Home
- Getting Started
- Configuring the Database
- Importing a Study
- Changing to a Different Study
- Deleting a Study
- Editing the Study
- Converting CHOP-fMRU Output to DICOM Files
To quickly get started with the application, simply download this zip file, which contains the current stable release version. Extract the folder to your file system and run the CHOP-fMRU_Assistant application.
The program maintains a directory containing the various studies that are imported. This must be configured the first time the program is used by a user on a particular workstation. First, create a directory in your file system that will be dedicated to this purpose and change this setting by choosing Settings from the menu.
Select Change Directory.
Select the directory that will contain the database and click OK.
Save the change.
The program will organize the studies within this directory by patient and by accession number. In the example database below, there are two patients, each of which contains a study.
The directory for each study contains an input_files directory, which contains the imported images. The input_files directory also contains an excluded directory. This is used when preparing the study for import into CHOP-fMRU and will contain portions of the study that do not need to be imported. The output_files directory will be used after functional analysis to prepare DICOM files for uploading to PACS.
Raw DICOM files must first be acquired from your PACS. While your imaging library may be able to perform this task for you, it is more convenient to configure a DICOM Network utility to download the files directly from PACS. We use the Santec DICOM Viewer, a free tool. Your PACS administrator will need to assist you with its configuration.
To import a study into the database, open the Study menu item and select Import Study.
Navigate to the directory containing the DICOM files and click OK.
The import process can be time consuming, as all DICOM headers are fixed when imported. Beware that the program will recursively add any DICOM study found in this directory. This means that if multiple studies are contained in one directory, even if they are contained in subdirectories, these will be imported into the database. Once finished, the last imported study will be selected. This can be seen in the status bar at the bottom of the main form.
##Changing to a Different Study To change to a different study within the database, open the Study menu item and select Change Study.
The studies are presented as a tree, with patient names as the roots and accession numbers as nodes. In this example, there is only one patient containing one study. Highlight the accession number of the desired study and click OK.
##Deleting a Study Simply change to the study of interest using the Change Study dialog as above. Once the study that you wish to remove is listed in the status bar at the bottom of the main form, open the Study menu item and select Delete Study. This will permanently delete the selected study from the database.
##Editing the Study The study can be edited to make importing into CHOP-fMRU feasible. Change to the study of interest using the Change Study dialog as above. Then, click the Study Editor button. The program will analyze all images for this study, which can be tracked with the progress bar at the bottom of the form. After processing is done, the Study Editor form will appear.
Different series in the study can be selected with the ComboBox in the top left. The series are listed based on their Series UIDs, which are normally hidden in a PACS environment. Selecting a series will show the series description underneath the ComboBox. The images for the study will be sorted by time and position and represented as a grid in the panel on the left. The selected image will be displayed on the right. The grid on the left can be navigated by clicking and using the arrow keys.
Series and images can be excluded, a useful tool to prepare the study for import into CHOP-fMRU. Excluded files are not deleted but are instead moved to the exclude directory within the input_files directory of the CHOP-fMRU_Assistant database. If you want to undo exclusion and reset the study to its original state, clicking Restore excluded portions will move all files from the exclude directory back to the parent input_files directory.
CHOP-fMRU requires that only dynamic images be imported. Other series can be excluded by clicking the Exclude series button. Do this until only dynamic images are left. The CHOP-fMRU creators also recommend high quality MIPs for inclusion, but we have not used these as the CHOP-fMRU will also generate MIPs from the individual dynamic images.
CHOP-fMRU also requires that the dynamic series be complete. That is, every slice position and every time within the square grid has an associated image. If there are missing images, the import will fail. This situation is represented in the grid of the Study Editor form with red cells.
This problem can be addressed by excluding any slice positions or times from the study that do not contain enough members. Select the desired image and click Exclude this time or Exclude this position, as desired.
CHOP-fMRU cannot handle an excessive number of images. This problem was encountered at our institution when the matrix size was set too large for a study. To address this, tools were also included to exclude images from before or after a certain time or slice position. The corresponding buttons are also available.
Once the fMRU analysis has been completed, it may be desirable to upload images of the results to PACS. While the paid version of IDL can create DICOM files, the free version cannot. The results can be exported as image files, however, and CHOP-fMRU_Assistant can then create DICOM files. These can be uploaded to PACS and will show up as an additional series in the original study.
First, change the study as above to the study of interest. This step is important, as the software will use the DICOM headers from the selected study to create new DICOM files. Choosing the wrong study in this step will cause the results to be associated with the wrong patient. Click the Images to DICOM button. Navigate to the directory containing the images exported from CHOP-fMRU and select all images that will be published to PACS, by either holding the Ctrl key and selecting multiple items or by pressing Ctrl+A to select all items. Click OK.
The DICOM files will be created and stored in the output_files directory for the study in the database. Upload these files to your PACS using a DICOM network utility. Again, we use the Santec DICOM Viewer for this purpose.