Ubuntu Manpage: medcon - MedCon conversion of medical image formats

NAME

       medcon - MedCon conversion of medical image formats

SYNOPSIS

       medcon [options] -f files ...

DESCRIPTION

  MedCon is a conversion utility intended for reconstructed nuclear medical images.

  The supported formats are:

                   Format                      Explanation                         Notation
                   ------                      -----------                         --------
                  Ascii       Raw ascii  image arrays without header           'ascii'
                  Binary      Raw binary image arrays without header           'bin'
                  Gif89a      annimated GIF with colormap                      'gif'
                  Acr/Nema    Papyrus, Siemens    (vers 2.0)                   'acr'
                  INW         RUG local format (vers 1.0)                      'inw'
                  ECAT        Siemens CTI ECAT 6                               'ecat6' or 'ecat'
                  ECAT        Siemens CTI ECAT 7                               'ecat7'
                  InterFile   version 3.3                                      'intf'
                  Analyze     with consideration to SPM software               'anlz'
                  DICOM       uses the VT-DICOM library                        'dicom'
                  PNG         Portable Network Graphics                        'png'
                  Concorde    Concorde/microPET                                'conc'
                  NIfTI       Neuroimaging Informatics Technology Initiative   'nifti'

FLAGS

       -f, --file, --files <files> ...
              Read  a list of files. In case of a dual file format, like InterFile and Analyze, just mention its
              header filename.

OPTIONS

-8, --indexed-color
This color mode forces 24-bit RGB color images being reduced to an 8-bit indexed colormap. For
color reduction in combination with dithering see the -dith option.

-24, --true-color
This color mode keeps a 24-bit image as is.

-alias, --alias-naming
Generate filenames based on patient and study information. The syntax of the resulting basename
is:

<patient_name>+<study_id>+<study_date>+<study_time>
and
<series>+<acquisition>+<instance>

with the latter three id's applied in case the originating format is DICOM or Acr/Nema. See also
-noprefix. Since Analyze does not have a patient_name, patient_id is used instead.

-anon, --anonymous
Make patient and study related entries anonymous (filled with 'X'). This option can not be used
with option -ident.

-b8, --unsigned-char

-b16, --signed-short

-b16.12
Force writing of Uint8 or Int16 pixels. The special option -b16.12 only uses 12 bits, as unsigned
however. With these options one can lose the quantified float values when the new format doesn't
support a global rescale factor or slope/intercept.

-big, --big-endian
Force writing of big endian files when supported by the format.

-byframe, --sort-by-frame
Set sort order in ECAT by frames, instead of the default anatomical sort (based on slice
location). Identical planes in each frame will be grouped together. You don't want this.

-c, --convert <format> ...
Convert with a list of formats to convert to. Use the notation without quotes as specified in the
above table. You can not use this option with -p.

-contrast, --enable-contrast
Apply (DICOM) window centre/width contrast remapping. Although this may improve the display of
images, any manufacturer independent pixel values (like HU, SUV) with quantitation options -qc or
-qs will be lost.

-cor, --coronal
Reslice the images of a volume into a coronal projection while preserving the real world
dimensions.

-crop=<X>:<Y>:<W>:<H>, --crop-images=<X>:<Y>:<W>:<H>
This option allows one to crop an equal frame from all images at <X>:<Y> where width and height
are <W>:<H>. The upper-left corner of an image is at 0:0.

-cs, --cine-sorting
Apply cine sorting, 1st image of each time frame, 2nd image of each time frame, 3rd image of each
time frame, ... (applicable on gated SPECT). Reapplying does NOT undo this sorting. For this you
need option -cu.

-cu, --cine-undo
Undo the cine sorting (as a result of the option -cs).

-cw=<centre>:<width>
Remap contrast using specified centre/width pair. No spaces are allowed within this option. See
also -contrast options.

-d, --debug
Show debug info. After reading a file, the program will display the contents of the internal
FILEINFO structure.

-db Only print main header of CTI ECAT files to standard output.

-dith, --dither-color
Use dithering to improve quality of color reduction (from RGB to 8-bit indexed).

-e, --extract [image ranges ...]
A routine to extract images interactively, unless you specify normal style image ranges directly
on the command-line separated by spaces. In normal style it is also possible to reorder the
sequence of images. You need to specify an output conversion format (see option -c). Note that the
extraction does NOT addapt the centre-centre slice separations. In other words, proper volume
measurements could be lost.

Selection Type? 1=normal 2=ecat

Normal Style
------------

- Any number must be one-based (0 = All reversed)
- Syntax of range : X...Y or X-Y
- Syntax of interval: X:S:Y (S = step)
- The list is sequence sensitive!

Give a list of images to extract?

Ecat Style
----------

- Any number must be one-based (0 = All)
- Syntax of range : X...Y or X-Y
- Syntax of interval: X:S:Y (S = step)

Give planes list?
Give frames list?
Give gates list?
Give beds list?

-ean, --echo-alias-name
A convenience function which quickly echoes the alias or human readable filename on screen,
without any delay of image processing. For the syntax of this alias filename, see option -alias.
The output could then be used in a script, for example to make interpretable links towards cryptic
numbered files resulting from a DICOM series.

-fb-none, --without-fallback

-fb-anlz, --fallback-analyze

-fb-conc, --fallback-concorde

-fb-dicom, --fallback-dicom

-fb-ecat, --fallback-ecat
Disable or specify a fallback read format in case autodetect failed.

-fh, --flip-horizontal

-fv, --flip-vertical
Flip images horizontal (-fh) along the X-axis, vertical (-fv) along the Y-axis respectively.
Parameters such as slice orientation are NOT changed. See also the -rs option.

-fmosaic=<W>x<H>x<N>, --force-mosaic=<W>x<H>x<N>
Enforce the mosaic file support for DICOM or Acr/Nema formats. The *stamps* will be split into
separate slices according to the values supplied on the command-line. See also extra options
-interl and -mfixv. The preset arguments are:

<W> = pixel width of image stamps (X)

<H> = pixel height of image stamps (Y)

<N> = total number of image stamps (Z)

medcon -f imagefile -fmosaic=64x64x30

-g, --make-gray
Remap coloured images to gray. This is necessary when you convert to formats which only support a
grayscale colormap!

-gap, --spacing-true-gap
The spacing between slices is the true gap/overlap between adjacent slices. In contrary to the
default behaviour where the spacing between slices is measured from the centre to centre of two
adjacent slices (including gap/overlap). Applied in DICOM & Acr/Nema.

-hackacr, --hack-acrtags
Enables you to hack a file that contains Acr/Nema tags hidden somewhere. Some proprietary image
formats do contain tags but are placed after some unknown headerinformation. This option will try
to find some readable tags in the first 2048 bytes after which it will give some possible hints to
get the images out of the file with the use of the interactive reading procedure (see option
`-i'). This experimental procedure can fail badly ...

-i, --interactive
Selects the interactive reading procedure. Normally the program automatically detects the format
or uses 'ecat' (or 'dicom') as default. With the interactive procedure it could be possible to
read an uncompressed, unsupported format by answering the following questions:

Number of images?
General header offset to binary data?
Image header offset to binary data?
Image header repeated before each image?
Swap the pixel bytes?
Same characteristics for all images?
Absolute offset in bytes? (overrides above, 0 = unused)
Image columns?
Image rows?
Pixel data type?
Redo input?

The GUI allows one to save such raw predef input (RPI) files, that can be used in a redirect statement:

medcon -f unsupported.img -c intf -i < predef.rpi

Doing so you can create small scripts that will read and convert your unsupported images at once.

-ident, --identify
An interactive routine to specify the patient and study related information. This option can not
be used with the option -anon. The questions asked are:

Give patient name?
Give patient id?
Select patient sex?
Give study description?
Give study id/name/p-number?
Give series description?

-implicit, --write-implicit
Another DICOM related option to enforce the implicit VR little transfer syntax as output, instead
of the default explicit transfer syntax.

-interl, --mosaic-interlaced
An extra option used in combination with forced mosaic (-fmosaic). The option indicates that the
slices in the original mosaic are in fact interlaced. See also options -fmosaic and -mfixv.

-little, --little-endian
Force writing of little endian files when supported by the format.

-lut, --load-lut <filename>
Load an external LUT color scheme.

-mh, --map-hotmetal
Selects the hotmetal colormap. This is only useful to GIF89a or PNG.

-mr, --map-rainbow
Selects the rainbow colormap. This is only useful to GIF89a or PNG.

-mc, --map-combined
Selects the combined colormap. This is only useful to GIF89a or PNG.

-mi, --map-inverted
Selects the invers colormap. This is only useful to GIF89a or PNG

-mfixv, --mosaic-fix-voxel
Another extra option used in combination with forced mosaic (-fmosaic). Choosing this options will
rescale the real world voxel dimensions by the mosaic factor. See also -fmosaic and -interl.

-mosaic, --enable-mosaic
Enable mosaic file support in DICOM or Acr/Nema format. The *stamps* will be splitted into
separate slices according to values found in the file. This autodetect routine will always fix the
voxel sizes. To support other type of mosaic files, see option -fmosaic.

-n, --negatives
Preserve negative values. When not selected, all negative values are put to zero. In combination
with quantitation (see -qs or -qc) the requested format must support pixels of type float, a
global rescale factor or the more generic slope/intercept concept in order to preserve the
(negative and positive) quantified values.

-nf, --norm-over-frames
Normalize with minimum/maximum values found over images in a frame group (in case the original
format has different frames). The default behaviour is normalization with minimum/maximum values
found over all images. This can be important when the requested format requires a rescaling to a
new pixeltype. The original pixel values then need to be rescaled to the new pixeltype boundaries
based on the minimum/maximum values.

-nometa, --write-without-meta
Write DICOM files without the part 10 meta header (group 0x0002).

-nopath, --ignore-path
Ignore absolute path mentioned in the "name of data file" key of an interfile header. Do make sure
then that the data file resides in the same directory as the header file.

-noprefix, --without-prefix
This option disables the numbered prefix in the output filename. In combination with the -alias
option, one could create human readable and alphabetical sorted files from DICOM or Acr/Name
multiple file volumes.

-o, --output-name <filename>
Changes output filename for all files to be created. It is allowed to specify a directory path as
well. However, a directory path disables unique filename prefixing.

-one, --single-file
Write header and image to same file; as allowed for InterFile.

-optgif, --options-gif
Define some GIF options when converting to the GIF format. Without this option a loop and
background color are defined by default. This interactive routine asks the following questions:

Select color map?
Insert a display loop?
Delay 1/100ths of a second?
Insert a transparent color?
Transparent color?
Background color?

-optspm, --options-spm
Define some SPM options (origins) when converting to the Analyze format. The quantification is not
set. See also '-spm' & '-ar'. The interactive routine asks the following questions:

Origin X?
Origin Y?
Origin Z?

-p, --print-values
Show some specified pixel values. This is an interactive routine. Calibration and negative pixels
are preserved automatically. You need to specify the -qs to preserve the quantification instead of
the calibration. You can not use this option with -c. See also -pa option for a non-interactive
routine.

- Any number must be one-based (0 = All)
- Syntax of range : X...Y or X-Y
- Syntax of interval: X:S:Y (S = step)

Selection Type? 1=normal 2=ecat

Normal Style
------------

Give a list of image numbers?
Give a list of pixels x,y ?

Ecat Style
----------

Give planes list?
Give frames list?
Give gates list?
Give beds list?
Give a list of pixels x,y ?

-pa, --print-all-values
Show all pixel values. This option is identical to -p, but doesn't require user input.

-pad, --pad-around

-padtl, --pad-top-left

-padbr, --pad-bottom-right
Increasing the slice matrix is done by padding an image with the lowest pixel value. The options
above enable different padding modes.

-preacq, --prefix-acquisition

-preser, --prefix-series
Respectivily use acquisition or series value in the numbered prefix of the new filename. This is
useful for alphabetical file ordering, where leading zeros in DICOM elements are missing. See also
-alias.

-q, --quantitation
Enable quantitation using all scale factors (for now alias for -qc option).

-qs, --quantification
A first scaling option to preserve the (ECAT) quantification (a) or to consider a first linear
scaling slope with intercept (b).

qpv = ppv * quant_scale [counts/second/pixel] (a)
qpv = ppv * slope + intercept (b)

qpv = quantified pixel value
ppv = plain pixel value

The "quant_scale" factor normalizes all images in the file; quite important for merging purposes. When
the corresponding format can not hold a rescale factor for each image, the quantified values are saved as
floats. Therefore, the highest pixel precision for correct quantitation is float, not double!

If the format does not support floats, the quantified pixel values get rescaled to an integer. Then only
formats that support a global scaling factor or slope/intercept pair will preserve those quantified
values.

Note that this option can not be used with -qc.

-qc, --calibration
A second quantitation option to preserve the (ECAT) quantification as well as the (ECAT)
calibration (a) or in general, using two rescale slopes with an intercept (b). These should
normally transform pixels into manufacturer independent values. So one can assume that after a
calibration, the new pixels will represent a real world unit (like concentration values (SUV),
hounsfield units (HU) and alike).

cpv = ppv * quant_scale * calibr_fctr [uCi/ml] (a)
cpv = ppv * slope1 * slope2 + intercept (b)

cpv = calibrated pixel value
ppv = plain pixel value
qpv = quantified pixel value = ppv * quant_scale

The "quant_scale" factor normalizes all images in the file; quite important for merging purposes. The
"calibr_fctr" rescales the qpv-values to a new unit. When the corresponding format can not hold a
compound factor for each image, the quantified values will be saved as floats. Therefore, the highest
pixel precision for correct quantitation is float and not double!

If the format does not support floats, the calibrated pixel values are rescaled to an integer type. Only
formats that support a global scaling factor or slope/intercept pair preserve those calibrated values.

Note that this option can not be used with -qs.

-r, --rename-file
Rename the file basename. This option is only useful in case of conversion.

-rs, --reverse-slices
Reverse all the slices along the Z-axis. Parameters such as slice orientation are NOT changed. See
also the -fh and -fv options.

-s, --silent
Suppress all message, warning and error dialogs.

-sag, --sagittal
Reslice the images of a volume into a sagittal projection while preserving the real world
dimensions.

-si=<slope>:<intercept>
Force remap of pixel values using specified slope/intercept (y = s*x + i). The quantitation option
-qc is enabled by default. No spaces are allowed within this option.

-skip1, --skip-preview-slice
Skip the first image in an InterFile. In other words, the first image in the array will simply be
ignored. Use this only when you are sure that the InterFile does contain an annoying/confusing
preview slice.

-split4d, -splitf, --split-frames

-split3d, -splits, --split-slices
Write out a study into separate files, one for each volume in a time frame (--split-frames) or
each image slice (--split-slices) individually. The names of the files created will have an extra
index number. See also -stack3d and -stack4d as opposite options.

-spm, --analyze-spm
Considering Analyze files for/from SPM. In this case the global scaling factor hidden in
imd.funused[1] will be used, as well as the hidden offset value in imd.funused[0].

In case of quantitation, the default output pixel type is float. This option allows one to write integers
combined with a global scale factor. To actually use this scaling factor, you must select a quantitation
option like -qs or -qc as well.

NOTES

When no conversion was specified, the program will display the header information of each image.

When conversion was specified, the program will automatically create new filenames in the current directory
with the following syntax:

mXXX-filename.ext

`XXX-' a number representing the XXX-th conversion
`ext' a corresponding extension of the new format

Binary raw -> .bin
Ascii raw -> .asc
Gif89a -> .gif
Acr/Nema -> .ima
INW -> .im
ECAT -> .img
Interfile -> .h33 + .i33
Analyze -> .hdr + .img
DICOM -> .dcm
PNG -> .png
CONC -> .hdr + .dat

Some special remarks related to reading from stdin or writing to stdout.

a) reading from stdin:

Enable this by using an "-" mark instead of the list of input files.

1. redirect: medcon -f - < inputfile

This is supported for all formats and shouldn't cause any particular problems. Interactive routines are
disabled because stdin is now in use by the image input.

2. pipes : cat inputfile | medcon -f - format

Actually, this way only one or two formats are supported since seek() calls are not possible during
pipes. The fact is that most of our formats are read using those seek() calls. In normal operation we
already need a quick sneak in the file to determine the format. Because this fseek() isn't allowed, you
must supply at least the input format too.

b) writing to stdout:

Enabled by using an extra "-" mark on the conversion list.

medcon -f inputfile -c - format

Only one inputfile is allowed. The converted output will be send to stdout.

In case of dual file formats such as Analyze or InterFile, the header information will be send to stderr.
The reference to the image file in the header of an InterFile will ofcourse be wrong (since the program
is not capable of knowing the resulting filename).

In case of RAW or ASCII output, the program will print the content of the internal FILEINFO struct to
stderr as well. Please note that the (t)csh shells do not allow to catch stderr or stdout separately. In
case of the bash shell, it is possible to say:

medcon -f inputfile -c - intf -b16.12 -qc 1>image 2>header

EXAMPLES

  1.  To display the image headers:
            medcon -f filename1 filename2

  2.  To convert the images:
            medcon -f filename1 filename2 -c gif acr intf

  3.  To read interactively
            medcon -i -f filename -c ecat

  4.  To extract alternate images:
            medcon -e 1:2:20 -f filename -c gif

  5.  To print out pixel values
            medcon -p -f filename

  6.  Convert to raw binary images, send to standard output:
            medcon -f filename -c - bin

FILES

  /usr/local/xmedcon/include/   Directory with header files.
  /usr/local/xmedcon/lib/       Directory with libraries.
  /usr/local/xmedcon/bin/       Directory with executables.
  /usr/local/xmedcon/man/       Directory with man-pages.
  /usr/local/xmedcon/etc/       Directory with rcfiles.

AUTHOR

  (X)MedCon project was originally written by Erik Nolf (eNlf) for the former  PET-Centre  at  Ghent  University
  (Belgium).

  e-mail:   enlf-at-users.sourceforge.net   www:   http://xmedcon.sourceforge.net

                                                                                                       MEDCON(1)