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.
36
39 -8, --indexed-color
40 This color mode forces 24-bit RGB color images being reduced to
41 an 8-bit indexed colormap. For color reduction in combination
42 with dithering see the -dith option.
43 -24, --true-color
46 This color mode keeps a 24-bit image as is.
47 -alias, --alias-naming
50 Generate filenames based on patient and study information. The
51 syntax of the resulting basename is:
52 <patient_name>+<study_id>+<study_date>+<study_time>
54 and
55 <series>+<acquisition>+<instance>
56 with the latter three id's applied in case the originating for‐
58 mat is DICOM or Acr/Nema. See also -noprefix. Since Analyze does
59 not have a patient_name, patient_id is used instead.
60 -anon, --anonymous
63 Make patient and study related entries anonymous (filled with
64 'X'). This option can not be used with option -ident.
65 -b8, --unsigned-char
68 -b16, --signed-short
70 -b16.12
72 Force writing of Uint8 or Int16 pixels. The special option
73 -b16.12 only uses 12 bits, as unsigned however. With these
74 options one can lose the quantified float values when the new
75 format doesn't support a global rescale factor or slope/inter‐
76 cept.
77 -big, --big-endian
80 Force writing of big endian files when supported by the format.
81 -byframe, --sort-by-frame
84 Set sort order in ECAT by frames, instead of the default anatom‐
85 ical sort (based on slice location). Identical planes in each
86 frame will be grouped together. You don't want this.
87 -c, --convert <format> ...
90 Convert with a list of formats to convert to. Use the notation
91 without quotes as specified in the above table. You can not use
92 this option with -p.
93 -contrast, --enable-contrast
96 Apply (DICOM) window centre/width contrast remapping. Although
97 this may improve the display of images, any manufacturer inde‐
98 pendent pixel values (like HU, SUV) with quantitation options
99 -qc or -qs will be lost.
100 -cor, --coronal
103 Reslice the images of a volume into a coronal projection while
104 preserving the real world dimensions.
105 -crop=<X>:<Y>:<W>:<H>, --crop-images=<X>:<Y>:<W>:<H>
108 This option allows to crop an equal frame from all images at
109 <X>:<Y> where width and height are <W>:<H>. The upper-left cor‐
110 ner of an image is at 0:0.
111 -cs, --cine-sorting
114 Apply cine sorting, 1st image of each time frame, 2nd image of
115 each time frame, 3rd image of each time frame, ... (applicable
116 on gated SPECT). Reapplying does NOT undo this sorting. For this
117 you need option -cu.
118 -cu, --cine-undo
121 Undo the cine sorting (as a result of the option -cs).
122 -cw=<centre>:<width>
125 Remap contrast using specified centre/width pair. No spaces are
126 allowed within this option. See also -contrast options.
127 -d, --debug
130 Show debug info. After reading a file, the program will display
131 the contents of the internal FILEINFO structure.
132 -db Only print main header of CTI ECAT files to standard output.
135 -dith, --dither-color
138 Use dithering to improve quality of color reduction (from RGB to
139 8-bit indexed).
140 -e, --extract [image ranges ...]
142 A routine to extract images interactively, unless you specify
143 normal style image ranges directly on the command-line separated
144 by spaces. In normal style it is also possible to reorder the
145 sequence of images. You need to specify an output conversion
146 format (see option -c). Note that the extraction does NOT addapt
147 the centre-centre slice separations. In other words, proper vol‐
148 ume measurements could be lost.
149 Selection Type? 1=normal 2=ecat
151 Normal Style
153 ------------
154 - Any number must be one-based (0 = All reversed)
156 - Syntax of range : X...Y or X-Y
157 - Syntax of interval: X:S:Y (S = step)
158 - The list is sequence sensitive!
159 Give a list of images to extract?
161 Ecat Style
163 ----------
164 - Any number must be one-based (0 = All)
166 - Syntax of range : X...Y or X-Y
167 - Syntax of interval: X:S:Y (S = step)
168 Give planes list?
170 Give frames list?
171 Give gates list?
172 Give beds list?
173 -ean, --echo-alias-name
176 A convenience function which quickly echoes the alias or human
177 readable filename on screen, without any delay of image process‐
178 ing. For the syntax of this alias filename, see option -alias.
179 The output could then be used in a script, for example to make
180 interpretable links towards cryptic numbered files resulting
181 from a DICOM series.
182 -fb-none, --without-fallback
185 -fb-anlz, --fallback-analyze
187 -fb-conc, --fallback-concorde
189 -fb-dicom, --fallback-dicom
191 -fb-ecat, --fallback-ecat
193 Disable or specify a fallback read format in case autodetect
194 failed.
195 -fh, --flip-horizontal
198 -fv, --flip-vertical
200 Flip images horizontal (-fh) along the X-axis, vertical (-fv)
201 along the Y-axis respectively. Parameters such as slice orienta‐
202 tion are NOT changed. See also the -rs option.
203 -fmosaic=<W>x<H>x<N>, --force-mosaic=<W>x<H>x<N>
206 Enforce the mosaic file support for DICOM or Acr/Nema formats.
207 The *stamps* will be splitted into separate slices according to
208 the values supplied on the command-line. See also extra options
209 -interl and -mfixv. The preset arguments are:
210 <W> = pixel width of image stamps (X)
212 <H> = pixel height of image stamps (Y)
214 <N> = total number of image stamps (Z)
216 medcon -f imagefile -fmosaic=64x64x30
218 -g, --make-gray
221 Remap coloured images to gray. This is necessary when you con‐
222 vert to formats which only support a grayscale colormap!
223 -gap, --spacing-true-gap
226 The spacing between slices is the true gap/overlap between adja‐
227 cent slices. In contrary to the default behaviour where the
228 spacing between slices is measured from the centre to centre of
229 two adjacent slices (including gap/overlap). Applied in DICOM &
230 Acr/Nema.
231 -hackacr, --hack-acrtags
234 Enables you to hack a file that contains Acr/Nema tags hidden
235 somewhere. Some proprietary image formats do contain tags but
236 are placed after some unknown headerinformation. This option
237 will try to find some readable tags in the first 2048 bytes
238 after which it will give some possible hints to get the images
239 out of the file with the use of the interactive reading proce‐
240 dure (see option `-i'). This experimental procedure can fail
241 badly ...
242 -i, --interactive
245 Selects the interactive reading procedure. Normally the program
246 automatically detects the format or uses 'ecat' (or 'dicom') as
247 default. With the interactive procedure it could be possible to
248 read an uncompressed, unsupported format by answering the fol‐
249 lowing questions:
250 Number of images?
252 General header offset to binary data?
253 Image header offset to binary data?
254 Image header repeated before each image?
255 Swap the pixel bytes?
256 Same characteristics for all images?
257 Absolute offset in bytes? (overrides above, 0 = unused)
258 Image columns?
259 Image rows?
260 Pixel data type?
261 Redo input?
262 The GUI allows to save such raw predef input (RPI) files, that can be
264 used in a redirect statement:
265 medcon -f unsupported.img -c intf -i < predef.rpi
267 Doing so you can create small scripts that will read and convert your
269 unsupported images at once.
270 -ident, --identify
273 An interactive routine to specify the patient and study related
274 information. This option can not be used with the option -anon.
275 The questions asked are:
276 Give patient name?
279 Give patient id?
280 Select patient sex?
281 Give study description?
282 Give study id/name/p-number?
283 Give series description?
284 -implicit, --write-implicit
287 Another DICOM related option to enforce the implicit VR little
288 transfer syntax as output, instead of the default explicit
289 transfer syntax.
290 -interl, --mosaic-interlaced
293 An extra option used in combination with forced mosaic (-fmo‐
294 saic). The option indicates that the slices in the original
295 mosaic are in fact interlaced. See also options -fmosaic and
296 -mfixv.
297 -little, --little-endian
300 Force writing of little endian files when supported by the for‐
301 mat.
302 -lut, --load-lut <filename>
305 Load an external LUT color scheme.
306 -mh, --map-hotmetal
309 Selects the hotmetal colormap. This is only usefull to GIF89a or
310 PNG.
311 -mr, --map-rainbow
314 Selects the rainbow colormap. This is only usefull to GIF89a or
315 PNG.
316 -mc, --map-combined
319 Selects the combined colormap. This is only usefull to GIF89a or
320 PNG.
321 -mi, --map-inverted
324 Selects the invers colormap. This is only usefull to GIF89a or
325 PNG
326 -mfixv, --mosaic-fix-voxel
329 Another extra option used in combination with forced mosaic
330 (-fmosaic). Choosing this options will rescale the real world
331 voxel dimensions by the mosaic factor. See also -fmosaic and
332 -interl.
333 -mosaic, --enable-mosaic
336 Enable mosaic file support in DICOM or Acr/Nema format. The
337 *stamps* will be splitted into separate slices according to val‐
338 ues found in the file. This autodetect routine will always fix
339 the voxel sizes. To support other type of mosaic files, see
340 option -fmosaic.
341 -n, --negatives
344 Preserve negative values. When not selected, all negative values
345 are put to zero. In combination with quantitation (see -qs or
346 -qc) the requested format must support pixels of type float, a
347 global rescale factor or the more generic slope/intercept con‐
348 cept in order to preserve the (negative and positive) quantified
349 values.
350 -nf, --norm-over-frames
353 Normalize with minimum/maximum values found over images in a
354 frame group (in case the original format has different frames).
355 The default behaviour is normalization with minimum/maximum val‐
356 ues found over all images. This can be important when the
357 requested format requires a rescaling to a new pixeltype. The
358 original pixel values then need to be rescaled to the new pixel‐
359 type boundaries based on the minimum/maximum values.
360 -nometa, --write-without-meta
363 Write DICOM files without the part 10 meta header (group
364 0x0002).
365 -nopath, --ignore-path
368 Ignore absolute path mentioned in the "name of data file" key of
369 an interfile header. Do make sure then that the data file
370 resides in the same directory as the header file.
371 -noprefix, --without-prefix
374 This option disables the numbered prefix in the output filename.
375 In combination with the -alias option, one could create human
376 readable and alphabetical sorted files from DICOM or Acr/Name
377 multiple file volumes.
378 -o, --output-name <filename>
381 Changes output filename for ALL files to be created. It is
382 allowed to specify a full directory path as well. However, a
383 full path disables unique filename prefixing.
384 -one, --single-file
387 Write header and image to same file; as allowed for InterFile.
388 -optgif, --options-gif
391 Define some GIF options when converting to the GIF format. With‐
392 out this option a loop and background color are defined by
393 default. This interactive routine asks the following questions:
394 Select color map?
396 Insert a display loop?
397 Delay 1/100ths of a second?
398 Insert a transparent color?
399 Transparent color?
400 Background color?
401 -optspm, --options-spm
403 Define some SPM options (origins) when converting to the Analyze
404 format. The quantification is not set. See also '-spm' & '-ar'.
405 The interactive routine asks the following questions:
406 Origin X?
408 Origin Y?
409 Origin Z?
410 -p, --print-values
412 Show some specified pixel values. This is an interactive rou‐
413 tine. Calibration and negative pixels are preserved automati‐
414 cally. You need to specify the -qs to preserve the quantifica‐
415 tion instead of the calibration. You can not use this option
416 with -c. See also -pa option for a non-interactive routine.
417 - Any number must be one-based (0 = All)
419 - Syntax of range : X...Y or X-Y
420 - Syntax of interval: X:S:Y (S = step)
421 Selection Type? 1=normal 2=ecat
423 Normal Style
425 ------------
426 Give a list of image numbers?
428 Give a list of pixels x,y ?
429 Ecat Style
431 ----------
432 Give planes list?
434 Give frames list?
435 Give gates list?
436 Give beds list?
437 Give a list of pixels x,y ?
438 -pa, --print-all-values
441 Show all pixel values. This option is identical to -p, but
442 doesn't require user input.
443 -pad, --pad-around
446 -padtl, --pad-top-left
448 -padbr, --pad-bottom-right
450 Increasing the slice matrix is done by padding an image with the
451 lowest pixel value. The options above enable different padding
452 modes.
453 -preacq, --prefix-acquisition
456 -preser, --prefix-series
458 Respectivily use acquisition or series value in the numbered
459 prefix of the new filename. This is useful for alphabetical file
460 ordering, where leading zeros in DICOM elements are missing. See
461 also -alias.
462 -q, --quantitation
465 Enable quantitation using all scale factors (for now alias for
466 -qc option).
467 -qs, --quantification
470 A first scaling option to preserve the (ECAT) quantification (a)
471 or to consider a first linear scaling slope with intercept (b).
472 qpv = ppv * quant_scale [counts/second/pixel] (a)
474 qpv = ppv * slope + intercept (b)
475 qpv = quantified pixel value
477 ppv = plain pixel value
478 The "quant_scale" factor normalizes all images in the file; quite
480 important for merging purposes. When the corresponding format can not
481 hold a rescale factor for each image, the quantified values are saved
482 as floats. Therefore, the highest pixel precision for correct quantita‐
483 tion is float, not double!
484 If the format does not support floats, the quantified pixel values get
486 rescaled to an integer. Then only formats that support a global scaling
487 factor or slope/intercept pair will preserve those quantified values.
488 Note that this option can not be used with -qc.
490 -qc, --calibration
493 A second quantitation option to preserve the (ECAT) quantifica‐
494 tion as well as the (ECAT) calibration (a) or in general, using
495 two rescale slopes with an intercept (b). These should normally
496 transform pixels into manufacturer independent values. So one
497 can assume that after a calibration, the new pixels will repre‐
498 sent a real world unit (like concentration values (SUV),
499 hounsfield units (HU) and alike).
500 cpv = ppv * quant_scale * calibr_fctr [uCi/ml] (a)
503 cpv = ppv * slope1 * slope2 + intercept (b)
504 cpv = calibrated pixel value
506 ppv = plain pixel value
507 qpv = quantified pixel value = ppv * quant_scale
508 The "quant_scale" factor normalizes all images in the file; quite
510 important for merging purposes. The "calibr_fctr" rescales the qpv-val‐
511 ues to a new unit. When the corresponding format can not hold a com‐
512 pound factor for each image, the quantified values will be saved as
513 floats. Therefore, the highest pixel precision for correct quantitation
514 is float and not double!
515 If the format does not support floats, the calibrated pixel values are
517 rescaled to an integer type. Only formats that support a global scaling
518 factor or slope/intercept pair preserve those calibrated values.
519 Note that this option can not be used with -qs.
522 -r, --rename-file
525 Rename the file basename. This option is only useful in case of
526 conversion.
527 -rs, --reverse-slices
530 Reverse all the slices along the Z-axis. Parameters such as
531 slice orientation are NOT changed. See also the -fh and -fv
532 options.
533 -s, --silent
536 Suppress all message, warning and error dialogs.
537 -sag, --sagittal
540 Reslice the images of a volume into a sagittal projection while
541 preserving the real world dimensions.
542 -si=<slope>:<intercept>
545 Force remap of pixel values using specified slope/intercept (y =
546 s*x + i). The quantitation option -qc is enabled by default. No
547 spaces are allowed within this option.
548 -skip1, --skip-preview-slice
551 Skip the first image in an InterFile. In other words, the first
552 image in the array will simply be ignored. Use this only when
553 you are sure that the InterFile does contain an annoying/confus‐
554 ing preview slice.
555 -split4d, -splitf, --split-frames
558 -split3d, -splits, --split-slices
560 Write out a study into separate files, one for each volume in a
561 time frame (--split-frames) or each image slice (--split-slices)
562 individually. The names of the files created will have an extra
563 index number. See also -stack3d and -stack4d as opposite
564 options.
565 -spm, --analyze-spm
568 Considering Analyze files for/from SPM. In this case the global
569 scaling factor hidden in imd.funused[1] will be used, as well as
570 the hidden offset value in imd.funused[0].
571 In case of quantitation, the default output pixel type is float. This
573 option allows to write integers combined with a global scale factor. To
574 actually use this scaling factor, you must select a quantitation option
575 like -qs or -qc as well.
576 See also -ar & -optspm.
578 -sqr, --make-square
581 Make all image matrices square, using the largest dimension.
582 Images are padded with the lowest pixel value. See also -pad
583 related options.
584 -sqr2, --make-square-two
587 Make all image matrices square, using the nearest power of two
588 (between 64, 128, 256, 512 and 1024). Images are padded with the
589 lowest pixel value. See also -pad related options.
590 -stack4d, -stackf, --stack-frames
593 -stack3d, -stacks, --stack-slices
595 Write separate studies into one file. The --stack-slices option
596 allows to write single image slice files into one 3D volume,
597 while the --stack-frames option allows volumes of different time
598 frames being written into one 4D file. The sequence of stacking
599 is based on the file sequence given at the argument line. See
600 also -split3d and -split4d as the opposite options.
601 -tra, --transverse
604 Reslice the images of a volume into a transverse projection
605 while preserving the real world dimensions.
606 -uin, --use-institution-name <namestring>
609 Change the program's default institution name which is applied
610 on studies without one. However, this does not override existing
611 values. For a namestring with spaces, group between double
612 quotes.
613 -v, --verbose
616 Verbose mode. Show some explaining messages during the reading
617 and writing of files.
618 -vifi, --edit-fileinfo
621 An interactive routine for editing voxel,array,slice and orient
622 related entries in the FILEINFO struct.
623 -w, --overwrite-files
626 Allow overwrite of existing files, without warning.
627
630 When no conversion was specified, the program will display the header infor‐
631 mation of each image.
632 When conversion was specified, the program will automatically create new
634 filenames in the current directory with the following syntax:
635 mXXX-filename.ext
637 `XXX-' a number representing the XXX-th conversion
639 `ext' a corresponding extension of the new format
640 Binary raw -> .bin
642 Ascii raw -> .asc
643 Gif89a -> .gif
644 Acr/Nema -> .ima
645 INW -> .im
646 ECAT -> .img
647 Interfile -> .h33 + .i33
648 Analyze -> .hdr + .img
649 DICOM -> .dcm
650 PNG -> .png
651 CONC -> .hdr + .dat
652 Some special remarks related to reading from stdin or writing to stdout.
654 a) reading from stdin:
656 Enable this by using an "-" mark instead of the list of input files.
658 1. redirect: medcon -f - < inputfile
660 This is supported for all formats and shouldn't cause any particular
662 problems. Interactive routines are disabled because stdin is now in use
663 by the image input.
664 2. pipes : cat inputfile | medcon -f - format
666 Actually, this way only one or two formats are supported since seek()
668 calls are not possible during pipes. The fact is that most of our for‐
669 mats are read using those seek() calls. In normal operation we already
670 need a quick sneak in the file to determine the format. Because this
671 fseek() isn't allowed, you must supply at least the input format too.
672 b) writing to stdout:
674 Enabled by using an extra "-" mark on the conversion list.
676 medcon -f inputfile -c - format
678 Only one inputfile is allowed. The converted output will be send to
680 stdout.
681 In case of dual file formats such as Analyze or InterFile, the header
683 information will be send to stderr. The reference to the image file in
684 the header of an InterFile will ofcourse be wrong (since the program is
685 not capable of knowing the resulting filename).
686 In case of RAW or ASCII output, the program will print the content of
688 the internal FILEINFO struct to stderr as well. Please note that the
689 (t)csh shells do not allow to catch stderr or stdout separately. In
690 case of the bash shell, it is possible to say:
691 medcon -f inputfile -c - intf -b16.12 -qc 1>image 2>header
693
695 1. To display the image headers:
696 medcon -f filename1 filename2
697 2. To convert the images:
699 medcon -f filename1 filename2 -c gif acr intf
700 3. To read interactively
702 medcon -i -f filename -c ecat
703 4. To extract alternate images:
705 medcon -e 1:2:20 -f filename -c gif
706 5. To print out pixel values
708 medcon -p -f filename
709 6. Convert to raw binary images, send to standard output:
711 medcon -f filename -c - bin
712
714 /usr/local/xmedcon/include/ Directory with header files.
715 /usr/local/xmedcon/lib/ Directory with libraries.
716 /usr/local/xmedcon/bin/ Directory with executables.
717 /usr/local/xmedcon/man/ Directory with man-pages.
718 /usr/local/xmedcon/etc/ Directory with rcfiles.
719
721 xmedcon(1), xmedcon-config(1)
722 m-acr(4), m-anlz(4), m-gif(4), m-inw(4), m-intf(4), m-ecat(4)
724 medcon(3)
726
728 (X)MedCon project was originally written by Erik Nolf (eNlf) for the former
729 PET-Centre at Ghent University (Belgium).
730 e-mail: enlf-at-users.sourceforge.net www: http://xmedcon.sourceforge.net
732 MEDCON(1)