Read Medical Files

Posted by Brett Shoelson, May 18, 2012

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Brett's Pick this week is the Medical Data Reader, by Dirk-Jan Kroon.

When I first saw Sean de Wolski's recommendation of Dirk-Jan's suite of medical file readers for Pick-of-the-Week recognition, I kicked myself; I should have thought of that one on my own. (I'm sure I would have gotten around to it eventually, but sooner is better--thanks for the suggestion, Sean. Your swag is on the way!)

My background is in medical research, and in my role as an application engineer, I regularly have opportunities to work with a lot of our medically-oriented customers. The medical field is teeming with specialized data formats--many of which we don't have pre-packaged readers for--and I've steered users to this file numerous times since Dirk-Jan first shared it.

When I present MATLAB to prospective users, I often point out that we provide access to low-level functions like fopen and fread, and that the lack of a pre-built data reader should rarely (if ever) prevent anyone from analyzing their data in the MATLAB environment. If there's a spec available for the file, it's often not too difficult to create a custom file reader.

Easier still, though, is finding that someone else has coded the file reader for you! In this package--one of his many highly-rated File Exchange submissions--Dirk-Jan provides read capabilities for file of type: DICOM ( .dcm , .dicom ), V3D Philips Scanner ( .v3d ), GIPL Guys Image Processing Lab ( .gipl ), HDR/IMG Analyze ( .hdr ), ISI ( .isi ) , NifTi ( .nii ), RAW ( .raw , .* ), VMP BrainVoyager ( .vmp ), XIF HDllab/ATL ultrasound ( .xif ), VTK Visualization Toolkit ( .vtk ), Insight Meta-Image ( .mha, .mhd ), Micro CT ( .vff ), and PAR/REC Philips ( .par, .rec). (Note that support for reading, writing, and querying DICOM files is provided by the Image Processing Toolbox.)

Sean wrote of Dirk-Jan's file: "It’s reliably had a function for every file type I’ve had to work with. In addition it’s well written and user-friendly." Nice synopsis, Sean! And thanks for the great effort, Dirk-Jan!

Please continue to steer us to your favorite File Exchange submissions ...we'll continue to consider your recommendations for Pick-of-the-Week recognition!

As always, comments to this blog post are welcome. Or leave a comment for Dirk-Jan here.

Published with MATLAB® 7.14