Training-AMIDE2.pdf

7/28/2019 Training-AMIDE2.pdf

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Hands-on training on AMIDE, a multimodality medical image analysis softwarepackage

Introduction

AMIDE is a medical imaging software tool for visualizing, analyzing, and registering medicalimaging data set acquired from different Imaging instruments. AMIDE is an open source

software tool written in C++. Source codes, compiled binaries for all operating systems (Linux,Mac OS X and Windows) and more detail documentation are available at

http://amide.sourceforge.net/.

Program startup

To start AMIDE double click the AMIDE icon. Æ Amide

o On program startup, a blank study window is

opened (see Figure 1). In this blank study

window, one or more related image data sets can be loaded and analyzed as required.

o A study, which represents a root object inAMIDE, is used for grouping a set of related

medical images and ROIs into logical unit. It also

keeps track of parameters that affect the whole

study.

Figure 1: Blank study window

o Using File -> New Study a new study can be opened to do multiple studies simultaneously.

Loading image data set

o A new image data set in typical medical image

format (e.g. DICOM, Analyze, Concorde, ECAT7, and InterFile) can be imported by selecting

File -> import File (guess) or

File -> import File (guess)

o Multiple image data with the same or different fileformat can be imported in each study (e.g PET,

SPECT, CT and/or MRI images). Figure 2 shows

imported PET and CT image data sets listed in the

study tree window.

Figure 2: Imported images into study tree

o Note that - for some image data, the file format has to be converted first to any of the typicalfile formats to be successfully loaded into AMIDE. This can be done by using data format

conversion programs . For example, a microCT scanner saves the reconstructed image in an

incomplete DICOM file format, a quick way to convert the image data is first to load the

microCT image data into GE MicroView or Amira and saving back the data set as Analyze

or DICOM file format .

http://amide.sourceforge.net/

http://amide.sourceforge.net/



Visualization/Manipulation of images

o To view/display the loaded images, select the

data set from the list of loaded images in thestudy tree. Using a fused/overlay selector,

multiple images can be selected to view in

fused or overlay form with fused/overlayselector (see Figure 3).

o The default main display window consists of three orthogonal slices taken from the data

(transverse, coronal and sagittal), but

AMIDE provide an option to display only

selected orthogonal views. A slider beloweach orthogonal view is used to browse across

the slices of plane images.

Figure 3: Selected images of PET and CT to

be displayed in the orthogonal view windows.

o AMIDE also allows to display multiple sets of the orthogonal views (figure 4) linked at thesame point in 3D space. In figure 4, three sets of display views shown after selecting a three

view display from the menu.

Figure 4: Three view displays

showing CT and PET images

separately and fused PET/CT

images on the third view

o Similarly, a set of operations can be selected such as color scale (threshold setting), zoom,

slice thickness setting, frame selector, interpolate (nearest neighbor or trilinear) from the topmenu to adjust the display for better visualization and navigate across the slices of 2D

images.

o AMIDE also includes important keyboard-mouse combination operations to better

manipulate the displayed data set. Some of this include:

• Shift-Left Mouse Button – shifts the active data usually used for aligning two data

sets. While holding Shift key, click left Mouse button and release on the display

window to move the data set within the display window. To complete the moveoperations click the right mouse button.

• Shift-Right Mouse Button - rotates the active data set usually used to align two datasets. Hold the shift key and click the middle mouse button

• Ctrl-Right Mouse Button – places an alignment points at the current cursor location

o To view a series of image data as function of space, time or gates use:

o View -> Series



o For viewing volume rendered images select:

o View -> Volume rendering

o Note that a good quality of volume rendered image can be generated by first using a

portion of the data set by selecting Tools -> Crop Active Data Set from the top

menu.

Image quantitation (ROI Analysis)

o The following ROI types are currently supported in AMIDE

• Ellipsoid

• Elliptic Cylinder

• Box

• Isocontour (2D and 3D)

• Freehand (2D and 3D)o To draw an ROI, first create a new ROI by

selecting the desired ROI under Edit ->add ROI or right click on the blank area

of the study tree. Figure 5: Shows an example of ROI’s added

into the study tree. o To adjust the size, placement and orientation

of already created ROI, either

• Click on the desired ROI and use Mouse operations (m1- shift, m2 – scale, m3 –

rotate), or

• Click m3 on the name of created ROI in the study list. This will bring up a dialogwindow with option of desired ROI modification.

o To calculate the statistics of ROI use Tools -> calculate ROI statistics. This will open up

dialog window to choose the ROI’s and the data sets for calculating the statistics.

Data alignment (image co-registration)

In AMIDE alignment of two data sets can be done either manually or using alignment wizard.o Manual alignment of data sets can be done by:

• Using shift-2 mouse combination to rotate the data sets to have the same transverse,coronal and sagittal view orientation, and

• Using shift-1 mouse combination to line up data sets appropriately, or

• Use data set modification dialog to perform fine manual alignment of two data sets.You can open data set modification dialog by right mouse click on the selected data

set in the study window.o To automatically align (co-register) two data sets:

• Draw at least three pairs of fiducial markers in each data set using Edit -> Add

Fiducial Mark or ctrl – right mouse click on any of the view windows.

• Give the same name for the corresponding fiducial markers in each data set. This is

required by the Alignment wizard, then

• Run Tools -> Alignment wizard to co-register the data sets.



Note that for better alignment using alignment wizard, each data set can first be cropped using

Tools -> Crop Active Data Set to include only desired image data for co-registration.

Figure 6: Shows alignment performed using alignment wizard for PET and CT data set.

Saving and exporting output data

o AMIDE saves studies in xif (Xml Image Format) in either single file or XIF directory. Toopen save file use File -> Open from the to menu.

o To export one of the views (transverse/cornola/sagittal) to a default jpeg image format use

o File -> Export view

o AMIDE allows also to export loaded image data into various typical file formats. To export

image data select the required data in the study tree and use

o File -> Export Data Set

Documents

Training-AMIDE2.pdf