tractography integration procedure can be set by the user The default value is proven to work properly for most of the cases The last parameter is the radius of the tube drawn to represent the fibers computed 6 4 Brute Force Tractography Using the Brute Force button the brute force tractography is computed using all the voxels over the FA th
15. Saturn User Manual Rub n C rdenes 29th January 2010 Image Processing Laboratory University of Valladolid Abstract Saturn is a software package for DTI processing and visualization provided with a graphic user in terface GUI This document describes the steps required to load DTI data and to operate with them compute and visualize scalar magnitudes derived from DTI data perform tractography perform auto matic fiber clustering perform glyph rendering compute measures over regions of interest ROIs and along fiber tracts and edit fibers and ROIs Contents Contents 1 Introduction 2 Input Output Formats al I sonoros ro rare ARA a ee eee oe e POC 6 gow eA he Ree EERE E E A A Boe IA PAE ETE ee Ree eee Eee Ee 24 Model Dad 2c kta edie dw eawen eee bee ee bh EOE DS Ow Owe ww 9 Visualization Windows 3 1 2D WINDOWS 4 aoaaa e 3 2 3D Window oaaae eee Scalar Magnitudes Scalar isosurfaces Tractography 6 1 Color options oaoa ban cd ma 6 2 ROL Edi ON esos Fede Pew e bos 6 3 Normal Tractography 6 4 Brute Force Tractography 6 5 Logic Operations Automatic Fiber Clustering Measures 8 1 ROIs Measures a a 8 2 Fibers Measures 2 00800 ee Fiber Edition 10 Fiber Properties 11 Glyphs 12 13 14 14 15 15 15 16 17 19 19 19 21 22 23 1 Introduction This document describes the features implemented in the DTI processing and visualization tool
16. ed by the label selected where Lm 1s the average fiber length and factor is set by the user with the factor slider e Resize fibers In the selected fiber tract reduce the selected fibers larger than a factor of the average length to that value All the fibers larger than the value factor Ly are reduced to that value removing points in order of storing position where Lm and factor are the same as in the previous case e Remove fibers In the selected fiber tract remove the selected fibers larger than a factor of the average length All the fibers larger than the value factor Lm are removed where Lm and factor are the same as in the previous cases e Cut fibers Six cut operations can be performed Cut the selected fibers in the sagittal direction from the position defined by the sagittal plane in the 3D viewer to the highest left position Cut the selected fibers in the sagittal direction from the position defined by the sagittal plane in the 3D viewer to the highest right position Cut the selected fibers in the coronal direction from the position defined by the coronal plane in the 3D viewer to the highest anterior position Cut the selected fibers in the coronal direction from the position defined by the coronal plane in the 3D viewer to the highest posterior position Cut the selected fibers in the axial direction from the position defined by the axial plane in the 3D viewer to the highest inferior p
17. ere are two implemented ways of controlling the selection of the glyphs to be represented Both can be enabled at the same time If no filter is enabled all the points in the data will be represented with a glyph a Spatial filtering Activate an interaction widget who defines the area where the glyphs will be shown This area can be oriented by orthogonal planes with the axial coronal and sagital check buttons By moving the axis sliders the widget will navigate along the data slices The widget can also be dragged around the scene with the left button of the mouse and moved along the normal axis with the central button The right button of the mouse scales the size of the widget b NN Tensorial invariants filtering The tensorial invariants are scalar magnitudes derived from DTI data This filter shows only the bunch of glyphs whose values lies around the factor selected on the factor slider The tensorial invariants who can be selected are Fractional Anisotropy FA Relative Anisotropy RA Mean Diffusivity ADC and Geometric Coefficients linear C planar C and spherical C 3 Parameters The parameters panel controls the basic aspects of each glyph There are four variables available The shape selector chooses the geometrical figure used for represent the tensor It can be Cones Boxes Spheres Arrows Ellipsoids and Toroids Simpler shapes like cones arrows or boxes require less resources than spheres or ellipsoids The
18. fore the same measures can be computed but this time they are computed using the fiber points instead of the voxel values Values 8 2 Fibers Measures A y FA 0 41005 0 RA 0 36507 O El 3 30434 3 E2 1 97090 2 E3 1 53677 2 MD 2 27067 2 D0 2 04425 2 Dl 0 07168 0 DZ 0 19563 O D3 2 01561 2 D4 0 07037 0 D5 2 75216 3 Cl 0 40886 O Cp 0 14080 0 Cs 0 45034 0 36599 31750 82873 43332 02751 76319 35717 DO198 00569 71067 25463 22172 37950 12515 49535 OOOrONnOOrrrrnNoo 31453 26883 65242 79163 41647 95351 91096 04718 03315 21474 03706 73483 31891 13921 54188 30246 25846 92558 99933 61215 17902 00028 01714 11125 38009 07658 15672 30904 13433 55663 OOOMNONMNOOMMIrrFNOO ROIs Measures OOOrONOONMrrFWOO 04 36047 0 40470 0 35792 31865 0 35910 0 31133 11927 3 22664 3 81500 184560 1 94479 2 43229 53878 1 50694 2 07690 16788 2 22612 2 77473 35075 1 97953 2 28819 04368 0 05457 0 07065 01448 0 02201 0 08416 19858 2 04197 2 70078 08894 0 03061 0 50854 95432 2 65686 3 33522 38179 0 40157 0 38186 10471 0 14468 0 10587 51349 0 45375 0 51227 Close Mi OOOrFONOOMrRrFEFENIOO 32650 27956 70708 79902 41219 97277 08334 16476 10242 21173 05333 Enano DS 32992 14185 52824 Figure 18 DTI measures over ROIs ODOOrONOOrRrNereNOO 29853 25383 8
19. he image horizontally e Show preferences Show the preferences panel e Zoom in Zoom in the image e Zoom out Zoom out the image e Translate right Translate right the image if zoom in is on e Translate left Translate left the image if zoom in is on e Translate up Translate down the image if zoom in is on e Translate down Translate down the image if zoom in is on e Show in Color Show the image in RGB color maps e Show in Gray Show the image in grayscale color maps 3 1 2D Windows 8 e Show anatomical labels Shows anatomical labels A P R L I S overlaid in the viewer e Expand the viewer Maximize the viewer to the maximum size of the visualization panel The scalar data can be shown in any of the viewers using the View button placed in the scalar data panel In figure 8 we show an example of this Once pressed the View button the scalar data currently selected in this case Volume FA 1s shown in the selected viewer upper right viewer To select a viewer just check the check button placed at the bottom right of each viewer as shown also in figure 8 W Saturn 1 x Saturn File View DTI DWI Help ieee tal Prefs Tract Prop Emn v tle TIF P alae clo AAA AA AAA IES ACE scatar Data v Semar Auto Stats Gon Scalar Data modelo tk FA modelo R TRN 7 Selected data S J A AA Y E OA v ter TIF Iy dar e RAS View Rename Delete 4 w View Out Do model
20. icients l Tensor Components Compute I Show Save file Figure 17 DTI measures control panel 8 1 ROIs Measures To perform measures over ROIs the user should draw or load ROIs These ROIs will de displayed overlaid with the data in any of the 2D viewers To obtain the measure results first go to the Tractography Auto panel and select the labels of the regions that are to be used Then go back to the Measures panel and use the Compute button The measures corresponding to the active check buttons FA RA MD Eigenvalues Geometric Coefficients and or Tensor components will be computed over the selected ROIs and shown in a separate window as the one in figure 18 The values obtained are the average measure values in the ROIs specified These measures can be recomputed using the Compute button if the ROIs are changed The measures are computed using the values at the voxels To show the measures window use the Show button The values can be saved to a text file using the Save file button By default only FA values will be computed To select and deselect all the check buttons use the Select All button Coherence values can be also obtained by activating the Coherence check button If this feature is active instead of computing the average values of each measure the coherence value for each measure will be computed 8 2 Fibers Measures The bottom section of the panel is designed to perform measures along fibers As be
21. image dimensions the pixel type and the byte order Image Information nl Scalar Data Image file name T2mhd Explore PA File Format M D choose format y Pixel components El Input Image 1 m Image 2 O Image 3 O ok Cancel View _ Rename Delete 4 view Out Do model a py Figure 2 Input scalar data dialog window a and scalar data browser b The image or volume loaded will appear in any of the three first 2D viewers placed in the visualization panel the bottom right viewer is reserved for color images You can select any of the three viewers to see the new images with the check buttons that appears in the open file dialog The loaded data will appear in the scalar data browser shown in figure 2b Any operation over scalar data will be performed over the data currently selected in the scalar data browser 2 2 Tensor Data 5 SOS Input Image parameters Image Image dimensions x p56 y 125 Voxel size x y e Pixel Type Byte order Choose pixel type M Choose M D N Figure 3 Input scalar data dialog window 2 2 Tensor Data To load tensor data use the menu item File gt Open Tensor The input tensor data format supported by Saturn are vtk and nrrd The input dialog window shown in figure 4a will appear to choose the file name and type The tensor data loaded will be listed in the tensor data browser see figure 4b and additionally a FA volume
22. input model data format supported by Saturn is vtk The loaded data will appear in the model data browser see figure 6 Any operation over model data will be performed over the data currently selected in that browser To save model data go to File gt Save Model and choose a file name for the model The model saved will be the one selected in the browser Model Data Figure 6 Model data browser 3 Visualization Windows 3 1 2D Windows Once the data is loaded it appears in one of 2D viewers of the visualization panel as the one shown in figure 7a These viewers always show 2D images but they are able to show orthogonal cuts of the volume loaded pressing the buttons 0 1 2 when the cursor is over them or using the selection box at the bottom right of each viewer There is also a slider at the bottom of each viewer that allows to change the slice shown in volume data Aux 1 iv tee rit y cialyclo Rast 2 DUO Aus a a TE MT slice au max B1 06 i 17 E 4 y min 0 00 1 a T Figure 7 2D Viewer a and independent window viewer b There exist also several buttons in the top of each viewer From left to right these buttons are e Show details button Shows image details overlaid in the viewer e Show value button Shows cursor position and image value at that position overlaid in the viewer e Flip vertically Flip the image vertically e Flip horizontally Flip t
23. n on the keyboard with the mouse left button and dragging 3 2 3D Window 11 center Coronal 11 Sagital Axial Color PP Lora pacity peaj e O gt e Gs 4 alee zoom Figure 10 3D Viewer e Spin the scene Pressing the CTRL button on the keyboard with the mouse left button and dragging e Pointing at the scene Using the mouse middle button and dragging e Predefined views using the A P L R I and S buttons 12 94 97 27 0 140498 7 a b Figure 11 3D viewer with oblique plane a and cursor value view b 4 Scalar Magnitudes The scalar magnitudes that can be derived from DTI data available in Saturn are controlled from the panel shown in figure 12 These are Fractional Anisotropy FA Relative Anisotropy RA Mean Diffustvity MD Color by Orientation Geometric Coefficients linear C7 planar Cp and spherical C eigenvalues ordered from high to low major Eig 1 middle Eig 2 and minor Eig 3 and tensor components D Dyy Dxz Dyy Dyz and Dzz Representing the tensor D as a positive semidefinite 3x3 matrix there exist only six independent components Dix Dyy Dyz D Dy Dy Dy Dy Dy Dz 1 IN X N There is a button for each scalar magnitude After a button is pressed the corresponding scalar data is computed and stored in the scalar data browser 2 except for the color by orientation In that case the resulting RGB image is shown in the fourth viewer bottom right
24. osition Cut the selected in the axial direction from the position defined by the axial plane in the 3D viewer to the highest superior position e Order Fib Ax Order the fiber points from inferior to superior and the fibers from anterior to posterior e Order Fib Sag Order the fiber points from inferior to superior and the fibers from left to right e Save Profile Save the fiber tract FA profile to a text file from inferior to superior direction previous ordering of fiber points is needed to ensure a valid profile 22 3D FIBERS DTI Fibers Edit Rosie monsests TY Save Profile Order Order Fibers Axial Extension Order Fibers Sagital sagital Distance Figure 20 Fibers edition control panel 10 Fiber Properties The panel for the control of the fiber properties is shown in figure 21 In the color section of this panel the fiber tracts can be assigned with different colors Three color modes can be used color by FA color by fibers size and predefined colors In the two first modes the color code varies from red to blue passing through green with red corresponding to low values blue to high values and green to intermediate values The range used to map the colors in these two cases can be set with the scalar range slider and the scalar range button Fourteen predefined colors can be selected with the rest of buttons included in this section The sliders of the last section allows to change the opacity diffuse
25. reshold as seeds The result of this operation is not possible to be shown due to the high amount of data obtained typically by this operation In order to show a set of fibers computed with the brute force algorithm the select fibers button is needed After clicking that button the fibers that pass through the ROIs drawn are visualized and stored in the model data browser 6 6 5 Logic Operations 16 6 5 Logic Operations The logic operations allow to use several ROIs with different labels or classes to refine the fiber tracts computation The logic operations are available using the Tract Logic button and it is only available if a brute force operation has been previously performed in the data Two operations are permitted here AND and NOT To use OR operation just use the Tract OR button The AND operation computes the fibers that pass trough the ROIs defined by both labels ROI1 and ROI2 The NOT operation excludes all the fibers that pass trough the ROI defined by the label in Ex If the Exclude All check button is activated all the regions are excluded except those defined by ROI and ROIT2 17 7 Automatic Fiber Clustering Automatic fiber Clustering is one of the most advanced features implemented in Saturn It can be performed from the Tractography Auto panel see figure 16 available with the Tractog Auto button or with the DTI gt Tractography Auto menu item The upper buttons marked as Tract and Measures connects this panel wi
26. th the Tractography panel and the Measures panel A list of fiber tracts 1s shown in this panel representing the main anatomical fiber tracts of the human brain Each of them has associated an index value that corresponds to a ROI label There are three external files required for this procedure model vtk ROIs mhd and ROIs raw that have to be located in the same path as the executable Saturn file To perform an automatic tractography over a loaded DTI data first select the regions to be computed with the check buttons Then use the Do Tract button This will perform a non rigid registration based on the FA model volume and the FA volume of the tensor data selected in the tensor data browser 4b which is computationally very expensive This process is known as normalization After that a brute force tractography is performed over the DTI data using the FA threshold of the Tractography panel and the tracts are computed using the corresponding warped ROIs If the Do Tract is pressed again the normalization and the brute force procedures are not recomputed The normalization process can be performed separately using the Normalize button In this latter case no fiber tracts are computed In order to refine the fiber tracts obtained the Auto Select button can be used instead of Do Tract in order to include automatically logic operations If the warped ROIs are available in a file from a normalization procedure made before over this data
27. tween the available visualization modes This document consists on the following sections First in section 2 the input output data formats are described then in section 3 the visualization modes and features are explained Then the following sections itis described how to compute and visualize DTI data in 2D and 3D modes In section 4 it is described how to compute scalar magnitudes from DTI while in the section 5 explains how to show this scalar magnitudes images as tridimensional isosurfaces In section 6 the tractography techniques are described at user level In section 7 it is described how to use the automatic fiber clustering method then section 9 describes the fiber edition procedures included and section 10 and then section 8 describes how to obtain different measures from DTI data The section 11 describes how to display the tensor values of DTI data as glyphs 2 Input Output Formats 2 1 Scalar Data To load scalar data use the menu item File gt Open Scalar The input scalar data formats supported by Saturn are JPEG TIFF PNG MetaFile Kretz Raw data DICOM and DICOM series In figure 2a it is shown the dialog window for the scalar data entry information The first three formats JPEG TIFF PNG can only load 2D images whereas the formats MetaFile Kretz Raw data DICOM and DICOM series support 2D or 3D data If the Raw data format is chosen a new dialog window figure 3 is opened where the user is asked to introduce the
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