mincpik(1) generate images from minc files


mincpik [options] <infile>.mnc [<image.type>]

mincpik generates image files from MINC volumes using the Imagemagick convert utility. Use -help or -man for more information and examples


mincpik generates image files from MINC volumes using the Imagemagick convert utility. For a complete list of output file types see the convert man pages.

EXAMPLES: To display a default view, axial (z) slicing, middle slice using display. (display is part of the Imagemagick package)

   mincpik infile.mnc PNG:- | display -

To generate a PNG file of the 15th coronal slice

   mincpik -slice 15 -coronal infile.mnc outfile.png

To generate a JPG file using the hotmetal lookup table with the image range 0 to 100

   mincpik -lookup '-hotmetal' -image_range 0 100 infile.mnc outfile.jpg

ImageMagick: http://www.wizards.dupont.com/cristy/ImageMagick.html
   NB: ImageMagick should be compiled without 16-bit quanta.

Currently if there is a time dimension in the file the image will only produced from the first time point

Problems or comments should be sent to: a.janke\@gmail.com


-v, --verbose
Be noisy when doing things
Print version number and exit
-?, --help
Dump some quick help output
Dump a man page
-c --clobber
overwrite the output file if it exists already
-f --fake
do a dry run, (echo cmds only). This is usually used in combination with -verbose to echo commands only
scaling factor for resulting image, by default images are output at twice their original resolution
autoscale the resulting image to have a fixed image width (in pixels)
bitdepth for resulting image 8 or 16 (MSB machines only!)
add a title to the resulting image, if just this option is specified the text used for the title is the name of the input image file.
use the input string for the title [default: input-filename]. This option must be used in conjunction with -title
font point size for the title
create an annotated bar to match the image (use height of the output image)

Image range and lookup table options

valid range of values for MINC file
range of image values to use for pixel intensity
automatically determine image range using a 5 and 95% PcT. (histogram)
arguments to pass to minclookup

Slicing options

-s --slice
slice number to get. (note this is in voxel co-ordinates)
-z --axial --transverse
get an axial/transverse (z) slice
-y --coronal
get a coronal (y) slice
-x --sagittal
get a sagital (x) slice

Triplanar options

-t --triplanar
create a triplanar view of the input file
pixel size for each image in a triplanar
offset the sagittal slice from the centre
offset the sagittal slice by a percentage from the centre
create a vertical triplanar view (Default)
create a horizontal triplanar view


Andrew Janke - [email protected]


Copyright 2012 by Andrew L Janke