EvIdent Tutorial

EvIdent Tutorial

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EvIdent Tutorial / Manual
Table of Contents
1 Introduction................................................................................................................. 3
2 Load Dataset................................................................................................................4
2.1 Load Options Dialog...........................................................................................4
2.2 LoSingle-Slice Dataset...................................................................................5
3 Single-Slice Viewer Window...................................................................................... 8
3.1 Zoom Tool...........................................................................................................8
4 ROI Manager.............................................................................................................10
4.1 ROI Tools..........................................................................................................11
4.2 ROI Table12
4.3 Active Analysis ROIs........................................................................................ 13
5 Saving a Project......................................................................................................... 14
6 Dataset Manager – Data File Viewers....................................................................... 14
6.1 Viewer Display Preferences............................................................. ...

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EvIdentTutorial / Manual Table of Contents1 Introduction ................................................................................................................. 3 2 Load Dataset................................................................................................................ 4 2.1 Load Options Dialog ........................................................................................... 4 2.2 Load Single-Slice Dataset ................................................................................... 5 3 Single-Slice Viewer Window...................................................................................... 8 3.1 Zoom Tool........................................................................................................... 8 4 ROI Manager............................................................................................................. 10 4.1 ROI Tools .......................................................................................................... 11 4.2 ROI Table .......................................................................................................... 12 4.3 Active Analysis ROIs........................................................................................ 13 5 Saving a Project......................................................................................................... 14 6DatasetManagerDataFileViewers.......................................................................146.1 Viewer Display Preferences .............................................................................. 15 6.2 Changing the Automatically Produced Number of TCs ................................... 17 7 Dataset Properties...................................................................................................... 20 7.1 Paradigm............................................................................................................ 20 8 EROICA (with Fuzzy Clustering Analysis).............................................................. 21 8.1 Time-Course Preprocessing .............................................................................. 22 8.2 Initial Partition - Parameter Viewer Window ................................................... 23 8.3 Principal Partition - Run EROICA (Clustering) ............................................... 24 1.1 Dataset Manager - Results Entry....................................................................... 24 8.4.................................................................................................................................. 24 9 EROICA (Clustering) Results Viewer ...................................................................... 25 9.1 Visible Maps Controls....................................................................................... 26 9.2 Plot Controls...................................................................................................... 29 9.3 Threshold Controls ............................................................................................ 33 9.4Time-CourseTool.............................................................................................359.5 Save TCs for Further Processing....................................................................... 36 9.6 Homogeneity Map............................................................................................. 37 9.7 Parameter Settings for Analysis Run ................................................................ 39 9.8 EROICA Log and Log Summary Files ............................................................. 40 9.9 Adding Map ROI to the Dataset........................................................................ 40 9.10SaveROIstoFile..............................................................................................439.11 Save TCs and Maps Data to File....................................................................... 44 10 TC Management for Processing ............................................................................ 49 10.1 Select TC In Viewer Using TC tool .................................................................. 49 10.2 Create TC From Paradigm ................................................................................ 52 11 Correlation Analysis.............................................................................................. 55 11.1 Correlation Results Viewer ............................................................................... 56 12 Exiting EvIdent, Loading a Project ....................................................................... 59 13 New Project ........................................................................................................... 61 13.1 Load Multiple-Slice Dataset.............................................................................. 61
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13.2 Multi-Slice Viewer Window ............................................................................. 63 13.3 Set Active and Visible Slices ............................................................................ 64 13.4 Zoom Tool......................................................................................................... 67 13.5ROITool...........................................................................................................6814 Set Active Time Instances..................................................................................... 69 15SetBaselineTimeInstances..................................................................................7216 EROICA (Multi-Slice Dataset) ............................................................................. 73 16.1 Multi-Slice Control and Viewer ........................................................................ 75 17 Printing .................................................................................................................. 79 18 Exit ........................................................................................................................ 80
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1 Introduction The following tutorial introduces users to common EvIdent tasks such as loading a dataset, setting dataset properties, executing EROICAs various options (preprocessing, initial data partition, principal partition with fuzzy clustering), and displaying the resulting activation maps. We strongly recommend that the user follow this tutorial systematically. The tutorial uses the test datasets included with the installation, but it is hoped that by completing the tutorial, users will be able to load and analyze their own datasets.
Dataset Manager Window
Upon startup, EvIdent displays the main menu bar with tool buttons and theDataset Managerwindow. Note: depending on your screen resolution, the EvIdent windows may not be sized exactly as shown.
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2 Load Dataset Currently EvIdent can load and analyze single-slice or multi-slice datasets. Only raw file formats can be loaded, with either short (2 byte), integer (4 byte) or float (4 byte) data. The file data formats are set via theOpen Data Filedialog window. When EvIdent loads a data file, certain preprocessing steps are done automatically. Users can deactivate these load options using theLoad Optionsdialog window. The latest load options are saved to the EvIdentPreferences File used for all subsequent dataset and load actions. 2.1 Load Options Dialog ¾Under theOptionsmenu select the Default Load Options entry.
This will display theLoad Optionsdialog window. Set the load options as shown and clickOK.
Scale DataWhen loading a data file, EvIdent will scale the intensity values by: multiplying each by a constant factor such that the median of the largest 10% of the data values matches the value specified in the field. This is usually done to avoid potential overflow problems when doing calculations with large MRI data values. Positive Data:shifted such that the largest negative value is setIf desired, all values are to zero. MRI data values are all positive, so to avoid unnecessary computation, do not set this.
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Calculate Mean:the time instances, for each slice, the average image of all  Calculates for display purposes. Activation maps will be displayed over the mean image. Auto-Threshold ROI: the regions of interest (brain slices for functional MRI) Usually do not take up the entire image area. For faster analysis, only time-courses (TCs) in the brain should be used. This option will use a simple, automatic image intensity thresholding algorithm, on a slice-by-slice basis, on the mean image if calculated, or on the first time instance image if not. The resulting ROIs, which can be used to specify the TCs to be analyzed, will be added to theROI Managerpanel. Erode ROI:For brain MRI, the skull is usually captured by the automatic threshold ROI algorithm. When this option is set, the outer voxel perimeter of the brain ROI is removed. Remove Outliers:voxels outside the brain are sometimes included in the Noise automatic-threshold ROI. When this option is set, singleton voxels will be removed. 2.2 Load Single-Slice Dataset The data file properties must be specified before opening a data file. Users may utilize an existing file properties entry if applicable (that is, the file properties entry matches the dimensionality and data type of the data file), or create a new file properties entry. EvIdent comes with two predefined data file properties. ¾In theDataset Managerwindow click on theLoad Functional Databutton.
If on a Unix system the Open Data File dialog should display the directory from where EvIdent was launched. On Windows NT, it will default to the user directory. Change the directory to the sample data that came with the EvIdent install files. On subsequent Load Functional Data actions the Open Data File dialog will display the contents of the last directory from which data was loaded. A list of previous data directories is kept in the Recent Directories drop list at the top of the Open Data File dialog window.
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¾Select the data file sample_3d provided with your install files. The Property Set drop-down list will display No Association the first time the file is to be loaded. There are two ways to associate a data file with a properties file description. One is to select from the drop-down list an existing set of properties.
¾Select the property sample_3d from theProperty Setdrop-down list. Click on theOpenbutton. The first time a data file is associated with a file property entry, EvIdent will ask if the specified data file is to be automatically associated with it the next time the data file is to be opened. ¾SelectYes. The data file sample_3d will automatically use the data file property amp _ s le 3d the next time it is loaded.
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EvIdent will attempt to load the selected data file using the specified file properties entry. Depending on the data file size, progress dialog windows will pop up and indicate what load options EvIdent is currently executing (scale data, mean image, auto-threshold ROI). Once the data file has been successfully loaded, theDataset Managerwindow is updated to include the newly loaded data file and ROI (if the load options were set to automatically threshold the image).
Datasets loaded and results
ROI Manager Displays ROIs for currently selected dataset.
The loaded data file becomes the currently selected dataset. Analysis will be performed on the voxels belonging to this dataset. The name of the currently selected dataset (which by default is the name of the data file) is displayed on EvIdents title bar.
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3 Single-Slice Viewer Window When a data file is loaded, EvIdent automatically displays the image. After the data file sample_3d is loaded, the following single-slice image viewer should appear:
The data viewer window drag bar displays the dataset name. At the bottom of the viewer, the current cursor position in voxel coordinates (0,0 is the bottom left corner) and the current data value corresponding to the crosshairs position are displayed. Data viewer windows currently open are also listed in theWindowsmenu. Use this menu to bring a window to the front of the screen.
Enlarging the viewer window, by dragging the corners or sides of the image viewer window, will automatically enlarge the image being displayed, while keeping the same aspect ratio and visible image area. 3.1 Zoom Tool You can select which area of the image will be visible in the viewer by using thezoomtool. Click on the magnifying glass icon or press F3.
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When this tool is selected, the cursor will change to a magnifying glass when it is over an image viewer. Clicking the image with the left mouse will magnify the image by a factor of two and will try to place the click point in the centre of the viewer. Enlarging the window will not make more of the image area visible, it will just enlarge the image to fit the new window size.Shift-Clickwith thezoom toolzoom out by a factor two.will ¾Using thezoom tool, drag the cursor over the image area that contains the brain. You can zoom back out (Shift-Click) and try again until the desired area is displayed.
The image will be zoomed such that the aspect ratio is maintained and the zoomed region is centered in the viewer. All future views of the dataset will use the current zoomed display area.
When an image is zoomed in, andNo Toolis selected (click the arrow icon or press the escape key), the image can be repositioned in the viewer by dragging the cursor in the viewer. ¾Press <ESC> (No Tooluntil it is centered in the viewer.) and drag the image
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4 ROI Manager TheROI Manageris part of theDataset Managerwindow. ROIs are associated with a particular dataset. When a dataset is selected in theDataset Managerwindow, the ROIs defined for the dataset are displayed in theROI Manager. ¾In theROI Tree,click the Auto-Threshold entry.
ROI Treedisplays ROI lists and sub-lists defined for the current dataset
ROI Tableshows ROI details of all the ROIs in the selected ROI lists
In the dataset image viewers, all the ROIs in theROI Table as visible, marked[V]checkbox, will be overlaid on the image using the specified colour, red by default.
. In EvIdent, all ROIs aresliceROI. That is, the (x,y) voxel coordinates of the ROI apply to one slice and indicate which TCs could be used in future dataset analysis.
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4.1 ROI Tools EvIdent will automatically determine an ROI for the voxels to use in processing. It uses a simple intensity thresholding algorithm to segment an image. Users can also create their own ROIs using one of the four ROI tools.
Contour ROI:To create a contour-based ROI, drag the cursor over the image to specify the perimeter of the desired ROI. Once the mouse button is released, the ROI perimeter is closed and the ROI added to theROI Manager. By default, the voxels inside and including the perimeter are part of the ROI. Polygon :This tool allows the user to specify the location of the polygon vertices in the image. Clicking on the image places one vertex. A straight line is drawn from the current vertex to a new vertex. A double-click places the last vertex and finishes the ROI by closing the polygon from the last vertex to the first vertex, and adds it to theROI Managerdefault, the voxels inside and including the perimeter are part of the ROI.. By Points :This tool allows the user to specify disjoint voxels as ROI. A single click over the image adds that voxel to the ROI. A double-click adds the voxel, completes the ROI, and adds it to theROI Manager.Rectangle : tool defines a rectangular ROI. The first click specifies the top left This corner of the rectangle. Drag the mouse to the desired location of the bottom right corner of the rectangle. When the mouse is released, the ROI is completed and added to theROI Manager. The voxels inside and including the perimeter are part of the ROI by default. ¾Ctrl-Click  theAuto Threshold entry in theROI Manager. This will deselect the ROI sub-lists and remove their entries from theROI Table. The ROIs are still active and will be used for analysis; they are just not displayed in the table and thus, not displayed on the image viewer for sample_3d. ¾Select the Contour ROI tool. TheFree Hand entry in theROI Treewill be selected automatically, with all of its sub-lists. All the ROIs in the sub-lists, if any, will be displayed in theROI Table.
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