MINC - Medical Image NetCDF or MINC isn't netCDF

INTRODUCTION

The MINC file format is a highly flexible medical image file format built on the HDF5 generalized data format. The format is simple, self-describing, extensible, portable and N-dimensional, with programming interfaces for both low-level data access and high-level volume manipulation. On top of the libraries is a suite of generic image-file manipulation tools. The format, libraries and tools are designed for use in a medical-imaging research environment : they are simple and powerful and make no attempt to provide a pretty interface to users.

Minc tools are hosted in https://github.com/BIC-MNI/minc-tools

Additional tools are available from the Montreal Neurological Institute (MNI).

https://packages.bic.mni.mcgill.ca/tgz

SUPPORT FOR HDF5 "MINC 2.0" FORMAT FILES

This change requires that HDF5 must be installed before MINC can be built. You can obtain HDF5 from, current version is 1.8.11:

https://www.hdfgroup.org/

You should NOT need to become an HDF5 expert to use MINC 2.0. However, two tools included with HDF5 may prove useful, "h5dump" and "h5ls". h5dump is roughly equivalent to netCDF's ncdump utility. There is no exact netCDF tool analogous to h5ls. h5ls is useful for exploring and extracting bits of the HDF5 hierarchy.

3. TENTATIVE ".mincrc" AND ENVIRONMENT VARIABLE SUPPORT

This is implemented as a way to control certain behaviors of the library which are not readily available through other means. These variables may be defined either in your environment, or in the .mincrc file in your home directory. The value in the environment should override the one in .mincrc.

Here's what exists so far:

Force output files to MINC 2.0 format, regardless of the "-2" option.

# MINC_FORCE_V2 = {1, 0}

Desired ZLIB compression level. Zero implies no compression, a value

of 4 gives a good tradeoff of compression and performance.

# MINC_COMPRESS = {0..9}

Desired HDF5 chunking dimension. This controls the size of the

"hypercube" used by HDF5 to store the file. If set to zero, the

file will not be stored in a chunked format, unless compression is

enabled. The chunk size will automatically be reduced if it exceeds

any actual dimension of the volume. If chunking is enabled

automatically because of compression, the default chunk dimension is

32.

# MINC_CHUNKING = {0..N}

Log file - path to the desirned output file for messages. The default

is the standard error (stderr) stream. To redirect to standard output,

set this variable to "stdout" or "-". Otherwise the variable is taken

to be the path to the desired log file. If the path name begins with

a '+' character, the log file should be appended rather than recreated.

# MINC_LOGFILE = [+]|stdout|-

Logging level. Not really useful yet, but intended to allow setting

of 'verbosity' of messages. A value of zero would inhibit all but

fatal messages, a value of 4 would allow debugging messages.

# MINC_LOGLEVEL = 0-4

Maximum memory buffer, used in some minc programs

# MINC_MAX_FILE_BUFFER_KB =

Maximum allocated memory, used in some minc programs

# MINC_MAX_MEMORY_KB =

Memory cache for MINC2 files, per open file

# MINC_FILE_CACHE_MB =

Creation of HDF5 checksums for the volume, only works for MINC2

file format

default 0

# MINC_CHECKSUM = {1,0}

Prefer using MINC2 API inside Volume IO

default 0

# MINC_PREFER_V2_API = {1,0}

DOCUMENTATION

https://en.wikibooks.org/wiki/MINC