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-.\" ========================================================================
-.\"
-.IX Title "MINCPIK 1"
-.TH MINCPIK 1 "2012-03-12" "perl v5.10.1" "User Contributed Perl Documentation"
-.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
-.\" way too many mistakes in technical documents.
-.if n .ad l
-.nh
-.SH "NAME"
-\&\fBmincpik\fR \- generate images from minc files
-.SH "SYNOPSIS"
-.IX Header "SYNOPSIS"
-\&\fBmincpik\fR [options] <infile>.mnc [<image.type>]
-.PP
-mincpik generates image files from \s-1MINC\s0 volumes using the Imagemagick
-convert utility. Use \-help or \-man for more information and examples
-.SH "DESCRIPTION"
-.IX Header "DESCRIPTION"
-\&\fBmincpik\fR generates image files from \s-1MINC\s0 volumes using the Imagemagick
-\&\fBconvert\fR utility. For a complete list of output file types see the
-\&\fBconvert\fR man pages.
-.PP
-\&\s-1EXAMPLES:\s0
-To display a default view, axial (z) slicing, middle slice
-using display. (display is part of the Imagemagick package)
-.PP
-.Vb 1
-\&   mincpik infile.mnc PNG:\- | display \-
-.Ve
-.PP
-To generate a \s-1PNG\s0 file of the 15th coronal slice
-.PP
-.Vb 1
-\&   mincpik \-slice 15 \-coronal infile.mnc outfile.png
-.Ve
-.PP
-To generate a \s-1JPG\s0 file using the hotmetal lookup table 
-with the image range 0 to 100
-.PP
-.Vb 1
-\&   mincpik \-lookup \*(Aq\-hotmetal\*(Aq \-image_range 0 100 infile.mnc outfile.jpg
-.Ve
-.PP
-ImageMagick:  http://www.wizards.dupont.com/cristy/ImageMagick.html
-   \s-1NB:\s0 ImageMagick should be compiled without 16\-bit quanta.
-.PP
-Currently if there is a time dimension in the file the image will
-only produced from the first time point
-.PP
-Problems or comments should be sent to: a.janke\e@gmail.com
-.SH "OPTIONS"
-.IX Header "OPTIONS"
-.IP "\fB\-v\fR, \fB\-\-verbose\fR" 4
-.IX Item "-v, --verbose"
-Be noisy when doing things
-.IP "\fB\-\-version\fR" 4
-.IX Item "--version"
-Print version number and exit
-.IP "\fB\-?\fR, \fB\-\-help\fR" 4
-.IX Item "-?, --help"
-Dump some quick help output
-.IP "\fB\-\-man\fR" 4
-.IX Item "--man"
-Dump a man page
-.IP "\fB\-c\fR \fB\-\-clobber\fR" 4
-.IX Item "-c --clobber"
-overwrite the output file if it exists already
-.IP "\fB\-f\fR \fB\-\-fake\fR" 4
-.IX Item "-f --fake"
-do a dry run, (echo cmds only). This is usually used in combination with \-verbose to echo commands only
-.IP "\fB\-\-scale\fR" 4
-.IX Item "--scale"
-scaling factor for resulting image, by default images are output 
-at twice their original resolution
-.IP "\fB\-\-width\fR" 4
-.IX Item "--width"
-autoscale the resulting image to have a fixed image width (in pixels)
-.IP "\fB\-\-depth\fR" 4
-.IX Item "--depth"
-bitdepth for resulting image 8 or 16 (\s-1MSB\s0 machines only!)
-.IP "\fB\-\-title\fR" 4
-.IX Item "--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.
-.IP "\fB\-\-title_text\fR" 4
-.IX Item "--title_text"
-use the input string for the title [default: input\-filename]. This option must be used in conjunction with \-title
-.IP "\fB\-\-title_size\fR" 4
-.IX Item "--title_size"
-font point size for the title
-.IP "\fB\-\-anot_bar\fR" 4
-.IX Item "--anot_bar"
-create an annotated bar to match the image (use height of the output image)
-.PP
-\fIImage range and lookup table options\fR
-.IX Subsection "Image range and lookup table options"
-.IP "\fB\-\-range\fR" 4
-.IX Item "--range"
-valid range of values for \s-1MINC\s0 file
-.IP "\fB\-\-image_range\fR" 4
-.IX Item "--image_range"
-range of image values to use for pixel intensity
-.IP "\fB\-\-auto_range\fR" 4
-.IX Item "--auto_range"
-automatically determine image range using a 5 and 95% PcT. (histogram)
-.IP "\fB\-\-lookup\fR" 4
-.IX Item "--lookup"
-arguments to pass to minclookup
-.PP
-\fISlicing options\fR
-.IX Subsection "Slicing options"
-.IP "\fB\-s\fR \fB\-\-slice\fR" 4
-.IX Item "-s --slice"
-slice number to get. (note this is in voxel co-ordinates)
-.IP "\fB\-z\fR \fB\-\-axial\fR \fB\-\-transverse\fR" 4
-.IX Item "-z --axial --transverse"
-get an axial/transverse (z) slice
-.IP "\fB\-y\fR \fB\-\-coronal\fR" 4
-.IX Item "-y --coronal"
-get a coronal (y) slice
-.IP "\fB\-x\fR \fB\-\-sagittal\fR" 4
-.IX Item "-x --sagittal"
-get a sagital (x) slice
-.PP
-\fITriplanar options\fR
-.IX Subsection "Triplanar options"
-.IP "\fB\-t\fR \fB\-\-triplanar\fR" 4
-.IX Item "-t --triplanar"
-create a triplanar view of the input file
-.IP "\fB\-\-tilesize\fR" 4
-.IX Item "--tilesize"
-pixel size for each image in a triplanar
-.IP "\fB\-\-sagittal_offset\fR" 4
-.IX Item "--sagittal_offset"
-offset the sagittal slice from the centre
-.IP "\fB\-\-sagittal_offset_perc\fR" 4
-.IX Item "--sagittal_offset_perc"
-offset the sagittal slice by a percentage from the centre
-.IP "\fB\-\-vertical\fR" 4
-.IX Item "--vertical"
-create a vertical triplanar view (Default)
-.IP "\fB\-\-horizontal\fR" 4
-.IX Item "--horizontal"
-create a horizontal triplanar view
-.SH "SEE ALSO"
-.IX Header "SEE ALSO"
-\&\fIconvert\fR\|(1) \fImincextract\fR\|(1) \fIdisplay\fR\|(1)
-.SH "AUTHOR"
-.IX Header "AUTHOR"
-Andrew Janke \- a.janke@gmail.com
-.SH "COPYRIGHTS"
-.IX Header "COPYRIGHTS"
-Copyright 2012 by Andrew L Janke
-.SH "POD ERRORS"
-.IX Header "POD ERRORS"
-Hey! \fBThe above document had some coding errors, which are explained below:\fR
-.IP "Around line 580:" 4
-.IX Item "Around line 580:"
-You forgot a '=back' before '=head3'
-.IP "Around line 582:" 4
-.IX Item "Around line 582:"
-\&'=item' outside of any '=over'
-.IP "Around line 599:" 4
-.IX Item "Around line 599:"
-You forgot a '=back' before '=head3'
-.IP "Around line 601:" 4
-.IX Item "Around line 601:"
-\&'=item' outside of any '=over'
-.IP "Around line 618:" 4
-.IX Item "Around line 618:"
-You forgot a '=back' before '=head3'
-.IP "Around line 620:" 4
-.IX Item "Around line 620:"
-\&'=item' outside of any '=over'