NAME

mincpik - generate images from minc files

SYNOPSIS

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

DESCRIPTION

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

OPTIONS

-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

SEE ALSO

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

AUTHOR

Andrew Janke - a.janke@gmail.com

COPYRIGHTS

Copyright 2012 by Andrew L Janke