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Manual Reference Pages  -  MINCPIK (1)

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mincpik - 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

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\


-v, --verbose Be noisy when doing things
--version Print version number and exit
-?, --help Dump some quick help output
--man 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
--scale scaling factor for resulting image, by default images are output at twice their original resolution
--width autoscale the resulting image to have a fixed image width (in pixels)
--depth bitdepth for resulting image 8 or 16 (MSB machines only!)
--title 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.
--title_text use the input string for the title [default: input-filename]. This option must be used in conjunction with -title
--title_size font point size for the title
--anot_bar create an annotated bar to match the image (use height of the output image)
Image range and lookup table options
--range valid range of values for MINC file
--image_range range of image values to use for pixel intensity
--auto_range automatically determine image range using a 5 and 95% PcT. (histogram)
--lookup 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
--tilesize pixel size for each image in a triplanar
--sagittal_offset offset the sagittal slice from the centre
--sagittal_offset_perc offset the sagittal slice by a percentage from the centre
--vertical create a vertical triplanar view (Default)
--horizontal create a horizontal triplanar view


convert(1) mincextract(1) display(1)


Andrew Janke -


Copyright 2012 by Andrew L Janke
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