CD Dialog

• Read Studies from CD or other locations
  • Demo
  • Purpose
  • Read Dicom
  • Save MIP
  • Delete
  • Setup

Read Studies from CD or other locations

Demo

There is a demo on youtube and a French demo on how to set up the program. A clean data demo has been added.

Purpose

The most common way to display studies is to drag the series folder to the Fiji status bar. Then there is a question if you want to create a stack which is answered "yes". The physicians asked for something easier. When a patient arrives with a CD from another hospital they don't want to be bothered drilling down through the directory structure to see series which they have no idea what each series might be. They just want to place the CD in the drive and get a list of studies where each study can have multiple series. Generally they just want to click on the study and bring up all the series. Furthermore, if this happens to be a PET-CT study, then the Pet-Ct Viewer should be brought up automatically.

Another good use of this program is if you are presenting studies at a conference. In that case you can make a directory with all your patients and studies and very quickly bring up the study you wish to show. This is the example shown below.

A third use could be to monitor a camera directory on the server, where the contents of the directory are frequently being updated. For all of these up to 12 "locations" can be defined and you can easily switch to the current location of interest.

Read Dicom

The Read from CD dialog, which appears under File->Import, appears as:

The first column is the patient name, where real names have been blackened out. This is followed by the study name, followed by the study date. The date is color coded, with "recent" studies being green and "old" studies being red. (The definition of "recent" is set in the Setup tab.)

There is a second color which can appear. Note in the green set there is a cyan entry and in the red set a magenta entry. The Brown fat, originally developed for brown fat but later extended to general ROI work, is indicated by the alternate colors. This allows the user to know, even before loading the studies, which Pet-Ct studies have been analyzed and which have not.

After the date is the series column. If the study has more than a single series, the icon will be displayed. If you Read a study with more than one series, all series will be read in. In order to read only a subset, first click in the series area (where appears), and the study will be "opened", displaying all series. You may then choose the desired subset and read only what is of interest.

Finally the patient ID is displayed (also blackened out).

You should notice that not all columns have the same width. This is because they have been resized. Indeed the whole dialog size may be changed, including the widths of all columns. Whenever the dialog is closed the current values are saved and used the next time the dialog is displayed.

The Clear button is used for a quick clear of all displayed studies. This is faster than X'ing out all individual studies.

On the bottom are the radio buttons for choosing your current location. Its name appears in the sunken box.

Save MIP

Calculating the MIP (Maximum Intensity Projection) can be a time consuming process, especially for newer studies with larger PET studies. While the MIP has to be calculated once, it can be saved so that subsequent reads will only need to read the previously calculated MIP, rather than recalculating it.

Before saving the MIP you may wish to Improve resolution to extend the 16 frame MIP to 32 frames, using Popup menu under MIP image. You right click on the MIP image to do this.

When a PET-CT study is read in, either a MIP data series is read in or not. If not the MIP is calculated and a Save MIP button will appear between the Read and Clear buttons . If you press this button the MIP will be saved to disk in the same parent directory as the study itself. Clearly if the study is read from a CD or some other read only device, no file can be saved.

The usual process when reading a study is to click on the entire study and read everything. The other option is to click on , which shows the individual series. Within the series you should see MIP data. Be sure to include this series. If not, the MIP will need to be recalculated.

Delete

A Delete tab has been added as a convenience. It can clear the entire location via the Delete All button, or it can clear individual series by highlighting them and then pressing the Delete button. Obviously a CD can't be deleted because the media is Read Only, but studies on disk can be erased.

Setup

Up to 12 locations can be defined by using the pull down Location number. It is given a name, in this example delback which appears in the sunken box on the Read tab. One then uses Browse to reach the directory with the data.

Red date, number of days is used to color code recent studies, as opposed to old studies. 30 days is the default for "recent". The studies are also color coded according to whether or not they have been processed. Processing means either adding annotations or Regions of Interest or both. The color key is

force use DicomDir may be useful in some cases where there is a log message that DicomDir will not be used. DicomDir varies from implementation to implementation and there are cases where forcing its use can allow displaying Pet Ct data which would otherwise not be displayed.

auto sort sorts the data first by name and then by reverse order date.

For whole body studies with an anterior and posterior view, it is clearly desirable to display the views as a montage rather than a stack. Make montage for series up to N slices lets you decide the limit where a montage is more desirable than a stack.

Tile properties allows you to automatically tile the series after they have been read. Many people prefer to make "postage stamps" out of the series. This allows them to see all the series and then to expand to full screen the particular one of interest. For example, if we chose 256 as a size then any image with resolution beyond 256 will be zoomed down to 256, but anything smaller will be left as is.

The Tile button performs an immediate rearrangement of the data into "postage stamps". The button is the same as the menu command using Plugins -> Nuclear Medicine -> Postage stamps. Postage stamps shows a similar button on the Fiji custom buttons.