Data Management - Processing Stream

Now we outline the procedure we have developed for processing and archiving images. All of the tools in this pipeline were developed in the lab with gui-based interfaces for ease of usage.

Dicom images are received on a windows machine running E-Film (a commercial product) that does a good job of logging incoming files by subject. This machine’s data drive is mounted onto our Linux processing machine. Here the incoming dicom files are read and converted by a dicom converter we developed in conjunction with Frank Ezekiel at UCSF. It also uses the dicom handling library of David Clunie. In our utility the dicom slice files are sorted by subject and converted into 3D image files. Various processing options are available including selecting the data format of the output files (analyze, interfile or quanta).

Next the 3D image files are given standardized names and depending on which study they belong to, they are moved to the correct data archives. We currently have four active studies: Framingham, Chap, Nomass and Whicap. In each study, images are archived in the same way. An individual subject is a subdirectory under the study directory. Below that are date directories each containing one or more image type (e.g. FLAIR, DSE, 3DT1) subdirectories. These contain the actual images along with any analysis files that are later created.

When someone does an analysis, a particular image file is “checked out” from one of these locations. This means that a copy is transferred to the analyst’s home directory and an annotation placed on the image in the archive so that anyone else wishing to check out this image is advised that it is already being worked on. After the analysis is completed, the file is “checked in” again along with the analysis files created and the annotation is removed.

The last step in this pipeline is to generate reports. We have developed a reporting utility which generates spreadsheet reports of subjects that have been analyzed. It can also query the archive by subject, date and image type to generate a list of what we currently possess in any of these categories.

Click on the thumbnail images above to see a close-up of the related tool.


Convert dicom files to 3D images.


Automatically archive images.



Query the image database, generate reports, check images in/out.

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