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The MINC (Medical Imaging NetCDF) 1.0 file format was designed as a file format for medical imaging data building upon the NetCDF (Network Common Data Format) standard [4]. MINC was designed specifically to provide the medical-imaging research community with a modality-neutral way to store medical images along with a rich and flexible set of supporting data.

While the the MINC 1.0 file format has been found to be both powerful and useful over the last decade, a number of limitations have been identified by its users. In particular, three of these limitations have driven the design of MINC 2.0, the next step in MINC's evolution.

The first of these limitations is the lack of support for files larger than 2 gigabytes in present versions of NetCDF. This is proving to be an important limitation for newer, high-resolution functional and anatomical imaging applications.

The second is the need to allow a single medical image file to contain data at several levels of resolution. This is useful for network image viewing applications, for example. HDF5's hierarchical organization and larger supported file sizes help to enable this feature.

The third motivation is the need for internal, transparent data compression. The MINC 1.0 library allows files to be compressed using an external program such as gzip, bzip2, etc. Unfortunately, external compression requires that the entire file be decompressed even if only a small portion of the image is to be examined. In addition, compression must be applied as an explicit post-processing step after a file is created. The impact of these problems increases with file size.

To address these and other issues, the MINC development team has chosen to implement support for HDF5 (Hierarchical Data Format 5) [2]. Compared to NetCDF, HDF5 provides enhanced support for complex file structure, hierarchical name spaces, structured and enumerated data types, and internal compression.

This document is intended to describe the specifics of the MINC 2.0 file format by defining the specific variables, attributes, organization, and conventions used by these files, as implemented as a specialization of the generic HDF5 format.

Much of the information in this document is excerpted from the MINC Programmer's Reference Manual by Peter Neelin [3].

NOTE: Throughout this document, literal MINC variable names, attribute names, and predefined values are set in a fixed-width font.

next up previous contents
Next: Coordinates and Dimensions Up: The MINC 2.0 File Previous: Contents   Contents
Robert VINCENT 2005-05-10