minc-toolkit documentation project

This is collection of documentation files for various minc tools. It was auto-converted from the legacy .man files to github-style markup format and then manually corrected.

Currently documented minc tools:

• minc file information
  • mincinfo - print out general information about a minc file
  • mincheader - print out complete header information for a minc file
  • mincstats - calculate simple statistics across voxels of a minc file
  • mincdiff - report differences between minc files
  • voxeltoworld - convert voxel coordinates to world coordinates
  • worldtovoxel - convert world coordinates to voxel coordinates
• file format conversion
  • rawtominc - converts a stream of binary image data to a minc format file
  • mincconvert - convert between MINC 1 to MINC 2 format
  • dcm2mnc - convert sets of DICOM files to one or more MINC format files
  • ecattominc - convert an ecat format file (version 6.x or 7.x) to a minc format file
  • minctoecat - convert a minc format file to an Ecat7 format file
  • minctoraw - copy data from a MINC file
  • mnc2nii- convert a MINC format file to a NIfTI-1 or Analyze format file
  • nii2mnc - convert a NIfTI-1 or Analyze 7.5 format file to a MINC format file
  • upet2mnc - convert a Concorde microPET format file to a MINC format file
  • vff2mnc - convert set of vff file(s) to one 3D MINC2.0 format file
• low-level file manipulation tools
  • minc_modify_header - modify the attributes in the header of a minc file
  • minccopy - copy minc image values from one minc file to another
  • mincdump - convert minc files to ASCII form (CDL)
  • mincedit - edit a MINC file header
  • mincexpand - expands a compressed minc file, if necessary
  • mincextract - dump a hyperslab of MINC file data
  • invert_raw_image - invert 2D image along either or both axes
  • mincgen - generate a MINC file from a CDL file
• mathematical operations on voxel level
  • minccalc - perform complex math operations on minc files
  • minccmp - compare one or more minc file using comparator operators
  • minclookup - perform lookup table conversions on minc files
  • mincmakescalar - convert vector minc files to scalar
  • mincmakevector - convert a list of scalar minc files into one vector file
  • mincmath - perform simple math operations on minc files
• higher level operations
  • mincconcat - concatenate minc files along a specific dimension
  • mincaverage - average minc files
  • mincblob - average minc files
  • mincblur - convolve an input volume with a Gaussian blurring kernel
  • autocrop - tool for extracting and manipulating bounds of a MINC file
  • mincbeast - BEaST brain extraction tool
• registration and resampling
  • mincresample - resamples a minc file along new spatial dimensions
  • mincreshape - cuts a hyperslab out of a minc file (with dimension re-ordering)
  • minctracc - estimates the spatial transformation required to register two volumes together
  • mritoself - intra-subject registration of two volumetric data sets
  • mritotal - performs multi-scale fitting of a normal human brain to a standard model
  • xfm2def - convert a MNI transform file to a deformation volume
  • xfmconcat - concatenate MNI transform files
  • xfminvert - invert an MNI transform file
  • xfmflip - flip an MNI transform file
  • transformtags - apply MNI transform to a tag file
• minc file viewing
  • mincview - view a MINC file (primitive viewer)
  • register - interactive volume display and point tagging program
• miscellanious
  • mincsample - generate samplings from minc files
  • mincwindow - limit voxel values to a given range