NAME

       mincmorph - MNI medical image format tools

SYNOPSIS

       mincmorph [options] <in.mnc> <out.mnc>

DESCRIPTION

       Command-specific options: General options:

       -verbose:
              be verbose

       -clobber:
              clobber existing files

       Outfile Options

       -filetype:
              Use data type of the input file.

       -byte: Write out byte data.

       -short:
              Write out short integer data. (Default)

       -int:  Write out long integer data.

       -float:
              Write out single-precision data.

       -double:
              Write out double-precision data.

       -signed:
              Write signed integer data.

       -unsigned:
              Write unsigned integer data.

       Kernel Options

       -2D04: Use a 2D 4-connectivity kernel.

       -2D08: Use a 2D 8-connectivity kernel.

       -3D06: Use a 3D 6-connectivity kernel. (default)

       -3D26: Use a 3D 26-connectivity kernel.

       -kernel:
              <kernel.kern> read in a custom kernel file

       Morphology Options

       -floor:
              lowwer value for binarising or clamping

              Default value: -1.79769e+308

       -ceil: upper value for binarising or clamping (incl)

              Default value: 1.79769e+308

       -range:
              range for binarising or clamping (incl)

              Default value: -1.79769e+308 1.79769e+308

       -foreground:
              foreground value

              Default value: 1

       -background:
              background value

              Default value: 0

   Single morphological operations:
       -binarise:
              binarise volume using the input range

       -clamp:
              clamp volume using the input range

       -pad:  pad volume with respect to the current kernel (-background to specify value)

       -erosion:
              do a single erosion

       -dilation:
              do a single dilation

       -median_dilation:
              do a single median dilation (note: this is not a median filter!)

       -open: open:            dilation(erosion(X))

       -close:
              close:           erosion(dilation(X))

       -lowpass:
              lowpass filter:  close(open(X))

       -highpass:
              highpass filter: X - lowpass(X)

       -convolve:
              convolve file with kernel

       -distance:
              distance transform

       -group:
              label groups in ascending order

   Successive morphological operations:
       -successive:
              Successive operations (Maximum: 100)

              B[floor:ceil:fg:bg]  -  binarise  in  the  range,  using  foreground and background
              K[floor:ceil:bg] - clamp between the specified range.  Set  other  voxels  to  'bg'
              (default:  0)  P[bg]  -  pad  volume  with respect to the current kernel using 'bg'
              (default: 0) E - erosion D - dilation M - median dilation O - open C -  close  L  -
              lowpass  filter  H  -  highpass  filter X - convolve F - distance transform (binary
              input only - not checked) G - Label the groups in the  volume  in  ascending  order
              R[TYPE|file.kern]  -  (2D04|2D08|3D06|3D26)  or read in a kernel file W[file.mnc] -
              write out current results I[cmp.mnc] - local xcorr between current file and cmp.mnc
              Default:  "B"

   Generic options for all commands:
       -help: Print summary of command-line options and abort

       -version:
              Print version number of program and exit

              mincmorph -help