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
AUTHOR
Andrew Janke - [email protected]COPYRIGHTS
Copyright 2012 by Andrew L Janke