{"id":3556,"date":"2012-05-18T08:41:12","date_gmt":"2012-05-18T13:41:12","guid":{"rendered":"https:\/\/blogs.mathworks.com\/pick\/?p=3556"},"modified":"2012-05-18T08:41:12","modified_gmt":"2012-05-18T13:41:12","slug":"read-medical-files","status":"publish","type":"post","link":"https:\/\/blogs.mathworks.com\/pick\/2012\/05\/18\/read-medical-files\/","title":{"rendered":"Read Medical Files"},"content":{"rendered":"
\r\n <\/introduction>\r\n

Brett<\/a>'s Pick this week is the Medical Data Reader,<\/a> by Dirk-Jan Kroon<\/a>.\r\n <\/p>\r\n

When I first saw Sean de Wolski's<\/a> recommendation of Dirk-Jan's suite of medical file readers for Pick-of-the-Week recognition, I kicked myself; I should have\r\n 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\r\n suggestion, Sean. Your swag is on the way!)\r\n <\/p>\r\n

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

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

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

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\r\n written and user-friendly.\" Nice synopsis, Sean! And thanks for the great effort, Dirk-Jan!\r\n <\/p>\r\n

Please continue to steer us to your favorite File Exchange submissions<\/a> ...we'll continue to consider your recommendations for Pick-of-the-Week recognition!\r\n <\/p>\r\n

As always, comments to this blog post<\/a> are welcome. Or leave a comment for Dirk-Jan here<\/a>.\r\n <\/p>