# The &app; User's Manual V&manrevision;

## Introduction

### Licensing

AMIDE is released under the terms of the GNU General Public Library (GPL).

The text of the license is fairly verbose. A quick summary follows:

1. You are free to run the program, for any purpose. Please note that, although the GPL makes no restrictions on use of the program, your government probably does. For instance, in the United States, AMIDE is not FDA approved and cannot be used clinically.

2. You are free to study the source code of the program, and adapt it to your needs.

3. You are free to redistribute the program.

4. You are free to release modified versions of the program, as long as you also redistribute the source code to the modified program, and you label your modified version of the program appropriately.

### Availability of Source Code

The source code for AMIDE is readily available from the AMIDE web site.

### Supported Platforms

In addition to source code, binary versions of AMIDE along with installation instructions can be found for several systems on the AMIDE web site. The currently supported systems are Linux/i386, Microsoft Windows, and Macintosh OS X (achieved through the use of the fink add-on packages).

### Contact Information

Questions and bug reports can be addressed to the AMIDE users list amide-users@lists.sourceforge.net. Information on joining the list and/or viewing archived messages can be found here.

## AMIDE Basics

As the use of AMIDE is bound to be completely intuitive only to the one who wrote the program (i.e. me), this section provides a brief overview of operating within the program. It assumes you already have a data set loaded in. For instructions on getting a data set into AMIDE, see importing_data_sets

### A Quick Theory of Operations

#### AMIDE Objects

AMIDE can work with and display a large number of objects simultaneous (limited only be available memory). The object types current implemented in AMIDE are as follows:

Data Set

- A data set object contains the raw information from a medical imaging study, along with the corresponding parameters needed for interpreting that information (thresholds, colormaps, etc.).

ROI

- A region of interest object defines a volume of space over which statistics can be calculated. All ROI's in AMIDE are volumetric. Currently, AMIDE implements ellipsoid, cylinderical, rectangular, and isocontour based ROI geometries.

Fiducial Mark

- A very simple object, fiducial marks encode only the location of a reference point in space, and are used for rigid body alignment.

Study

- Each AMIDE session has a single study object, which is used for grouping together a number of related data sets, ROI's, and fiducial marks.

#### Object Tree

##### Study Tree

An example of a study's tree structure within AMIDE. The two data sets (FDG PET and microCT) and 1 ROI (bladder) are children of the study object (m2862). The remaining ROI's are children of the data sets.

In order to facilitate working with a large number of objects simultaneously, AMIDE conceptually groups all objects into a tree hierarchy, with the study object as the root of the tree (see studytree-fig). Data set objects will generally be primary branches off of the study object, while ROI's can be branches off of the study object or off of individual data sets. Why is this important? Because the structure of the tree determines how movements are mapped within the program. If a data set is moved relative to the rest of the study, the ROI's that are branches from that data set object will be correspondingly moved, so that they will maintain the correct orientation and position with respect to the data set that is their parent.

#### Real World Units

An important thing to realize when working with AMIDE is that the program will try to abstract away the underlying digital format of the data as much as possible. When you listen to digital audio, the CD player automatically converts the series of 0's and 1's encoded on the compact disc into an analog format so that you don't have to worry about the underlying digital format. Similarly, AMIDE presents the digital data to you in analog form. When ever possible, units are given in terms of real world units (e.g. mm's, seconds), and most operations are not constrained by the discrete nature of the underlying data. For example, data in AMIDE is viewed in terms of "slices", not fixed image planes. These slices can be taken from the data set at arbitary angles, and can be of any thickness (they are not constrained to be integer multiples of the underlying voxel size). You may be used to looking at medical images in terms of voxels and integers, but remember that the object or subject scanned is an item in the real world, and AMIDE tries to recreate this "analog signal" for you.

The only place the abstraction starts to break down is when dealing with dynamic data sets. Einstein understood time to be a "special" dimension, and AMIDE agrees. The reason for this, is that trying to represent dynamic data as anything but separate frames of data becomes overly complex from a computational standpoint, primarily because dynamic data is generally not equally spaced. While moving 1 voxel in the x, y, or z directions will always move you a constant unit of measurement (say 0.4 mm) in the appropriate direction, moving 1 voxel in the t direction may move you 30 seconds or 30 minutes in time, depending on what frame you're looking at. Because of this, AMIDE deals with dynamic data in terms of frames, although it should always tell you the time that those frames correspond to.

### Components of the Display

#### AMIDE Main Window

A diagram pointing out the salient features of the main window

#### Context Sensitive Help

Located in the lower left corner of the window, the context sensitive help window shows what different mouse buttons and key strokes can accomplish given the current cursor position. Note that mouse buttons are labelled in UNIX fashion. Buttons 1, 2, and 3 correspond to the left, middle, and right mouse buttons, respectively. Under Macintosh OS X, the middle and right buttons are emulated by pressing the option key or the open apple key, respectively, while pressing the mouse button.

#### Tree View of Study Data

Located on the left side of the window is a tree listing of all the objects in the study. The tree structure shows how movements will be propogated to other objects in the study. For instance, if a data set is rotated, all of its children will be correspondingly rotated.

Objects in the tree can be selected for display by left clicking on the name of the object. Middle clicking on a data set will make that data set the "active" data set. The "active" data set is designated by being highlights, and when a function is chosen that can logically apply to only one data set (e.g. filtering), the active data set is the one chosen.

Object modification dialog boxes can be brought up by right clicking on the corresponding object. ROI's can be added by right clicking on the blank area of the tree, or shift-right clicking on one of the objects. These functions are further described in data_sets and rois.

#### Orthogonal Views

Most of the main window display consists of the orthogonal views used for visually displaying the data sets being studied. Data is usually presented as three orthogonal slices taken from the data sets, but the user can choose to display fewer of these views if desired by using the view selector (described below in view_selector). The three views shown are the transverse, coronal, and sagittal planes. Note that the views may be incorrectly labeled for you. This could be because the data in the file you imported was not in the order that AMIDE expected it to be in. It could also be because you want to use the transverse/coronal/sagittal terminology differently then the program does (e.g. a coronal section of a rat brain is not the same as a coronal section of a rat).

Below the views are sliders for adjusting where in the data set the slices are being taken from. The location can also be changed by directly clicking on any of the canvases. The appropriate mouse clicks are as follows

Left Mouse Button

- Changes the location in the data set that the slices are taken from, without changing the thickness of the slices.

Middle Mouse Button

- Change the location in the data set that the slices are taken from, along with setting the thickness of the slices to the minimum reasonable.

Right Mouse Button

- Clicking an dragging with this button changes the thickness of the slices without changing the location. The thickness of the viewed slices can also be altered by adjusting the slice thickness setting spin button (see slice_thickness_setting).

Other

- Additional functionality of the mouse buttons for manipulating data sets and ROI's is explained in data_sets and rois

#### View Selector

Which of the three orthogonal views are shown can be selected by using these toggle buttons. By default, all three views are shown.

#### Linked Viewing

In addition to the three orthogonal views, AMIDE can display mutiple sets of these orthogonal views, all looking at the same point ("linked") in three dimension space. This is most often used for looking at fusion images of two data sets, with one set of views used for the first data set, the next set of views used for the second data set, and the third set of views used for the fusion of the two data sets.

#### Thresholding Tool

This button on the toolbar will pop-up a thresholding and colormap selection dialog for the currently active data set. In the dialog, the maximum and minimum thresholding levels can be changed by either directly typing in the values (in absolute or percentage units), or by using sliders on the color bar. The color scale can be changed using the corresponding drop-down menu. A log normalized histogram is shown to give an idea of the distribution of the data set's value. Finally, the thresholding type can be changed. The thresholding type determines how the maximum and minimum threshold values are applied to the data set, and are:

Per Slice

- The max and min threshold values will be applied in proportion to the max and min values in the current slice of data

Per Frame

- The max and min threshold values will be applied in proportion to the max and min values in the current frame of the data set

Interpolate Between Frames

- This threshold mode only makes sense for dynamic studies. In this mode, two sets of max and min threshold values are specified, along with which frame of data each of these sets corresponds to. For data frames before and including the first reference frame, the first set of threshold values are used. For data frames after and including the second reference frame, the second set of threshold values are used. For data frames between the two reference frames, the max and min threshold values are derived by interpolating (as a function of time) between the two sets of thresholding values.

Global

- The max and min threshold values will be applied in proportion to the max and min values in the entire data set

If the data set's modality is set to CT, buttons will be shown for applying bone and soft tissue windows as the thresholds.

#### Zoom Selector

This specifies how much to enlarge the views. AMIDE tries to make an educated guess about how large the display of the data should be, by using the smallest voxel dimension from the data set with the largest voxels to correspond to a displayed pixel. Zoom can be used in addition to that guesswork.

#### Slice Thickness Setting

Thickness specifies how deep the slices displayed on the views are. The minimum slice thickness is determined by the smallest voxel dimension of any of the data sets in the study.

#### Frame Selector

This button pops up a dialog for picking which frames of data to show from a dynamic data set. A frame (i.e. time period) to display can be selected by clicking on a list element. Multiple frames can be selected by holding down the shift key and selecting additional frames. Note, that for each data set selected for view, at least one frame from that data set will be displayed. If the choosen time period does not encompass a frame from that data set, the closest appropriate frame will be choosen.

#### Gate Selector

This button pops up a dialog for picking which gates of data to show from a gated data set. A gate to display can be selected by clicking on a list element. Multiple gates can be selected by holding down the shift key and selecting additional frames. Note that by using the entries, a span of gates can be choosen that loops around (e.g. gates 8, 0, and 1).

#### Target Selector

The target cross hairs are generally only displayed when one of the mouse buttons is depressed. With this toggle button, you can tell the program that you want the target cross hairs left on the views.

#### Interpolation

Interpolation refers to the method whereby AMIDE extracts data from the original medical imaging data set in order for it to be viewed on the screen. The interpolation selection button lets the user specify what type of interpolation to use when generating slices from the active data set. Nearest neighbor is faster, while tri-linear interpolation produces better looking (smoother) images with the penalty of being ~8x slower.

#### Rendering

Three rendering methods are available, MPR (multiplanar reformation), MIP (maximum intensity projection), and MINIP (minimum intensity projection). These rendering algorithms are utilized to combine data in the depth direction of the slice and/or over multiple frames of data. As such, the effects are most noticeable when the view thickness of the slices is increased and/or several frames of data are being combined. For MPR, each displayed pixel corresponds to the weighted average of the underlying data. For MIP and MINIP, each displayed pixel corresponds to the maximum or minimum value of the underlying data, respectively.

#### Fusion/Overlay Selector

By default, AMIDE displays multiple data sets as fused images. With the fused/overlay selector, you can tell AMIDE that you want the active data set to simply be overlayed on the other data sets, rather than fused.

#### Preferences Dialog Box

Underneath the edit menu is the preferences menu item. This will pop-up a dialog box that allows you to change preferences as to how things in AMIDE are displayed. The preferences will be saved in a configuration file for use by future AMIDE sessions (note: saved preferences are not currently supported on MS Windows).

ROI/View Preferences

- Here are several preferences for changing how ROI's are the view canvas are drawn, more thoroughly described in study-dialog. Note that these preferences are only used when a new study is created. To change these preferences for an existing study, you need to use the study modification

Threshold Windows

- The window preferences are more throughly described in data-set-dialog. Note that these preferences are only used for new data sets. To change the window levels for an existing data set, use the data set modification dialog.

Default Colortable Preferences

- The program uses the specified color tables by default on a newly imported data set.

Misc. Preferences

- The "Send Warning Messages to Console" option does exactly that. This is useful if enough warning messages are popping up that they're becoming annoying.

  With the "Don't Prompt for 'Save Changes' on Exit" option, you can tell the program to not prompt you to save changes done on the study when exiting an AMIDE session.

  The "Which Default Directory" controls which directory the file chooser dialog (used for save/import/open operations) will use as it's default location. "None" will cause the file chooser to show a list of recent locations as default. "Specified Directory" will cause the file chooser to utilize the directory specified as the default directory. "Working Directory" will utilize the directory from which the AMIDE program was executed as the default directory - this is most useful if you're often envoking AMIDE from the command line.

## Importing Data and Saving Studies

### Importation of Data Sets

AMIDE uses its own format (described below: xif-files) for saving data between session. To get new data into AMIDE, it needs to be imported (located under the file menu). You can either let AMIDE try to guess the file format (which works for most data types) or tell AMIDE explicitly which format the file to be imported is suppose to be in. Importing of all data types except for raw data is done using Erik Nolf's (X)medcon medical imaging conversion library.

#### Raw Data Files

AMIDE will generally attempt to load any file ending in ".dat" or ".raw" as a raw data file. The user will be prompted for the dimensions of the study, the offset of the data in the file, and the data format of the data in the file. Both big endian, little endian, and PDP endian files can be loaded (endian refers to the order in which bytes are arranged in memory).

The following data formats are supported: 8 bit signed or unsigned integer, 16 bit signed or unsigned integer, 32 bit signed or unsigned integer, 32 bit IEEE floating point, 64 bit IEEE floating point, and ASCII data.

#### ECAT Files

Static and dynamic ECAT 6.4 and 7.2 files are supported through (X)MedCon. AMIDE will generally try to load any file ending in ".img" as ECAT 6.4, and any file ending in ".v" as ECAT 7. Please note that ECAT 6.4 files are very difficult to autodetect, so if the file does not end in .img, you will probably have to tell AMIDE explicitly to import the file as ECAT 6.4.

Although not compiled in by default, AMIDE can be configured to use the z_matrix_7/libecat library for handling ECAT files instead of (X)MedCon.

#### DICOM Files

DICOM 3.0 is supported through (X)MedCon, which actually uses a slightly modified version of Tony Voet's VT-DICOM library. The level of support for DICOM 3.0 is entirely determined by (X)MedCon/VT-DICOM.

DICOM data is often distributed as a series of single slice data files. To read these into AMIDE as a single data set, you will need to stack these slices into a single, volumetric file. Notes on how to do this can be found at the (X)medcon website.

#### Concorde microPET files

Concorde format files are generated by the Concorde company's series of microPET scanners. It's a two file format (a data file and a header file), with the header in easily read ASCII format. Please note that you will need to tell AMIDE to open the header file (.img.hdr), not the raw data file (.img).

#### Acr/Nema 2.0, Analyze (SPM), InterFile3.3, Gif87a/89a

A variety of additional file formats are supported through (X)MedCon, including: Acr/Nema 2.0, Analyze (SPM), InterFile3.3, and Gif87a/89a. For more information, please see the (X)MedCon documentation, or the corresponding webpage (http://xmedcon.sf.net) .

### XIF Files

AMIDE saves studies in an extensible XML based format called XIF (Xml Image Format). This format can be stored as either a single file (flat file format XIF) or as a XIF directory. The flat file format is the default, and simplifies file moving and handling.

The directory format on the other hand allows easy access to the raw study data external to the AMIDE program, and will be of interest to developers. The directory format can be utilized via the "Save as XIF Directory" and "Open XIF Directory" menu items under the File menu.

In any case, these files or directories will characteristically end with ".xif", and are treated identically within the AMIDE program.

#### Opening Studies

From the main window, select "File->Open", and a file selection widget will open up. Select an XIF filename in the right column, and then hit the "OK" button (or double click on the filename).

#### Saving Studies

To save a study, from the study window select "File->Save As" and a file selection dialog will appear. Look at the "selection:" line near the bottom of the window, if this is the desired XIF filename, hit "OK" and the file will be saved. If this is not the desired XIF filename, select or enter in the correct XIF study, and hit the "OK" button.

Note that the original data set files are no longer needed by AMIDE, as all the information AMIDE needs is saved inside the .XIF file. You should however still archive the original data files, as AMIDE only reads in and stores the information from the header that it needs (which is generally not all the information enclosed within the header).

#### XIF Directory Format

Although admittedly annoying from a data transfer standpoint, using a directory structure for saving study information has the decisive advantage of making the saved information easily accessible using standard command-line utilities and text-based tools.

Each XIF directory contains a file called "study_*.xml" which contains the basic study parameters. Additional files can also be found in the XIF directory, such as ROI_*.xml files which contain ROI's, and data-set_*.xml files and their corresponding data-set_*_raw-data files, which contain the image data set parameters and the raw data respectively. The raw data file format is arbitrary (double/float/int, 64/32/16/8 bit, little or big endian, per plane/per frame/single scale factor), and is determined by the format of the originally imported data.

#### XIF Flat File Format

The flat file format is basically a concatenation of the information enclosed within the directory format. It is not meant to be editable or developer friendly. Instead, it allows easy management of studies for casual users. If you wish to access the information in a XIF flat file external to AMIDE, you'll be much better off resaving the data as in XIF directory format.

The format is as follows: The first 64 bytes of the file contain a magic string for format identification. The next 16 bytes contain 2 64bit unsigned little endian integers, the first one being the location of the study xml data within the file, and the second integer being the size of this xml data. Within the study xml data, is encased the information as to where in the file the children's xml data is. And within the children's xml data, is enclosed the location information of the raw data and subchildren.

### Exporting a View to JPEG/PNG

To export one of the views (transverse/coronal/sagittal) to an external image file, select "File->Export View->[view]" from the menu. The saved data format by default is jpeg. If the saved filename ends in ".png", the saved data format will be PNG.

## Manipulating Medical Data Sets

After being loaded in, medical images can be manipulated in a variety of ways with AMIDE. An important point to remember is that AMIDE deals with all data sets as 3 or 4 dimensional data sets. While 2D slices extracted from the the data set are displayed on the computer screen, at no time does AMIDE handle images as anything less than 3 dimensional data.

### Manipulating Data Sets on Screen

#### Displaying Data Sets

When initially loaded into the program, a data set is not displayed on the canvases. Rather, the name of the data set is contained in the study list, and the user needs to select the data set in the study list so that it is displayed on the canvases.

Displaying multiple data sets is as simple as importing more than one data set, and then selecting the data sets that you wish to view from the study list.

The time period over which the slices are drawn is determined by the time dialog, described in more detail in frame-dialog

#### Pertinent Mouse Actions

The following mouse actions can be used when the mouse is hovering over a data set on any of the orthogonal views

Shift-Left Mouse Button

- This combination allows shifting of the active data set in space (usually used for aligning two data sets). While holding the shift key, left click (and release) on the canvas, and you'll grab the active data set. You can now shift the active data around on the canvas. At this point, to enact the shift, click the right button (button 3). Any other mouse button will cancel the shift action.

Shift-Right Mouse Button

- This combination allows rotating of the active data set in space (usually used for aligning two data sets). While holding the shift key, middle click (and release) on the canvas, and you'll grab the active data set. You can now rotate the active data around on the canvas. At this point, to enact the rotation, click the right button (button 3). Any other mouse button will cancel the rotation.

Ctrl-Right Mouse Button

- This combination will place an alignment point at the current cursor location. A dialog will popup for entry of the alignment point's name.

### Manually Aligning Data Sets

What follows is a quick guide to manually aligning data sets in AMIDE

1. First rotate each of the data sets so that they are level with respect to the transverse, coronal, and sagittal views. This is easily done using the shift-2 mouse combination, but can also be done from the data set modification dialog.

2. Choose one of the data sets to be the active data set. The other data set will be the "fixed" data set.

3. Shift the active data set so that the two data sets line up appropriately. This is easily done using the shift-1 mouse combination, but can also be done from the data set modification dialog.

4. If fine tuning adjustments are needed, these are best done from the data set modification dialog.

### Data Set Modification Dialog

To modify parameters of a data set, right click on the name of the data set in the study tree to pop-up the data set modification dialog box. Parameters that can be modified are divided into the following pages.

Basic Info

- On this page are options to alter the data set name, type of modality, subject name, subject id, subject date of birth (DOB), conversion factor, and the interpolation type to use for this data set (described at interpolation). The conversion factor is a parameter that is multiplied to the data set before it is used for viewing or quantitation. Since the data set is in ECAT/MAP/abitrary scale units, the conversion factor can be used in order to analyze the data set in another type of reference unit (e.g. Percent Injected Dose [%ID]). There is also a built in calculator, where parameters such as subject weight and injected dose can be entered, and the conversion factor will be generated. Note that 1 cc is assumed to equal 1 g when generating the %ID/g and SUV.

Center

- The data set can be shifted by respecifing the center of the data set with respect to the origin. The x, y, and z dimensions are in millimeters.

Voxel Size

- The size of the data set's voxels (again, in millimeters) can be altered on this page. The "keep aspect ratio" button specifies that when altering the size of any voxel component (x, y, or z), the relative sizes between the components should be kept the same.

Rotate

- The data set can be rotated around its center in this page. There is one dial for each of the three slice planes. The transverse dial will spin the data set in the transverse plane (i.e. rotate on the z-axis). The coronal dial will spin the data set in the coronal plane (i.e. rotate on the y-axis). And the sagittal dial will spin the data set in the sagittal plane (i.e. rotate on the x-axis). The "reset to default" button allows the data set to be rotated back to the default orientation. On the bottom of this page is a matrix showing the coordinate frame of the data set with respect to the base coordinate frame.

Colormap/Threshold

- This page is analogous to the thresholding tool dialog (described at threshold_dialog) above).

Time

- From this page, the timing information of the data set can be altered. Scan start time can be used for altering the start time of the scan with respect to other data sets. Corrections in the duration of each data frame can also be made on this page.

Windowing Preferences

- The max and min threshold levels used for the bone and soft tissue CT window buttons can be explicitly set here. The "Insert Current Thresholds" button will reset the max and min values with the data set's currently used threshold levels.

Immutables

- This panel lists information about the data set that cannot be altered. The underlying internal data format of the data set and the data set dimensions in voxels are displayed on this page.

## Using Regions of Interest (ROI's)

ROI stands for Region of Interest. An ROI designated a volume in space over which statistics should be calculated.

### ROI Types

The following ROI types are currently supported in AMIDE:

#### Geometric ROI's

Ellipsoid

- An ellipsoid is similar to a sphere, but with a diameter specified for each direction [x,y,z]. In the case of x=y=z, the ellipsoid is a sphere.

Elliptic Cylinder

- An elliptic cylinder is similar to a regular cylinder, except it has an ellipse as its base instead of a circle.

Box

- Exactly what it says, a 3D box.

#### Isocontour ROI's

Isocontour ROI's are regions selected from the data set such that the edge values of the ROI are always the same value. There are two types, 2D and 3D isocontours. Additionally, both these ROI types can be defined so that they encompass all neighboring values either above a certain minimum value, below a certain maximum value, or between a minimum and maximum value. After drawing of these ROI's, they can be modified by using manual drawing or erasing operations.

2D Isocontour

- A 2D isocontour is derived by considering a value on one of the displayed 2D slices. The depth of a 2D isocontour is specified initially by the depth of the viewed slices.

3D Isocontour

- A 3D isocontour is derived by considering a value on the current frame of the active data set.

#### Freehand ROI's

Freehand ROI's are regions of interest that are drawn manually.

2D Freehand

- A 2D Freehand ROI is similar to a 3D Freehand, except that it is constrained to be only one voxel thick. By default, the depth is the current slice thickness, although this can be changed by the user.

3D Freehand

- An ROI that can be drawn freely in all 3 dimensions..

### Drawing ROI's

To draw an ROI, you first need to create a new ROI. You can add a new ROI to either the study, or a particular data set. To add an ROI to the study, you can either select the ROI desired under the "Edit->add ROI:" menu item, or right click on the blank area of the study tree. To add an ROI to a data set, shift-right click on the data set that you'd like to add the ROI to. In both cases, a dialog box will pop-up for you to enter in the new ROI's name.

When first added, the new (undrawn) ROI will be selected in the study tree. When an undrawn ROI is selected in the study tree, the program will use the next mouse input on any of the displayed views to begin the process of drawing this ROI.

For ellipsoid, elliptic cylinder, and box ROI's, a click with the left button will begin an edge-to-edge drawing, while a click with the middle button will begin a center-out drawing. The x and y dimensions of the ROI are determined by this process. The z dimension (thickness) of the ROI can be specified by the pop-up dialog that will appear on the completion of the mouse movement.

For isocontour's, the value of the data set at the clicked upon location will be used to derive the isocontour.

For freehand's, the point on the screen that is clicked upon will be included in the ROI.

### Manipulating ROI's

After an ROI is drawn, it can be further manipulated to adjust its size, placement, and orientation. You can directly manipulate the ROI by clicking on it in any of the viewing windows. Mouse button 1 is used to shift ROIs. Mouse button 2 is used for zooming ellipsoid, elliptic cylinder and box ROI, and is used for entering drawing mode for isocontour and freehand ROI's. Mouse button 3 is used to rotate ellipsoid, elliptic cylinder, and box ROIs, and for redefining the isocontour value for isocontour ROI's.

For isocontour and freehand ROI's, drawing mode can be entered by using thie middle mouse button (button 2). Once entered, points can be added or removed from the ROI by using the left (button 1) or right (button 3) mouse buttons, respectively. Holding down the shift key while using these buttons increases the size of the action. The middle button (button 2) allows the user to leave drawing mode.

You can also edit the ROI size/placement/orientation/name etc. by clicking on mouse button 3 while over the ROI's name in the study item list. This brings up the ROI modification dialog (described at roi-dialog).

### Calculating Statistics

Statistics on an ROI can be calculated via the "Tools->calulate ROI statistics" menu item. Choosing this will pop-up a dialog that lets you choose which ROI's (selected or all) and which data sets (selected or all) you'd like to calculate statistics over. You will also have three options as to how you what the values to be calculated.

1. Calculate over all voxels.

2. Calculate over highest x percent of voxels. For example, if you choose this and pick 25% as the number, your ROI will be calculated from the 25% of the voxels in the ROI that have the highest values.

3. Calculate for voxels >= % of Max. This method is based on Lee, Madsen, Bushnel, and Menda, Nuc Med Comm 2000, 21:685-690. As an example, if you choose this and pick 50% as the number, the highest valued voxel in the ROI will be found, and then the ROI statistics will be calculated for all voxels that are greater or equal to 50% of the highest valued voxel.

4. Calculate for voxel >= Value. This algorithm only does calculations for voxels in the ROI that have a value greater than the value specified.

There's also a check box to enable "more accurate quantitation". The default algorithm (corresponding to unchecked) makes some approximations in deciding which voxel are in our out of the ROI. If this check boxed is checked, the ROI results will be more accurate, but will take much longer to compute.

After hitting execute, the program will crank for a while, and then show the calculated values in a new dialog window. Hitting "Save as" button allows saving these values as a tab separated values (TSV) file. This file should be easily imported into most spreadsheet applications (Excel's a little stupid, you may have to explicitly tell it you're importing a TSV file). Pressing the "Copy" button copies the information into the operating systems clipboard, allowing pasting of the results into other programs. The "Save Raw Values" button allows you to export the underlying raw data values for the ROI's in case you wish to do your own statistical analysis.

#### Gotcha's to ROI calculations

##### Variance and Standard Deviation Fallacies

Currently, AMIDE generates variance and standard deviation values that may occasionally be of interest to imaging physicists. It is very important to remember, that these numbers represent the noise in the data set, NOT the noise in your experiment.

The variance of an experiment can only truly be measured by taking multiple samples (i.e. performing multiple scans) and calculating the variance between these different samples.

##### Changing Calculated Volume

Short story: The calculated volume shown by the ROI statistics dialog is correct. Use this value as the volume of the ROI, not the value you might calculate by hand based on the ROI's dimensions.

Long story: AMIDE calculates ROI's by translating the ROI's dimensions into the data set's coordinate space. It then computes statistics for all the data set voxels that are in the ROI. For voxels that lie on the edge of the ROI, AMIDE will subdivide the voxel into a finite number of subvoxels, and calculate over the subvoxels. This approach yields correct statistics, but it is important to realize that the computed ROI is a discrete representation of the specified analytical ROI. So while the true volume of an ellipse is pi*r1*r2*r3, the computed volume of the ellipse in AMIDE will depend on the number of voxels and subvoxels that were determined to lie within the ellipse, which in turn can depend on the orientation of the ROI with respect to the data set in question. Since the computed volume given by AMIDE represents the volume in the data set that was used for the ROI calculation, you will want to use that value (not the real ellipse value).

##### Why isn't a "total" statistic calculated for the ROI?

AMIDE doesn't present the "total" value in the ROI, as it doesn't necessarily know what the units of the underlying data are. If you're using PET or SPECT data, your voxel values are most likely proportional to activity/volume/time. To calculate the total in your ROI, you should multiple the mean value of the ROI times the ROI volume and the frame duration. If you're using CT data, your values are probably proportional to density, so to calculate the total you would multiple the mean ROI value by the ROI volume.

#### Explanations of ROI Statistical Values

Median

- This is the median value of all the voxels that are enclosed (partially or totally) within the ROI. For an even number of voxels, the median is defined as the average of the center 2 values.

Mean

- The mean value of the voxels in the ROI. Voxels that are partially enclosed within the ROI are appropriately weighted.

Variance

- The variance of the voxels in the ROI. This is a weighted variance calculation so that voxels that are partially enclosed within the ROI are correctly handled.

Standard Deviation

- The square root of the variance.

Standard Error

- The square root of the variance, divided by the square root of the total number of voxels in (totally or partially) the ROI.

Minimum/Maximum

- The minimum and maximum values for all voxels enclosed totally or partially within the ROI.

Size

- The volume of an ROI (mm^3). Details as to its calculation are above in: roi-volume-calculation.

Fractional Voxels

- The is the sum of the voxel weights, and gives an indication of how large the ROI is in voxel space.

Voxels

- This is the total number of voxels used in calculating the ROI, both partial and total. In contrast to the "Fraction Voxels" measure, the "Voxels" measure gives a better indication of the statistical validity of the mean, variance, etc.

### ROI Modification Dialog

To directly modify parameters of an ROI, right click on the name of the ROI in the study tree to pop-up the modification dialog. Parameters that can be modified are divided into the following pages.

Basic Info

- The name and type of ROI can be altered on this page.

Center

- The center of the ROI can be shifted with respect to the origin on this page. The x, y, and z parameters are in millimeters.

Dimensions

- The size of the ROI can be altered from this page. The x', y', and z' dimensions are in millimeters and are orientated with respect to the orientation of the ROI.

Rotate

- The ROI can be rotated around its center in this page. There is one dial for each of the three slice planes. The transverse dial will spin the ROI in the transverse plane (i.e. rotate on the z-axis). The coronal dial will spin the ROI in the coronal plane (i.e. rotate on the y-axis). And the sagittal dial will spin the ROI in the sagittal plane (i.e. rotate on the x-axis). The "reset to default" button allows the ROI to be rotated back to the default orientation. On the bottom of this page is a matrix showing the coordinate frame of the ROI with respect to the base coordinate frame.

## The Study

The "Study object" in AMIDE is used for grouping a set of related data sets and ROI's. Note that the use of the word "Study" here diverges from the traditional nuclear medicine use of the word, in which study generally connotates a single scan (or occasionally multiple but highly coupled scans) done on a single patient. A study in AMIDE is often used to group an entire experiment (several patients, several animals, whatever) into a single file. The study object itself is used mostly for storing parameters that effect all other objects stored in the study.

### Study Modification Dialog

Similarly to the data set and ROI modification dialogs, the study modification dialog can be used to alter parameters relevant to the entire study. Right click on the name of the study in the study tree to pop-up the study modification dialog box. Parameters that can be modified are divided into the following pages.

Basic Info

- On this page are options to alter the name and creation date of the study.

View Center

- From this page, the point that the study is currently viewing can be explicitly changed. The x, y, and z dimensions are in millimeters.

Rotate

- The entire study (including all objects within it) can be rotated around the view center in this page. There is one dial for each of the three slice planes. The transverse dial will spin the study in the transverse plane (i.e. rotate on the z-axis). The coronal dial will spin the study in the coronal plane (i.e. rotate on the y-axis). And the sagittal dial will spin the study in the sagittal plane (i.e. rotate on the x-axis). The "reset to default" button allows the study to be rotated back to the default orientation. On the bottom of this page is a matrix showing the coordinate frame of the study with respect to the base coordinate frame.

ROI/View Preferences

- The width of the line used to draw geometric ROIs can be altered here (1-5 pixels). This parameter is not relevant for isocontour ROI's. For isocontour ROI's, you can choose to have them draw as filled in or hollow.

  Canvas layout allows you to switch the three views (transverse, coronal, and sagittal) between a linear style layout more commonly seen in PET software, and an orthogonal style layout more commonly seen in MRI software. "Maintain view size constant" allows you to pick if you want the size of the view to remain constant or not. If not checked, the size of the views shown will depend only on the data sets selected. If the checkbox is checked, the size of the views will depend on all the data sets in the study. Finally, "target empty area" is for setting the size of the empty area in the middle of the target (the crosshairs on the views when changing the view location).

Immutables

- This panel lists information about the study that cannot be altered. "Voxel dim" is the preferred voxel dimension, this is what the canvas will use as the "basic" voxel dimension, from which the zoom factor is relative too.

## Viewing Series of Slices

Instead of looking at three orthogonal slices through the data set, a series of slices (all of the same orientation) can also be examined. Select: "View->Series", and a dialog box will come up allowing you to pick which objects you'd like to display on the series viewer, along with if you'd like to display the slices over space, time, or gates. The thickness of the slices are determined at the time the series window is brought up. A slider appears on the top of the window which allows moving through the data set. Note that since slices are cached in memory after being displayed, already displayed slices do not need to be regenerated from the data set and reviewing these slices is significantly faster.

## Rendering Data

Rendering in AMIDE is accomplished using the Volpack volume rendering library. This software library is both portable, and provides for true volume rendering (as opposed to the surface rendering used by many other libraries and hardware accelerators).

To start a rendering window, select the "View->Rendering" menu item. A small dialog window will pop-up allowing you to select which objects you'd like rendered, along with some additional options. The first "Set values greater than max threshold to zero" allows you to strip high level voxels out of the rendering process. In general you won't want this, but it might be useful if you have high valued areas in your data set that obscures what you'd like to see. The second option "Accelerate Rendering" tells VolPack to use a faster method for doing the volume rendering. You will in general want to use this option, as it causes a significance performance enhancement (around 10 fold). It does, however, require around 3 fold as much rendering as the non-accelerated option, so if you're running out of memory, you'll want to try to rendering without the acceleration. The third option "Initial opacity functions only density dependent" sets things such that the initial gradient opacity function does not contribute to the rendering. This is useful for data sets (e.g. PET) where one is more interested in having an accurate view of the data, rather than a view where gradients in the data set are highlighted.

After hitting "Execute" the program will reslice the data sets and ROI's into a data structure that the volpack library can handle, and then perform some initial renderin gcalculations. For data sets, the interpolation type specified for the data set will be used. This whole process will take some time, so be patient. Please also note that, when converting the data set, the data is scaled between the current minimum and maximum threshold, with all data above the current maximum threshold set to the maximum threshold value (or zero, if specified), and all data below the current minimum threshold set to the minimum threshold value. This scaling can be relative to the data set's "Global" maximum and minimum, to the "Per Frame" maximum and minimum, or can be from maximum and minimum values "Interpolated Between Frames". "Per slice" scaling does not make sense in the context of volume rendering, and is interpreted as "Global" scaling.

When all this is completed, the rendering window should pop-up. Its use is described below.

### Rendering Window

#### Main Rendering Canvas

The result of the rendering process is presented on the canvas in the center of the window. This canvas can accept user input to change the orientation of the rendering. Button 1 allows rotating on the x and y axis, and button 2 allows rotating on the z axis.

#### Spin Sliders

You should notice two slider type widgets, one on top of the rendered image, and one on the right side. These are both appropriately labeled with the axis around which the rendering will be spun if they are changed. Additionally you should notice a dial widget (labeled 'z'). The dial is for rotating on the z axis (which comes out of the plane of the display). Note that the effect of rotations are cumulative.

#### Reset Axis

This button will reset the rendering's orientation back to the default orientation.

#### Toolbar

##### Transfer Function Button

This will pop-up a dialog with a panel for each object being rendered. The available options are described below:

Return Type

- This setting determines whether the rendering returns an image which looks more analogous to an x-ray (the "opacity" setting), or returns an image which looks more like a surface (the "grayscale" setting). The "grayscale" setting does this by specifying a light source, material properties, and using depth cueing.

Color Table

- The color table of each rendered object can be changed here.

Classification Functions

- This is the most confusing part of rendering, so hang on here. The classification functions are used to map between the value in each voxel and how much that voxel should be represented in the final rendered image. On the x axis is the possible values of the different voxels. On the y-axis is the opacity that will be given a voxel based on its value.

  Both classification functions have several buttons on the right side of their graphs. The top button allows the classification function to be drawn as a spline. The second button allows the classification function to be drawn as a series of straight lines. Finally, the last button resets the classification function to a straight line.

  There are two classification functions:

  - Density Dependent: This function tells you how opaque each voxel will be based on its current value. In a sense, this is analogous to an x-ray, where the amount of the x-rays that are absorbed in a structure is related to the density of that structure. of the display.

  - Gradient Dependent: Instead of relating the density of a voxel to its opacity, this function relates the gradient of a voxel (how much the value changes between this voxel and its neighbors) to its opacity. This has the effect of giving added weight to surfaces.

##### Monoscopic/Stereoscopic Buttons

You can choose between generating a single rendered image (monoscopic), or a stereoscopic image pair. A stereoscopic image pair is a pair of images that have been generated at slightly different angles. When viewed correctly, these two images can be interpreted by the viewer's eyes as a single image containing depth information.

##### Zoom

Determines the size at which the resultant rendered image will be displayed. Note that changing the zoom will not affect the speed of the rendering, and increasing the zoom past 1 will not increase the resolution of the rendered image.

#### Rendering Menus

##### File->Export Rendering

This menu item allows you to export the rendered image to an external image file. The saved data format is jpeg.

##### File->Create Movie

This causes the movie generation dialog box to pop up. This dialog box is further described below: rendering-movie-dialog.

##### Edit->Rendering Parameters

This causes the rendering parameters dialog box to pop up. This dialog box is described below: rendering-dialog.

### Rendering Parameters Dialog

#### Speed versus Quality

With this drop-down menu, the user can choose between rendering speed and rendering quality. To increase speed, voxels with values either close to zero or close to unity can be counted as completely translucent or completely opaque, respectively. The highest quality doesn't use this approximation at all, the lowest quality setting uses this approximation big-time.

#### Stereosopic parameters

These parameters are used for controlling the results when the "stereoscopic" option has been chosen.

##### Stereo Angle

This is the angle offset (in degrees) between a pair of rendered images. Increasing this number will generally give a greater sensation of depth in the image pair. A Reasonable value for this parameter is between 2 and 5 degrees. Note that this parameter will be saved between different sessions of the program (not currently done on MS Windows).

##### Eye Width (mm)

Ideally, this should be (roughly) the distance between the two rendered images, and corresponds to the distance between the user's eyes. It is impossible for a person to resolve a stereoscopic pair if the images are farther apart then the person's eyes, since human eyes cannot move independently. While this parameter is specified in millimeters, the actually distance between the pair of images that gets displayed on the monitor depends on the setup of the computer. If the monitor information reported by the operating system is not correct (usually the case), the "eye width" parameter will not be in true millimeters. Note that this parameter will be saved between different sessions of the program (not currently done on MS windows).

#### Depth Cueing

These parameters are only used if the "grayscale" output type has been chosen.

##### Enable/Disable Depth Cueing

Specify whether or not we want depth cueing. Depth cueing puts in a "fog" that causes more distant voxels to appear less bright.

##### Front Factor

This is the transparency of the fog at the front of the data set. If this number is greater than 1.0, voxels toward the front of the data set will be brightened. If this parameter is less than 1.0, voxels toward the front of the data set will be darker, respectively.

##### Density

This is how thick the "fog" is. The thicker the fog, the darker distant objects seem.

### Rendering Movie Dialog

#### Frames

How many frames should be in the MPEG1 movie. The MPEG1 movies generated will be set to run at 30 frames/second, so the default of 300 frames will give a ten second movie.

#### Rotations on [x,y,z]

This setting determines how many times the data set will be rotated around the given axis over the course of the movie. The rotation for each frame is done in x->y->z order (rotate on x first, then y, then z).

#### Dynamic Movie: No/Over Time/Over Frames Smoothed/Over Gates

This option allows a rendered movie to be made over a time period, which is useful for dynamic data sets.

Note that every time a frame boundary in the data set is passed over, the rendering process must slice and load in a new frame of data. This makes creating a rendered movie over time significantly slower than a movie with just rotations.

Picking "over time" will allow entry of a start and end time for which the data from the data sets should be drawn. With the "over time" option, each second is given equal waiting in terms of how many images from that time period are generated for the output movie.

Picking "over frames" allows entry of a start and end frame (note that this really only makes sense with a single data set). The advantage of "over frames", is that each frame is weighted equally in terms of how many images are generated for the output movie, so for data sets were the dynamics of interest correspond closely to the dynamics of the data set framing sequence, "over frames" may give a more appealing result.

The "over frames smoothed" option is almost the same as "over frames", except that data will be interpolated between frames. This makes for a smoother movie (no jumps) but takes much longer as nearly every movie frame has to be reloaded.

## Additional Tools

### Alignment Wizard

In addition to manually aligning data sets (described at manual_alignment), data sets can also be aligned using the alignment wizard utilizing either mutual information or fiducial markers.

#### Alignment with Mutal Information

A rigid body alignment can be performed utilizing mutual information between two data sets. This algorithm works by taking orthogonal slices from one data set (transverse, coronal, and sagittal) and computing a transform to best allow matching of these slices to the second data set. This algorithm works best when the two data sets have already been roughly aligned. Note that the orthogonal slices utilized for the matching are derived utilizing the current viewing parameters (current viewing location, slice width, interpolation method, etc).

#### Alignment with Fiducial Markers

A rigid body alignment can be performed utilizing fiducial markers. The process is basically:

1. Draw at least three pairs of fiducial makers between the two data sets that you wish to align. Drawing fiducial markers is described below as fiducial-marker.

2. Run the alignment wizard (under tools->alignment wizard). For the alignment wizard to recognize two fiducial markers as a pair, they must have exactly the same name. So if you have a marker labeled "1" under the first data set, you will need another marker, also labeled "1", under the second data set.

#### Drawing Fiducial Markers

Fiducial markers can be added to any of the data sets in the study in a variety of ways. For the currently active data set, hitting the "Edit->Add fiducial mark" menu item will drop a fiducial maker at the currently viewed location. Fiducial marks can be added for the active data set directly from the views by pressing ctrl-right mouse button, which will drop a fiducial marker at the point that the mouse is currently at. Finally, fiducial markers can be added to non-active data sets by pressing ctrl-right mouse button while hovering over a data set's name in the study list.

After being created, the fiducial marker can be moved by clicking on the marker point shown in any of the views.

#### Fiducial Marker Modification Dialog Box

To modify parameters of a fiducial mark, right click the point in the study list to pop-up the Fiducial Marker Modification Dialog. From this dialog, the name and location of the fiducial marker can be altered.

### Crop Wizard

Coming soon. Note that only what is strictly inside the cursor lines is saved. What's underneath and outside the cursor lines is cropped away.

### Factor Analysis Wizard

The factor analysis wizard is currently being developed. It probably won't work for you, and is only included in AMIDE for those who might be interested in working on it (rather than with it).

### Filter Wizard

Nothing written yet...

### Fly Through Wizard

Nothing written yet...

Note, will generally get much better results for fly through if using trilinear interpolation.

### Profile Tool

A complete description of this tool has not yet been written.

The left and right limits of the gaussian fit can be altered by clicking on the profile with the left and right mouse buttons, respectively. The x value used for initializing the gaussian fit can be picked by clicking on the profile with the middle mouse button.

Note that the line profile is extracted from the currently viewed image, not the underlying raw data itself. This means things like the current interpolation and FOV will effect the line profile that's generated, and as such may effect the FWHM that's fitted.

### ROI Statistics

A description of the ROI statistics tool can be found at: roi_statistics.