MINC 2.0: A Flexible Format for Multi-Modal Images

It is often useful that an imaging data format can afford rich metadata, be flexible, scale to very large file sizes, support multi-modal data, and have strong inbuilt mechanisms for data provenance. Beginning in 1992, MINC was developed as a system for flexible, self-documenting representation of neuroscientific imaging data with arbitrary orientation and dimensionality. The MINC system incorporates three broad components: a file format specification, a programming library, and a growing set of tools. In the early 2000's the MINC developers created MINC 2.0, which added support for 64-bit file sizes, internal compression, and a number of other modern features. Because of its extensible design, it has been easy to incorporate details of provenance in the header metadata, including an explicit processing history, unique identifiers, and vendor-specific scanner settings. This makes MINC ideal for use in large scale imaging studies and databases. It also makes it easy to adapt to new scanning sequences and modalities.


DETAILS OF THE COORDINATE TRANSFORMATION
The direction cosines for spatial axis i is a normalized vector in three space such that: (1) Using δ i to represent the value of the step attribute for spatial axis i, and defining s i similarly for the 2 start attribute, the vector → v i between adjacent elements along that axis is: and the origin (0,0,0) in voxel coordinates is located at world coordinates (o x , o y , o z ) as given by: Finally, any homogeneous coordinate in voxel space (v x , v y , v z , 1) can be transformed to its equivalent in 5 world space using the equation: Each of these attributes are mandatory for any MINC standard variable, with the following exceptions:

10
• The signtype attribute is required only for variables of integral type.

11
• The parent children attributes are required only for variables of class group or 12 var-attribute.

13
These seven attributes are considered structural:

MINC 2.0 format
• admitting diagnosis -A string description of the admitting diagnosis.

61
• attending physician -A string giving the name of the physician administering the examination.

62
• department -A string identifying the department conducting the study.

63
• device model -A string specifying the model of the imaging device.

64
• institution -A string identifying the institution conducting the study.

65
• manufacturer -A string specifying the name of the imaging device manufacturer.

68
• operator -A string giving the name of the operator of the imaging device.

69
• procedure -A string description of the procedure employed.

70
• radiologist -A string giving the name of the radiologist interpreting the examination.

71
• referring physician -A string giving the name of the patient's primary physician.

75
• station id -A string identifying the specific imaging system that generated the image.

76
• study id -A string identifying the study.

82
• address -A string giving the patient's address.

83
• age -A number giving the patient's age in years.

84
• birthdate -A string specifying the patient's birthdate in the form YYYYMMDD.

85
• full name -A string specifying the full name of the patient.

86
• identification -A string specifying identification information for the patient.

87
• insurance id -A string giving the patient's insurance plan id.

88
• other ids -A string giving other identification information for the patient.

89
• other names -A string giving other names for the patient.

91
• sex -A string specifying the patient's sex: male , female or other .

92
• size -A number giving the patient's height or length in meters.

93
• weight -A number giving the patient's weight in kilograms.

109
• image type -A string giving the type of this image. See DICOM (0008,0008).

110
• imaged nucleus -A string specifying the nucleus that is resonant at the imaging frequency.

111
• imaging frequency -A number giving the precession frequency in Hz of the imaged nucleus.

112
• injection length -A number giving the time duration of the injection (in seconds).

113
• injection time -A string giving time (and date) of injection, in the same format as 114 study:start time.

115
• injection dose -Total dose of radionuclide or contrast agent injected (in units specified by 116 dose units).

117
• injection route -A string identifying administration route of injection.

118
• injection volume -A number giving the volume of injection in milliliters.

119
• inversion time -A number giving the time in seconds after the middle of the inverting RF pulse 120 to the middle of the 90 degree pulse to detect the amount of longitudinal magnetization.

123
• num averages -A number of times a given pulse sequence is repeated before any parameter is

134
• pixel bandwidth -A number specifying the inverse of the sampling period, in hertz per pixel.

136
• protocol -A string description of the protocol for image acquisition.

Frontiers 4
Vincent et al.

MINC 2.0 format
• radionuclide -A string specifying the isotope administered.

138
• radionuclide halflife -A number giving the half-life of the radionuclide in seconds.

139
• receive coil -A string giving the name of the receive coil used in an MR acquisition.

140
• repetition time -A number giving the time in seconds between pulse sequences.

141
• scanning sequence -A string description of type of data taken.

142
• series description -A string giving the text description of the series.

143
• series time -A string giving the start time of this series, in the same format as 144 study:start time.

145
• slice order -A string specifying the order of acquisition of individual slices, one of 146 descending, ascending, or interleaved.

147
• SAR -A number specifying the specific absorption rate in watts per kilogram.

148
• slice thickness -A number giving the slice thickness in millimeters.

149
• start time -A string giving the start date and time for the overall acquisition, in the same format 150 as study:start time.

151
• tracer -A string identifying tracer labeled with radionuclide that was injected.

152
• transmit coil -A string identifying the transmit coil used in an MR acquisition.

153
• window center -A number specifying a linear conversion for the pixels. Specifically note that in this image, the xspace dimension variable is a vector of length 176, containing