1MEDCON(1) General Commands Manual MEDCON(1)
2
6 medcon - MedCon conversion of medical image formats
7
9 medcon [options] -f files ...
10
12 MedCon is a conversion utility intended for reconstructed nuclear medical
13 images.
14 The supported formats are:
16 Format Explanation Notation
18 ------ ----------- --------
19 Ascii Raw ascii image arrays without header 'ascii'
20 Binary Raw binary image arrays without header 'bin'
21 Gif89a annimated GIF with colormap 'gif'
22 Acr/Nema Papyrus, Siemens (vers 2.0) 'acr'
23 INW RUG local format (vers 1.0) 'inw'
24 ECAT Siemens CTI ECAT 6 'ecat6' or 'ecat'
25 ECAT Siemens CTI ECAT 7 'ecat7'
26 InterFile version 3.3 'intf'
27 Analyze with consideration to SPM software 'anlz'
28 DICOM uses the VT-DICOM library 'dicom'
29 PNG Portable Network Graphics 'png'
30 Concorde Concorde/microPET 'conc'
31 NIfTI Neuroimaging Informatics Technology Initiative 'nifti'
32
34 -f, --file, --files <files> ...
35 Read a list of files. In case of a dual file format, like Inter‐
36 File and Analyze, just mention its header filename.
37
40 -8, --indexed-color
41 This color mode forces 24-bit RGB color images being reduced to
42 an 8-bit indexed colormap. For color reduction in combination
43 with dithering see the -dith option.
44 -24, --true-color
47 This color mode keeps a 24-bit image as is.
48 -alias, --alias-naming
51 Generate filenames based on patient and study information. The
52 syntax of the resulting basename is:
53 <patient_name>+<study_id>+<study_date>+<study_time>
55 and
56 <series>+<acquisition>+<instance>
57 with the latter three id's applied in case the originating for‐
59 mat is DICOM or Acr/Nema. See also -noprefix. Since Analyze does
60 not have a patient_name, patient_id is used instead.
61 -anon, --anonymous
64 Make patient and study related entries anonymous (filled with
65 'X'). This option can not be used with option -ident.
66 -b8, --unsigned-char
69 -b16, --signed-short
71 -b16.12
73 Force writing of Uint8 or Int16 pixels. The special option
74 -b16.12 only uses 12 bits, as unsigned however. With these
75 options one can lose the quantified float values when the new
76 format doesn't support a global rescale factor or slope/inter‐
77 cept.
78 -big, --big-endian
81 Force writing of big endian files when supported by the format.
82 -byframe, --sort-by-frame
85 Set sort order in ECAT by frames, instead of the default anatom‐
86 ical sort (based on slice location). Identical planes in each
87 frame will be grouped together. You don't want this.
88 -c, --convert <format> ...
91 Convert with a list of formats to convert to. Use the notation
92 without quotes as specified in the above table. You can not use
93 this option with -p.
94 -contrast, --enable-contrast
97 Apply (DICOM) window centre/width contrast remapping. Although
98 this may improve the display of images, any manufacturer inde‐
99 pendent pixel values (like HU, SUV) with quantitation options
100 -qc or -qs will be lost.
101 -cor, --coronal
104 Reslice the images of a volume into a coronal projection while
105 preserving the real world dimensions.
106 -crop=<X>:<Y>:<W>:<H>, --crop-images=<X>:<Y>:<W>:<H>
109 This option allows one to crop an equal frame from all images at
110 <X>:<Y> where width and height are <W>:<H>. The upper-left cor‐
111 ner of an image is at 0:0.
112 -cs, --cine-sorting
115 Apply cine sorting, 1st image of each time frame, 2nd image of
116 each time frame, 3rd image of each time frame, ... (applicable
117 on gated SPECT). Reapplying does NOT undo this sorting. For this
118 you need option -cu.
119 -cu, --cine-undo
122 Undo the cine sorting (as a result of the option -cs).
123 -cw=<centre>:<width>
126 Remap contrast using specified centre/width pair. No spaces are
127 allowed within this option. See also -contrast options.
128 -d, --debug
131 Show debug info. After reading a file, the program will display
132 the contents of the internal FILEINFO structure.
133 -db Only print main header of CTI ECAT files to standard output.
136 -dith, --dither-color
139 Use dithering to improve quality of color reduction (from RGB to
140 8-bit indexed).
141 -e, --extract [image ranges ...]
143 A routine to extract images interactively, unless you specify
144 normal style image ranges directly on the command-line separated
145 by spaces. In normal style it is also possible to reorder the
146 sequence of images. You need to specify an output conversion
147 format (see option -c). Note that the extraction does NOT addapt
148 the centre-centre slice separations. In other words, proper vol‐
149 ume measurements could be lost.
150 Selection Type? 1=normal 2=ecat
152 Normal Style
154 ------------
155 - Any number must be one-based (0 = All reversed)
157 - Syntax of range : X...Y or X-Y
158 - Syntax of interval: X:S:Y (S = step)
159 - The list is sequence sensitive!
160 Give a list of images to extract?
162 Ecat Style
164 ----------
165 - Any number must be one-based (0 = All)
167 - Syntax of range : X...Y or X-Y
168 - Syntax of interval: X:S:Y (S = step)
169 Give planes list?
171 Give frames list?
172 Give gates list?
173 Give beds list?
174 -ean, --echo-alias-name
177 A convenience function which quickly echoes the alias or human
178 readable filename on screen, without any delay of image process‐
179 ing. For the syntax of this alias filename, see option -alias.
180 The output could then be used in a script, for example to make
181 interpretable links towards cryptic numbered files resulting
182 from a DICOM series.
183 -fb-none, --without-fallback
186 -fb-anlz, --fallback-analyze
188 -fb-conc, --fallback-concorde
190 -fb-dicom, --fallback-dicom
192 -fb-ecat, --fallback-ecat
194 Disable or specify a fallback read format in case autodetect
195 failed.
196 -fh, --flip-horizontal
199 -fv, --flip-vertical
201 Flip images horizontal (-fh) along the X-axis, vertical (-fv)
202 along the Y-axis respectively. Parameters such as slice orienta‐
203 tion are NOT changed. See also the -rs option.
204 -fmosaic=<W>x<H>x<N>, --force-mosaic=<W>x<H>x<N>
207 Enforce the mosaic file support for DICOM or Acr/Nema formats.
208 The *stamps* will be split into separate slices according to the
209 values supplied on the command-line. See also extra options
210 -interl and -mfixv. The preset arguments are:
211 <W> = pixel width of image stamps (X)
213 <H> = pixel height of image stamps (Y)
215 <N> = total number of image stamps (Z)
217 medcon -f imagefile -fmosaic=64x64x30
219 -g, --make-gray
222 Remap coloured images to gray. This is necessary when you con‐
223 vert to formats which only support a grayscale colormap!
224 -gap, --spacing-true-gap
227 The spacing between slices is the true gap/overlap between adja‐
228 cent slices. In contrary to the default behaviour where the
229 spacing between slices is measured from the centre to centre of
230 two adjacent slices (including gap/overlap). Applied in DICOM &
231 Acr/Nema.
232 -hackacr, --hack-acrtags
235 Enables you to hack a file that contains Acr/Nema tags hidden
236 somewhere. Some proprietary image formats do contain tags but
237 are placed after some unknown headerinformation. This option
238 will try to find some readable tags in the first 2048 bytes
239 after which it will give some possible hints to get the images
240 out of the file with the use of the interactive reading proce‐
241 dure (see option `-i'). This experimental procedure can fail
242 badly ...
243 -i, --interactive
246 Selects the interactive reading procedure. Normally the program
247 automatically detects the format or uses 'ecat' (or 'dicom') as
248 default. With the interactive procedure it could be possible to
249 read an uncompressed, unsupported format by answering the fol‐
250 lowing questions:
251 Number of images?
253 General header offset to binary data?
254 Image header offset to binary data?
255 Image header repeated before each image?
256 Swap the pixel bytes?
257 Same characteristics for all images?
258 Absolute offset in bytes? (overrides above, 0 = unused)
259 Image columns?
260 Image rows?
261 Pixel data type?
262 Redo input?
263 The GUI allows one to save such raw predef input (RPI) files, that can
265 be used in a redirect statement:
266 medcon -f unsupported.img -c intf -i < predef.rpi
268 Doing so you can create small scripts that will read and convert your
270 unsupported images at once.
271 -ident, --identify
274 An interactive routine to specify the patient and study related
275 information. This option can not be used with the option -anon.
276 The questions asked are:
277 Give patient name?
280 Give patient id?
281 Select patient sex?
282 Give study description?
283 Give study id/name/p-number?
284 Give series description?
285 -implicit, --write-implicit
288 Another DICOM related option to enforce the implicit VR little
289 transfer syntax as output, instead of the default explicit
290 transfer syntax.
291 -interl, --mosaic-interlaced
294 An extra option used in combination with forced mosaic (-fmo‐
295 saic). The option indicates that the slices in the original
296 mosaic are in fact interlaced. See also options -fmosaic and
297 -mfixv.
298 -little, --little-endian
301 Force writing of little endian files when supported by the for‐
302 mat.
303 -lut, --load-lut <filename>
306 Load an external LUT color scheme.
307 -mh, --map-hotmetal
310 Selects the hotmetal colormap. This is only useful to GIF89a or
311 PNG.
312 -mr, --map-rainbow
315 Selects the rainbow colormap. This is only useful to GIF89a or
316 PNG.
317 -mc, --map-combined
320 Selects the combined colormap. This is only useful to GIF89a or
321 PNG.
322 -mi, --map-inverted
325 Selects the invers colormap. This is only useful to GIF89a or
326 PNG
327 -mfixv, --mosaic-fix-voxel
330 Another extra option used in combination with forced mosaic
331 (-fmosaic). Choosing this options will rescale the real world
332 voxel dimensions by the mosaic factor. See also -fmosaic and
333 -interl.
334 -mosaic, --enable-mosaic
337 Enable mosaic file support in DICOM or Acr/Nema format. The
338 *stamps* will be splitted into separate slices according to val‐
339 ues found in the file. This autodetect routine will always fix
340 the voxel sizes. To support other type of mosaic files, see
341 option -fmosaic.
342 -n, --negatives
345 Preserve negative values. When not selected, all negative values
346 are put to zero. In combination with quantitation (see -qs or
347 -qc) the requested format must support pixels of type float, a
348 global rescale factor or the more generic slope/intercept con‐
349 cept in order to preserve the (negative and positive) quantified
350 values.
351 -nf, --norm-over-frames
354 Normalize with minimum/maximum values found over images in a
355 frame group (in case the original format has different frames).
356 The default behaviour is normalization with minimum/maximum val‐
357 ues found over all images. This can be important when the
358 requested format requires a rescaling to a new pixeltype. The
359 original pixel values then need to be rescaled to the new pixel‐
360 type boundaries based on the minimum/maximum values.
361 -nometa, --write-without-meta
364 Write DICOM files without the part 10 meta header (group
365 0x0002).
366 -nopath, --ignore-path
369 Ignore absolute path mentioned in the "name of data file" key of
370 an interfile header. Do make sure then that the data file
371 resides in the same directory as the header file.
372 -noprefix, --without-prefix
375 This option disables the numbered prefix in the output filename.
376 In combination with the -alias option, one could create human
377 readable and alphabetical sorted files from DICOM or Acr/Name
378 multiple file volumes.
379 -o, --output-name <filename>
382 Changes output filename for all files to be created. It is
383 allowed to specify a directory path as well. However, a direc‐
384 tory path disables unique filename prefixing.
385 -one, --single-file
388 Write header and image to same file; as allowed for InterFile.
389 -optgif, --options-gif
392 Define some GIF options when converting to the GIF format. With‐
393 out this option a loop and background color are defined by
394 default. This interactive routine asks the following questions:
395 Select color map?
397 Insert a display loop?
398 Delay 1/100ths of a second?
399 Insert a transparent color?
400 Transparent color?
401 Background color?
402 -optspm, --options-spm
404 Define some SPM options (origins) when converting to the Analyze
405 format. The quantification is not set. See also '-spm' & '-ar'.
406 The interactive routine asks the following questions:
407 Origin X?
409 Origin Y?
410 Origin Z?
411 -p, --print-values
413 Show some specified pixel values. This is an interactive rou‐
414 tine. Calibration and negative pixels are preserved automati‐
415 cally. You need to specify the -qs to preserve the quantifica‐
416 tion instead of the calibration. You can not use this option
417 with -c. See also -pa option for a non-interactive routine.
418 - Any number must be one-based (0 = All)
420 - Syntax of range : X...Y or X-Y
421 - Syntax of interval: X:S:Y (S = step)
422 Selection Type? 1=normal 2=ecat
424 Normal Style
426 ------------
427 Give a list of image numbers?
429 Give a list of pixels x,y ?
430 Ecat Style
432 ----------
433 Give planes list?
435 Give frames list?
436 Give gates list?
437 Give beds list?
438 Give a list of pixels x,y ?
439 -pa, --print-all-values
442 Show all pixel values. This option is identical to -p, but
443 doesn't require user input.
444 -pad, --pad-around
447 -padtl, --pad-top-left
449 -padbr, --pad-bottom-right
451 Increasing the slice matrix is done by padding an image with the
452 lowest pixel value. The options above enable different padding
453 modes.
454 -preacq, --prefix-acquisition
457 -preser, --prefix-series
459 Respectivily use acquisition or series value in the numbered
460 prefix of the new filename. This is useful for alphabetical file
461 ordering, where leading zeros in DICOM elements are missing. See
462 also -alias.
463 -q, --quantitation
466 Enable quantitation using all scale factors (for now alias for
467 -qc option).
468 -qs, --quantification
471 A first scaling option to preserve the (ECAT) quantification (a)
472 or to consider a first linear scaling slope with intercept (b).
473 qpv = ppv * quant_scale [counts/second/pixel] (a)
475 qpv = ppv * slope + intercept (b)
476 qpv = quantified pixel value
478 ppv = plain pixel value
479 The "quant_scale" factor normalizes all images in the file; quite
481 important for merging purposes. When the corresponding format can not
482 hold a rescale factor for each image, the quantified values are saved
483 as floats. Therefore, the highest pixel precision for correct quantita‐
484 tion is float, not double!
485 If the format does not support floats, the quantified pixel values get
487 rescaled to an integer. Then only formats that support a global scaling
488 factor or slope/intercept pair will preserve those quantified values.
489 Note that this option can not be used with -qc.
491 -qc, --calibration
494 A second quantitation option to preserve the (ECAT) quantifica‐
495 tion as well as the (ECAT) calibration (a) or in general, using
496 two rescale slopes with an intercept (b). These should normally
497 transform pixels into manufacturer independent values. So one
498 can assume that after a calibration, the new pixels will repre‐
499 sent a real world unit (like concentration values (SUV),
500 hounsfield units (HU) and alike).
501 cpv = ppv * quant_scale * calibr_fctr [uCi/ml] (a)
504 cpv = ppv * slope1 * slope2 + intercept (b)
505 cpv = calibrated pixel value
507 ppv = plain pixel value
508 qpv = quantified pixel value = ppv * quant_scale
509 The "quant_scale" factor normalizes all images in the file; quite
511 important for merging purposes. The "calibr_fctr" rescales the qpv-val‐
512 ues to a new unit. When the corresponding format can not hold a com‐
513 pound factor for each image, the quantified values will be saved as
514 floats. Therefore, the highest pixel precision for correct quantitation
515 is float and not double!
516 If the format does not support floats, the calibrated pixel values are
518 rescaled to an integer type. Only formats that support a global scaling
519 factor or slope/intercept pair preserve those calibrated values.
520 Note that this option can not be used with -qs.
523 -r, --rename-file
526 Rename the file basename. This option is only useful in case of
527 conversion.
528 -rs, --reverse-slices
531 Reverse all the slices along the Z-axis. Parameters such as
532 slice orientation are NOT changed. See also the -fh and -fv
533 options.
534 -s, --silent
537 Suppress all message, warning and error dialogs.
538 -sag, --sagittal
541 Reslice the images of a volume into a sagittal projection while
542 preserving the real world dimensions.
543 -si=<slope>:<intercept>
546 Force remap of pixel values using specified slope/intercept (y =
547 s*x + i). The quantitation option -qc is enabled by default. No
548 spaces are allowed within this option.
549 -skip1, --skip-preview-slice
552 Skip the first image in an InterFile. In other words, the first
553 image in the array will simply be ignored. Use this only when
554 you are sure that the InterFile does contain an annoying/confus‐
555 ing preview slice.
556 -split4d, -splitf, --split-frames
559 -split3d, -splits, --split-slices
561 Write out a study into separate files, one for each volume in a
562 time frame (--split-frames) or each image slice (--split-slices)
563 individually. The names of the files created will have an extra
564 index number. See also -stack3d and -stack4d as opposite
565 options.
566 -spm, --analyze-spm
569 Considering Analyze files for/from SPM. In this case the global
570 scaling factor hidden in imd.funused[1] will be used, as well as
571 the hidden offset value in imd.funused[0].
572 In case of quantitation, the default output pixel type is float. This
574 option allows one to write integers combined with a global scale fac‐
575 tor. To actually use this scaling factor, you must select a quantita‐
576 tion option like -qs or -qc as well.
577 See also -ar & -optspm.
579 -sqr, --make-square
582 Make all image matrices square, using the largest dimension.
583 Images are padded with the lowest pixel value. See also -pad
584 related options.
585 -sqr2, --make-square-two
588 Make all image matrices square, using the nearest power of two
589 (between 64, 128, 256, 512 and 1024). Images are padded with the
590 lowest pixel value. See also -pad related options.
591 -stack4d, -stackf, --stack-frames
594 -stack3d, -stacks, --stack-slices
596 Write separate studies into one file. The --stack-slices option
597 allows one to write single image slice files into one 3D volume,
598 while the --stack-frames option allows volumes of different time
599 frames being written into one 4D file. The sequence of stacking
600 is based on the file sequence given at the argument line. See
601 also -split3d and -split4d as the opposite options.
602 -tra, --transverse
605 Reslice the images of a volume into a transverse projection
606 while preserving the real world dimensions.
607 -uin, --use-institution-name <namestring>
610 Change the program's default institution name which is applied
611 on studies without one. However, this does not override existing
612 values. For a namestring with spaces, group between double
613 quotes.
614 -v, --verbose
617 Verbose mode. Show some explaining messages during the reading
618 and writing of files.
619 -vifi, --edit-fileinfo
622 An interactive routine for editing voxel,array,slice and orient
623 related entries in the FILEINFO struct.
624 -w, --overwrite-files
627 Allow overwrite of existing files, without warning.
628
631 When no conversion was specified, the program will display the header infor‐
632 mation of each image.
633 When conversion was specified, the program will automatically create new
635 filenames in the current directory with the following syntax:
636 mXXX-filename.ext
638 `XXX-' a number representing the XXX-th conversion
640 `ext' a corresponding extension of the new format
641 Binary raw -> .bin
643 Ascii raw -> .asc
644 Gif89a -> .gif
645 Acr/Nema -> .ima
646 INW -> .im
647 ECAT -> .img
648 Interfile -> .h33 + .i33
649 Analyze -> .hdr + .img
650 DICOM -> .dcm
651 PNG -> .png
652 CONC -> .hdr + .dat
653 Some special remarks related to reading from stdin or writing to stdout.
655 a) reading from stdin:
657 Enable this by using an "-" mark instead of the list of input files.
659 1. redirect: medcon -f - < inputfile
661 This is supported for all formats and shouldn't cause any particular
663 problems. Interactive routines are disabled because stdin is now in use
664 by the image input.
665 2. pipes : cat inputfile | medcon -f - format
667 Actually, this way only one or two formats are supported since seek()
669 calls are not possible during pipes. The fact is that most of our for‐
670 mats are read using those seek() calls. In normal operation we already
671 need a quick sneak in the file to determine the format. Because this
672 fseek() isn't allowed, you must supply at least the input format too.
673 b) writing to stdout:
675 Enabled by using an extra "-" mark on the conversion list.
677 medcon -f inputfile -c - format
679 Only one inputfile is allowed. The converted output will be send to
681 stdout.
682 In case of dual file formats such as Analyze or InterFile, the header
684 information will be send to stderr. The reference to the image file in
685 the header of an InterFile will ofcourse be wrong (since the program is
686 not capable of knowing the resulting filename).
687 In case of RAW or ASCII output, the program will print the content of
689 the internal FILEINFO struct to stderr as well. Please note that the
690 (t)csh shells do not allow to catch stderr or stdout separately. In
691 case of the bash shell, it is possible to say:
692 medcon -f inputfile -c - intf -b16.12 -qc 1>image 2>header
694
696 1. To display the image headers:
697 medcon -f filename1 filename2
698 2. To convert the images:
700 medcon -f filename1 filename2 -c gif acr intf
701 3. To read interactively
703 medcon -i -f filename -c ecat
704 4. To extract alternate images:
706 medcon -e 1:2:20 -f filename -c gif
707 5. To print out pixel values
709 medcon -p -f filename
710 6. Convert to raw binary images, send to standard output:
712 medcon -f filename -c - bin
713
715 /usr/local/xmedcon/include/ Directory with header files.
716 /usr/local/xmedcon/lib/ Directory with libraries.
718 /usr/local/xmedcon/bin/ Directory with executables.
719 /usr/local/xmedcon/man/ Directory with man-pages.
720 /usr/local/xmedcon/etc/ Directory with rcfiles.
721
723 xmedcon(1), xmedcon-config(1)
724 m-acr(4), m-anlz(4), m-gif(4), m-inw(4), m-intf(4), m-ecat(4)
726 medcon(3)
728
730 (X)MedCon project was originally written by Erik Nolf (eNlf) for the former
731 PET-Centre at Ghent University (Belgium).
732 e-mail: enlf-at-users.sourceforge.net www: http://xmedcon.sourceforge.net
734 MEDCON(1)