EvIdent Tutorial
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EvIdent Tutorial

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EvIdent Manual / Tutorial
1. Introduction.................................................................................................................3
2. Loading Datasets.........................................................................................................4
2.1. Load Options Dialog........................................................................................... 4
2.2. Load Single-Slice Dataset................................................................................... 5
2.3. Single-Slice Viewer Window ............................................................................. 8
2.4. Zoom Tool..........................................................................................................9
2.5. Load Multi-Slice Dataset .................................................................................. 10
2.6. Multi-Slice Viewer Window11
2.7. Resizing Multi-Slice Image Viewers................................................................ 12
2.8. Switching Dataset Viewer Windows 13
3. Dataset Manager.......................................................................................................14
4. ROI ............................................................................................................15
4.1. ROI Tools..........................................................................................................16
ROI Table.......................................................... ...

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EvIdentManual / Tutorial 1. Introduction................................................................................................................. 3 2. Loading Datasets......................................................................................................... 4 2.1. Load Options Dialog........................................................................................... 4 2.2. Load Single-Slice Dataset................................................................................... 5 2.3. Single-Slice Viewer Window ............................................................................. 8 2.4. Zoom Tool .......................................................................................................... 9 2.5. Load Multi-Slice Dataset .................................................................................. 10 2.6. Multi-Slice Viewer Window............................................................................. 11 2.7. Resizing Multi-Slice Image Viewers ................................................................ 12 2.8. Switching Dataset Viewer Windows ................................................................ 13 3. Dataset Manager ....................................................................................................... 14 4. ROI Manager ............................................................................................................ 15 4.1. ROI Tools.......................................................................................................... 16  ROI Table.............................................................................................................. 17 4.2.................................................................................................................................. 17 4.3. Active Analysis ROIs ....................................................................................... 17 5. Saving and Loading a Project ................................................................................... 19 6. Dataset Manager  Dataset Viewers ....................................................................... 20 6.1. Viewer Display Preferences.............................................................................. 20 7. Dataset Properties ..................................................................................................... 23 7.1. Experimental Paradigm..................................................................................... 23 7.2. Active Time Instances....................................................................................... 24 7.3. Baseline Time Instances ................................................................................... 27 8. EROICA.................................................................................................................... 28 8.1. Time-Course Preprocessing .............................................................................. 29 8.2. Initial Partition .................................................................................................. 29 8.3. Principal Partition ............................................................................................. 29 8.4. Parameter Viewer Window............................................................................... 29 8.5. Run EROICA .................................................................................................... 30 8.6. Dataset Manager  Results Entry.................................................................... 30 9. EROICA (Clustering) Results Viewer...................................................................... 31 9.1. Visible Maps Controls ...................................................................................... 32 9.2. Plot Controls ..................................................................................................... 34 9.3. Threshold Controls............................................................................................ 37 9.4. Time-Course Tool ............................................................................................. 38 9.5. Set Default Display ........................................................................................... 39 9.6. Save TCs for Further Processing ...................................................................... 39 9.7. Homogeneity Map ............................................................................................ 40 9.8. Parameter Setting and EROICA Log Files for Analysis Run........................... 43 9.9. Adding Map ROIs to the Dataset...................................................................... 43 9.10. Save/Load ROIs ............................................................................................ 45 9.11. Save TCs and Map Data to File .................................................................... 46 10. TC Management for Processing............................................................................ 50 10.1. Select TC in Viewer using TC Tool ............................................................. 50 10.2. Create TC from Paradigm ............................................................................. 53
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11. Correlation Analysis ............................................................................................. 55 11.1. Correlation Results Viewer........................................................................... 56 12. Multi-Slice Data Analysis..................................................................................... 58 12.1. Set Active and Visible Slices ........................................................................ 58 12.2. Zoom Tool .................................................................................................... 61 12.3. ROI Tool ....................................................................................................... 62 13. EROICA (Multi-Slice Dataset)............................................................................. 64 13.1. Multi-Slice Control and Viewer.................................................................... 65 14. Printing.................................................................................................................. 73 15. Multi-Dataset Analysis ......................................................................................... 75 16. EROICA Analysis Post-Processing ...................................................................... 81 16.1. Correlation .................................................................................................... 81 16.2. Region Growing............................................................................................ 83
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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 on the functional images. 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. Loading Datasets 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. 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 EvIdent evidentPreferencesfile and used for all subsequent dataset load actions. 2.1. Load Options Dialog Under theOptionsmenu select the Default Load Options entry.
This will display theLoad Options dialog window. Set the load options as shown and clickOK.
Scale Dataloading a data file, EvIdent will scale the intensity values by: When multiplying each voxel 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. Default setting istrue. Positive Data:If desired, all values are shifted such that the largest negative value is set to zero. MRI data values are all positive, so to avoid unnecessary computation, do not set this. Default setting isfalse. Calculate Mean: the average image of all the time instances, for each slice, Calculates for display purposes. Activation maps will be displayed over the mean functional images. Default setting istrue.
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All Points ROI:a rectangle ROI so that entire image, for each slice, is used forDefines analysis. Since for most fMRI datasets the interesting regions are inside the brain, the default setting isfalse. The resulting ROIs, which can be used to specify the time-courses (TCs) to be analyzed, will be added to theROI Managerpanel. Auto-Threshold ROI:slices for fMRI) do not takeUsually the regions of interest (brain up the entire image area. For faster analysis, only 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 first time instance image, or on the mean image if its calculated. The resulting ROIs, which can be used to specify the TCs to be analyzed, will be added to the ROI Managerpanel, one ROI per slice. Default setting istrue. 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. Default setting istrue. 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. Default setting istrue. 2.2. Load Single-Slice Dataset In the Dataset Manager window click on the Load Functional Data button.
If on a Unix system, theOpen Data Fileshould display the directory from wheredialog EvIdent was launched. On Windows NT, it will default to the user directory. Change the directory to the sample_ datafolder that came with the EvIdent install files. On subsequentLoad Functional Data the actions,Open Data File will display dialog the contents of the last directory from which data was loaded. A list of previous data directories is kept in theRecent Directories drop list at the top of theOpen Data Filedialog window.
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Previous data directoriesCurrent data director
Data file descriptionSelect the data file sample_3d provided with your install files. TheProperty Setdrop-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 way is to select from the drop-down list an existing properties entry.
Select the property sample_3d from theProperty Set drop-down list. Click on the Openbutton. 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. SelectYes. The data file sample_3d will automatically use the data file property sample_3d the next time it is loaded.
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EvIdent will attempt to load the selected data file using the specified file format. 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 active dataset. Analysis will be performed on the voxels belonging to this dataset. The name of the currently selected dataset (the same name as the data file by default) is displayed on EvIdents title bar.
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2.3. Single-Slice Viewer Window When a dataset is loaded, EvIdent automatically displays the image. After the data file sample_3d is loaded, the following single-slice image viewer should appear:
The image viewer window drag bar displays the dataset name. At the bottom of the viewer, the current crosshairs position in voxel coordinates (0,0 is the bottom left corner) and the current data value are displayed. 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.
Drag corners to enlarge window
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2.4. Zoom Tool You can select which area of the image will be visible in the viewer by using thezoomtoolthe magnifying glass icon or press F3.. Click on
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.lickft-CSihwith thezoom toolwill zoom out by a factor two. Using thezoom tool, drag the cursor over the image area that contains the brain. You can zoom back out (kcilC-tfihS) 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, the image can be repositioned in the viewer by dragging the cursor in the viewer. Press <ESC> (No Tool) and drag the image until it is centered in the viewer.
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2.5. Load Multi-Slice Dataset EvIdent expects the entire dataset to reside in one file. Single slice data (3D), is expected to be stored (X,Y,T), the entire image (X,Y) for a time instance (T), before the image for the next time instance. Multi-slice data (4D) may be stored (X,Y,Z,T) or (X,Y,T,Z). In the first case, the entire volume (X,Y,Z) is stored for one time instance (T) before the next volume. In the second case, the entire time series for one slice (X,Y,T) is stored before the time series for the next slice (Z). In theDataset Manager window, click on theLoad Functional Data button. Select samp _ d.This will display thedialog window where datasetfile propertiesmaybe set.  le 4
Enter 4 in theNumber of Dimensionsfield and press <ENTER>.
sample 4ddataset, each slice 128x128 pixels, and 100 time instances. is a 4-slice Change theLabel,Size,Type andUnits as shown below. The dataset is stored entries (X,Y,Z,T), and analysis is done along the temporal dimension. Make sure the Timedimension is selected as theAnalysisd.onsienim
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The data is stored as 4-byte floating point data, in high byte order. Unix-based systems, such as Sun or Silicon Graphics, store data in high byte order. Intel based systems (Windows, Linux) store data in low byte order. EvIdent needs to know on what system the data wasstored. Usually it will be a high-byte system. EvIdent performs a basic byte order test, it may display a message that the byte order is backwards. You may ignore the warning message and try loading. If it displays the images in inverse colour, try changing the byte order and loading again. Set theData Format as  informationBinary, Float and high-byte order as shown. Click on theSave Asbutton and when prompted, save the file properties as sample_4d. ClickOKwhen done.
TheData FileProperties dialog window will close and theProperty Set entry in the Open Data Filedialog will be updated to sample_4d. ClickOpento load the dataset. In attempting to load a data file, EvIdent checks whether the file size matches the specified dimension and data type. It also checks whether the byte order makes sense. EvIdent will display appropriate messages when file data and/or file properties mismatch. 2.6. Multi-Slice Viewer Window All the slices are displayed in one window. The viewer will be sized to the screen as best as possible. When best possible isnt satisfactory resizing the window will reposition
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