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.
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 the section called “Frame Selector”
The following mouse actions can be used when the mouse is hovering over a data set on any of the orthogonal views
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.
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.
This combination will place an alignment point at the current cursor location. A dialog will popup for entry of the alignment point's name.
What follows is a quick guide to manually aligning data sets in AMIDE
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.
Choose one of the data sets to be the active data set. The other data set will be the "fixed" data set.
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.
If fine tuning adjustments are needed, these are best done from the 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.
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 the section called “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.
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.
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.
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.
This page is analogous to the thresholding tool dialog (described at the section called “Thresholding Tool”) above).
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.
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.
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.