The IBSR provides raw image files and manual segmentation result (label) files. Check the README file that comes with each data set for more information on that specific data. The image files are two formats, "raw" and Analyze. The Analyze file format can be read by many medical image processing programs such as the Analyze Program from the Mayo Clinic and 3D Slicer (the format is described in detail in ANALYZE75.pdf). A long list of image analysis tools is available at the Internet Analysis Tools Registry.
Files in the "raw" image format are easily opened by, for instance, a short C program, but they can also be opened by many commercially available programs (Matlab, Photoshop, etc.) if you provide extra information like the image size and data type. The raw format files are just a series of values where the data type is indicated by the suffix:
".bchar" - binary char (8-bit)All of these file formats (except ".img") have an associated ".hdr" text file that provides four numbers:
".buchar" - binary unsigned character (8-bit)
".bshort" - binary short integer (16-bit)
".bushort" - binary unsigned short integer (16-bit)
".bfloat" - binary floating point ".img" - binary unsigned short (16-bit) 256 rows by 256 columns
Where:rows columns slices endian
"rows" is the number of rows in the 3D data setThe ".img" format does not have a ".hdr" file because it is always a big endian file containing a single slice with 256 rows by 256 columns.
"columns" is the number of columns in the 3D data set
"slices" is the number of slices in the 3D data set, and
"endian" is the byte order with 0 for big endian and 1 for little endian
Note: The Analyze image format consist of ".hdr" header files and ".img" image data files. However, the raw image format files can also end in ".hdr" and ".img". These file types are not the same, so be careful when you download them. This unfortunate mixture of naming conventions is due to hysterical historical reasons.
Some downloads contains ".otl" outline files. These files are the result of semi-automated segmentation techniques performed by an expert using the program 'cardviews'. These files contain lists of points that define certain structures in each scan image. The files are text and have a general header followed by specific headers and outline data points for each structure. Each structure has a label, e.g. "LABEL Right Cerebral Exterior". The general header gives the size used for the outlines; in this case it is 512x512. This means the outlines were created using images that were doubled in size. The outline data points are given as one point per line: "x y" with the origin of the image located in the upper left corner and x as the horizontal axis.
Some downloads contain "info" files in the "gdf" file format. This is a format created at the CMA and more information can be seen here.
Any kind of publication that uses IBSR data must acknowledge the IBSR as the source. Please see the README file that came with the downloaded data for specific instructions. In general, the reference should go something like this: "The description_of_data was provided by the Center for Morphometric Analysis at Massachusetts General Hospital and is available at http://www.cma.mgh.harvard.edu/ibsr/."