Stacked Image Set.. 1

Definition. 1

Coordinate System.. 1

New.. 2

Computed Scout Views. 3

Orientation Labels. 3

Edit 4

Selection of a stacked image set 5

Stacked Image Set Options. 5

Distance Tool 5


Stacked Image Set


A stacked image set consists of a series of images taken sequentially without patient motion along an axis of the body.All the images must be coplanar, but need not be the same size.A stacked image set may consist of all coronal, sagittal, or transverse images, but not a mixture.It is necessary that each image be specified in relationship to some common coordinate system.The Dicom standard requires this for all images in the same series.Such images are here considered stackable to form a three dimensional model of the patient.Normally you would only pull the images from a single series.However, the capability is provided to pull images together from anywhere, as might be the case if a body technique changed to a head technique when the head is encountered.However, the head images must be specified to the same coordinate system as the body images in this example and so should be part of the same series.The program has no way of knowing the relationship between different series, and the user must not combine images outside of a series unless it is known apriori that all the images meet the above conditions.CT transverse scans may be taken with the gantry rotated, as long as all images are parallel to each other.The program will not allow non-coplanar images to be together in a stacked image set.Nor may two images occupy the same plane within a stacked image set.

Coordinate System

Each image file must consist of patient orientation information and the coordinates specifying the plane of the image relative to a common patient coordinate system.Dicom 3 specifies that positive Z axis pointing towards the patientís head, with the Y axis pointing down (for a supine patient) in the posterior direction, X axis to the patientís left.Be aware that this program uses the IEC coordinate system with the positive Z axis pointing anterior, Y axis toward the patientís head, and X axis to the patientís left.Dicom 2 and 1 specified images relative to the imaging equipment, not the patient.In that instance we must rely on designations within the file as to feet first or head first, supine or prone.


To create a stacked image set select New under Stacked Image Sets on the main tool bar.A name unique to the patient must be provided by the user.A patient may have any number of stacked image sets.To select images for a stacked image set, the program will provide a file selection box starting at the directory specified in the file NewImagesDirectory.loc in the program resource directory.


Choosing a directory on the left of the popup will show the files in that directory on the right.Navigation is also possible with the filter function at the top of the popup.Note on the bottom that the files may be copied or moved into the patient directory.Moving means that the file in the images directory will be erased after it is successfully copied into the patientís directory under the new stacked image set name.The entire file is copied or moved unchanged.


Select Images Files for a Stacked Image Set Popup


Normally you should configure your Dicom input so that a patientís series is stored in a separate directory under the new images directory.


After you have selected all the images for a stacked image set, the images will all be displayed on a screen.

Computed Scout Views

For stacked image sets with more than one image, a coronal, sagittal, and transverse scout view is computed.The plane for these scout views is through the center of the volume of the image set.Each scout view is computed by considering parallel (non-diverging) rays through the image set and averaging the pixel value of the pixels that the ray goes through.Pixels with a value less than a threshold specified in the program resource file ComputedScoutImages are not averaged.This is to reduce the dynamic range of the resulting image.


Upon display of a new image set, the computed scout views may be useful in locating errors due to patient motion during the imaging process, as discontinuities may result and be discernable in the scout views.

Orientation Labels

For each plane displayed, the edges of the image will be labeled among anterior, posterior, superior, inferior, right, and left.To see the labels you may have to enlarge the frame or an image to full screen by hitting the button in the upper right hand corner of the frame.The text for these labels comes from the program resource file PatientOrientationLabels (under the language subdirectory).†† For oblique planes the labels may be combined for the dominate directions, such as Ant-Sup.


It is absolutely essential that the orientation labels on the two dimensional images be verified.†† Although one is unlikely to confuse anterior and posterior, left and right is another matter, particularly in the head and pelvis.†† Even in the thorax, there are rare individuals whose organs are reversed left to right from the norm.


We strongly recommend that a protocol be established with the imaging center to place a marker consistently on one side of the body to eliminate any possibility of confusion between left and right.


If patient orientation is critical in any way, you must have some means of verifying the correctness of the orientation shown on the image display.


As a corrective measure you may flip the stacked image set across any of the three orthogonal planes in a x,y,z coordinate system.However, be extremely cautious if you do so, as it is unlikely that the display would be wrong.An error would have to been made during the imaging process in specifying the patient orientation to the imaging system, such as a patient placed feet first instead of head first but specified as being head first.Or an error occurred in writing out the Dicom files.


Do not flip an image set unless you know precisely where and what caused the orientation labels to be wrong and that you know precisely how to flip the image set to correct the error.It would not do to create a mirror image of the patient, or create an error when there was none, or create a different error.


Be sure the labels are correct before you do any further processing.


As an aid, routine rlDicomDump is provided to dump the contents of a Dicom image file, with decoding of some pertinent fields.Type rlDicomDump followed by the file name to read.rlDicomDump may be found in the subdirectory tools.dir.


You may edit an image set at any time.However, we recommend that you complete the image set before any further processing is done.†† Otherwise confusion may result, for example, if an outline is made on an image but then the image is deleted from the image set. Besides flipping an image set as described above, you can delete an image from an image set if there is some reason to do so.Normally you would want the most complete model for the patient, but an image file may have been corrupted or mistakenly included in the image set.


Edit Stacked Image Set Toolbar shown with the Flip Image Set Popup


You may also add images to the image set.But, as noted above, these images must be stackable, taken of the patient during the same imaging process without patient motion.This function is provided as a means to correct a situation where all the images were accidentally not included in the original selection of the image set.

Selection of a stacked image set

The program allows for displaying more than one image set.Consequently, through out the program there are instances where an image set must be specified.For example, in reformatting an image the program has to know which image set the image is to be reformatted from.Be careful of situations where an image set is selected and then a new tool bar is pushed.You will operating on the selected image set.

Stacked Image Set Options

Controls are found under the Stacked Image Sets pulldown on the main menu and are described throughout this manual.


Under Options is the Options toolbar.

Stacked Image Set Options Toolbar

The options selected here are covered under the appropriate chapters in this manual for the particular topic that is selected for each choice presented in the toolbar.


Distance Tool

The distance tool under the Stacked Image Sets pull down will compute the distance between any two selected points.You click the left mouse on the first point and then on the second.The two points do not have to be on the same image but do have to be two points in the same stacked image set or between two fused image sets.




In addition to computing the geometric distance between the two points, the water equivalent path length is also computed. The first instance is the water equivalent computed path length based upon the CT number to density conversion curve.The path is computed in the stacked image set that the first point was in.The second text box below that is the water equivalent path also taking into account the density of any ROI volume that the path might have gone through that had been assigned a density.The ratio between the geometric distance and the water equivalent distance is then also shown in the text box with the water equivalent path.†† In this example shown here, the path did not transverse any ROI volumes that had an assigned density.


The distance tool under the Images pull down on the Main Toolbar, simply computes the geometric distance between two points on the same image.