1M-INTF(4) Kernel Interfaces Manual M-INTF(4)
2
6 m-intf - InterFile 3.3 medical image format (MedCon)
7
9 The file consists of two parts, the administrative data in ASCII and the
10 binary image data. It is possible to put both in one file, but we prefer to
11 separate the data into two files. The administrative data in a file with
12 extension `.h33' and the binary data in a file with extension `.i33'.
13 This is a wonderful feature! Because of the separate header in ASCII you
15 could write your own header for any raw image data you may have. I regularly
16 use InterFile for turning unsupported formats into a supported format. Try
17 to extract the raw image data from the unknown format and add an appropriate
18 header with all information you know about.
19 The basic defines for the format:
21 ---------------------------------------------------------------------------
23 #define MDC_INTF_MAXKEYCHARS 256
25 char keystr[MDC_INTF_MAXKEYCHARS];
27 /* the data type */
29 #define MDC_INTF_STATIC 1
30 #define MDC_INTF_DYNAMIC 2
31 #define MDC_INTF_GATED 3
32 #define MDC_INTF_TOMOGRAPH 4
33 #define MDC_INTF_CURVE 5
34 #define MDC_INTF_ROI 6
35 /* the process status */
37 #define MDC_INTF_ACQUIRED 1
38 #define MDC_INTF_RECONSTRUCTED 2
39 /* gated spect nesting outer level */
41 #define MDC_INTF_NESTING_SPECT 1
42 #define MDC_INTF_NESTING_GATED 2
43 typedef struct MdcInterFile_t {
45 int data_type, process_status, pixel_type, gspect_nesting;
47 Uint32 width, height, images_per_dimension, time_slots;
48 Uint32 data_offset, data_blocks, imagesize, number_images;
49 Uint32 energy_windows, frame_groups, time_windows, detector_heads;
50 float pixel_xsize, pixel_ysize, slice_thickness, centre_centre_separation;
51 float study_duration, image_duration, image_pause, group_pause, ext_rot;
52 Int8 patient_rot, patient_orient, slice_orient;
53 double version;
54 } MDC_INTERFILE;
56 ---------------------------------------------------------------------------
58 What does the format support or not support:
60 ===========================================================================
62 Item Supported Not Supported
63 ===========================================================================
64 Color Map : grayscale -
65 File Endian : little or big -
66 Pixeltypes : 1-bit, all intergers -
67 float, double, ASCII
68 ===========================================================================
69 Scaling factors : quantify & calibrate factors/image are NOT supported,
70 unless you define your own key-value pairs
71 ---------------------------------------------------------------------------
72 Dimensions/Image : different dimensions for each image are supported
73 ---------------------------------------------------------------------------
74 Pixeltypes/Image : different pixeltypes for each image are supported, but
75 decoders are not required to be able to read.
76 MedCon does support different pixeltypes per image.
77 ===========================================================================
78 Underneath you will find a description of the format.
80 1. ADMINISTRATIVE DATA
82 ===================
83 a) The administrative data are only composed of key-value pairs and
85 exist in the form of ASCII text. The administrative data should be
86 terminated with a <Ctrl-Z).
87 b) All administrative data are to be supplied in the form of key-
89 value pairs in ASCII with delimiters. A `key' is the name of a
90 parameter taking a specific `value', an example being:
91 patient name := Elvis Presley <cr><lf>
93 c) The maximum permitted number of characters for a key or a value or
95 a comment is 255 characters.
96 d) Neither keys nor values are to be treated as case sensitive. The
98 characters <space> <tab> <underscore> <!> may all be treated as
99 white space and ignored.
100 e) All relevant keys should be included in the intermediate file. A
102 null value is permitted which will invoke the default where speci‐
103 fied. The required keys are preceded by an exclamation mark.
104 f) A hole line or key-value pairs may have comments appended to them
106 by preceding the comment with a semicolon <;>.
107 g) A required key ("name of data file") is included to point to the
109 image data file, even if the binary data is in the same file of
110 the administrative data.
111 h) The two alternate keys ("data starting block") or ("data offset in
113 bytes") are used to indicate the offset of the binary data in the
114 file as specified by the key ("name of data file"). The ("data
115 starting block") represents the offset in number of blocks or
116 2048 bytes. The use of the key ("data offset in bytes") permits
117 the offset to the binary data to be freely specified.
118 2. IMAGE DATA
120 ==========
121 a) The order of the pixel data shall increment by column from left to
123 right, and then by row, from top to bottom.
124 b) Image data shall be in either bit, signed or unsigned integer for‐
126 mat, IEEE floating point format (float or double) or ASCII. When
127 the data pixels are written in ASCII, the text line must not
128 exceed 255 characters.
129 c) The default value for the key ("imagedata byte order") is BIGEN‐
131 DIAN, but LITTLEENDIAN is allowed. The byte order must be
132 respected for integer and floating point numbers.
133 d) Bit data will stored in a single byte, representing 8 pixel values
135 and ordered such that the most significant bit corresponds to the
136 leftmost pixel.
137 3. LIST OF KEYS - VERSION 3.3 (Updated for Gated SPECT)
139 ==========================
140 !INTERFILE := <NULL>
142 ;to indicate that this is an Interfile file
143 !imaging modality := <ASCII> nucmed
145 ;only nucmed is defined for the purpose of this document
146 !originating system := <ASCII>
148 ;eg.GAMMA-11, MDS, ADAC, etc.
149 !version of keys := <Numeric> 3.3
151 ;future versions shall increment
152 date of keys := <DateFormat> 1996:09:26
154 ;date of version 3.3 in date format
155 conversion program := <ASCII>
157 ;name of program used
158 program author := <ASCII>
160 ;your chance of fame and fortune
161 program version := <Numeric>
163 ;to keep track of conversion programs
164 program date := <DateFormat>
166 ;date of program
167 !GENERAL DATA := <NULL>
169 ;required but can be treated as comment
170 original institution := <ASCII>
172 ;name of hospital etc.
173 contact person := <ASCII>
175 ;another chance of fame (and fortune?)
176 data description := <ASCII>
178 ;whatever you want
179 !data starting block := <Numeric> 0
181 ;the value is the offset in blocks of 2048 bytes in either the
182 ;administrative or the data file depending on the key value for
183 ;name of data file (see below)
184 | ;OR
185 !data offset in bytes:= <Numeric> 0
186 ;as above but the offset may be specified freely in bytes
187 !name of data file := <ASCII> <NULL>
189 ;<NULL> if no image data exists
190 ;key is a name of the file where the data are present, either when
191 ;in a separate binary data file, or when in a combined
192 ;administrative/binary data file
193 patient name := <ASCII>
195 ;last name, first name (recommended)
196 !patient ID := <ASCII>
198 ;as used in your hospital
199 patient dob := <DateFormat>
201 ;date of birth
202 patient sex := <ASCIIlist> Unknown M|F|Unknown
204 ;default is Unknown!
205 !study ID := <ASCII>
207 ;as local conditions dictate
208 exam type := <ASCII>
210 ;description of procedure as above
211 data compression := <ASCII> none
213 ;name of algorithm if present- e.g. JPEG, etc.
214 data encode := <ASCII> none
216 ;name of method of encoding if present- e.g. uuencode etc.
217 organ := <ASCII> none
219 ;ENLF: for mapping with DICOM tag (0018,0015) BodyPartExamined
220 isotope := <ASCII> | <ASCII>/<ASCII> none
222 ;ENLF: for mapping with DICOM radionuclide/radiopharmaceutical entries.
223 dose := <Numeric> 0
225 ;ENLF: for mapping with DICOM tag (0018,1074) RadionuclideTotalDose [MBq]
226 !GENERAL IMAGE DATA := <NULL>
228 ;again required but treated as comment
229 !type of data := <ASCIIlist> Other
231 Static|Dynamic|Gated|Tomographic|Curve|ROI|GSPECT|Other
232 ;important - this key is used for many conditionals
233 !total number of images := <Numeric>
235 ;how many images are there altogether in total in the associated
236 ;data file (for all windows etc.). This overrides any other way of
237 ;calculating the total number of images.
238 study date := <DateFormat>
240 ;date of the first image included in the data file
241 study time := <TimeFormat>
243 ;time for the start of first image specified
244 imagedata byte order := <ASCIIlist> BIGENDIAN
246 BIGENDIAN|LITTLEENDIAN
247 ;BIGENDIAN is the default if unspecified
248 process label := <ASCII> none
250 ;ENLF: for mapping with DICOM tag (0008,103E) SeriesDescription
251 quantification units := +1.696265e-05
253 ;ENLF: global scale factor for mediman dialect
254 NUD/rescale slope := +1.696265e-05
256 ;ENLF: global scale factor for NUD systems
257 NUD/rescale intercept := +0.000000e+00
259 ;ENLF: global scale intercept for NUD systems
260 number of energy windows := <Numeric> 1
262 ;defaulted to one if unspecified
263 for ( number of energy windows, energy window)
265 {
266 energy window[<energy window>] := <ASCII>
267 ;ASCII text- for example "Tc99m"
268 ;this starts as "energy window [1]" and then increments to
269 ;energy window[2]:= <ASCII>
270 ;and then on to
271 ;energy window[3]:= <ASCII>
272 ;etc. etc.
273 energy window lower level [<energy window>] := <Numeric>
275 ;value of lower energy level in keV for the corresponding window
276 ;starts off as "energy window lower level [1]"
277 ;and continues [2],[3] .. as above
278 energy window upper level [<energy window>] := <Numeric>
280 ;value of upper energy level in keV for the corresponding window
281 ;starts off as "energy window upper level [1]"
282 ;and continues [2],[3] .. as above
283 flood corrected := <ASCIIlist> Y Y|N
286 ;corrected if unspecified
287 decay corrected := <ASCIIlist> N Y|N
289 ;not corrected if unspecified
290 if( type of data = "Static"|"ROI")
292 {
293 !STATIC STUDY (General) := <NULL>
294 ;label to indicate that this is the static definition
295 number of images/energy window := <Numeric> 1
297 ;number of images in THIS energy window
298 for ( number of images/energy window )
300 {
301 !Static Study (each frame) := <NULL>
302 ;included at the beginning of the definition of
303 ;each new static frame
304 !image number := <Numeric>
306 ;starting from 1 [see above]
307 ;- must be specified!!
308 ;starts from 1 and increments though all
309 ;windows to its maximum value which equals the
310 ;total number of images in the file!!
311 !matrix size [1] :=< Numeric>
313 ;matrix size across (number of columns)- previously x
314 ;32, 64, 128 etc. but not necessarily powers of 2
315 !matrix size [2] := <Numeric>
317 ;matrix size down (number of rows)- previously y
318 ;32, 64, 128 etc. but not necessarily powers of 2
319 !number format := <ASCIIlist> unsigned integer
321 signed integer|unsigned integer
322 |long float|short float|bit|ASCII
323 ;as specified
324 !number of bytes per pixel := <Numeric>
326 ;e.g. 1|2|4.. [this key ignored for bit data]
327 scaling factor (mm/pixel) [1]:= <Numeric>
329 ;size of pixel across- previously x
330 scaling factor (mm/pixel) [2] := <Numeric>
332 ;size of pixel down- previously y
333 image duration (sec) := <Numeric>
335 ;eg. 120.0 i.e. normally a float, for each image
336 image start time := <TimeFormat>
338 ;time for each image
339 label := <ASCII>
341 ;eg Anterior
342 maximum pixel count := <Numeric>
344 ;for scaling purposes, for each image
345 total counts := <Numeric>
347 ;either an integer or a float, for each image
348 }
350 ;End of frame loop -Repeat for each subsequent frame
351 }
352 ;End of static definitions
353 if( type of data = "Dynamic")
356 {
357 !DYNAMIC STUDY (general) := <NULL>
358 ;label to indicate that this is a dynamic study
359 !number of frame groups := <Numeric> 1
361 ;defaults to 1
362 for( number of frame groups, frame group number)
364 {
365 !Dynamic Study (each frame group) := <NULL>
366 ;Repeated for each group of frames as
367 ;indication of the start of the
369 ;definition of the new group
370 !frame group number := <Numeric>
372 ;numbering starts from 1 (must be specified)
373 !matrix size [1] := <Numeric>
376 ;matrix size across (number of columns)
377 ;-previously matrix size x
378 ;32, 64, 128 etc. but not necessarily powers of 2
379 !matrix size [2] := <Numeric>
381 ;matrix size down (number of rows)- previously y
382 ;32, 64, 128 etc. but not necessarily powers of 2
383 !number format := <ASCIIlist> unsigned integer
385 signed integer|unsigned integer|
386 long float|short float|bit|ASCII
387 ;as specified
388 !number of bytes per pixel := <Numeric>
390 ;e.g. 1|2|4.. [this key ignored for bit data]
391 scaling factor (mm/pixel) [1]:= <Numeric>
393 ;size of pixel across- previously x
394 scaling factor (mm/pixel) [2] := <Numeric>
396 ;size of pixel down- previously y
397 !number of images this frame group := <Numeric>
399 ;for each frame group
400 ;(for each energy window)
401 !image duration (sec) := <Numeric>
403 ;eg 0.2, for each frame group
404 ;(for each energy window)
405 pause between images (sec) := <Numeric> 0.0
407 ;eg 0.0, default is 0.0
408 pause between frame groups (sec) := <Numeric> 0.0
410 ;eg 5.0 default 0.0, time between last
411 ;frame group (or start of study) and this frame group
412 !maximum pixel count in group := <Numeric>
414 ;eg 1234 (for scaling purposes)
415 ;maximum pixel for all frames in this
416 ;group and this window!!
417 }
419 ;Repeat for each subsequent frame group
420 }
421 ; End of dynamic definitions
423 if( type of data = "Gated")
426 {
427 !GATED STUDY (general) := <NULL>
428 ;again a flag to indicate a gated study
429 !matrix size [1] := <Numeric>
431 ;matrix size across (number of columns)- previously x
432 ;32, 64, 128 etc. but not necessarily powers of 2
433 !matrix size [2] := <Numeric>
435 ;matrix size down (number of rows)- previously y
436 ;32, 64, 128 etc. but not necessarily powers of 2
437 !number format := <ASCIIlist> unsigned integer
439 signed integer|unsigned integer|
440 long float|short float|bit|ASCII
441 ;as specified
442 !number of bytes per pixel := <Numeric>
444 ;e.g. 1|2|4|..> [this key ignored for bit data]
445 scaling factor (mm/pixel) [1]:= <Numeric>
447 ;size of pixel across- previously x
448 scaling factor (mm/pixel) [2] := <Numeric>
450 ;size of pixel down- previously y
451 study duration (elapsed) sec := <Numeric>
453 ;eg 300, total elapsed time for whole study
454 number of cardiac cycles (observed) := <Numeric>
456 ;total number of cycles if known, for this
457 ;energy window
458 number of time windows := <Numeric> 1
460 ;defaults to 1 if unspecified- number of different
461 ;sets of time intervals
462 for ( number of time windows, time window number)
464 {
465 !Gated Study (each time window) := <NULL>
466 !time window number := <Numeric>
468 ;starting from 1
469 !number of images in time window := <Numeric>
471 ;eg 24
472 !image duration (sec) := <Numeric>
474 ;eg 0.04 for each frame in THIS time window
475 framing method := <ASCIIlist> Forward
477 Forward|Backward|Mixed|Other
478 ;default is forward
479 time window lower limit (sec) := <Numeric>
481 ;float normally expected, for THIS time window
482 time window upper limit (sec) := <Numeric>
484 ;float normally expected
485 % R-R cycles acquired this window := <Numeric>
487 ;if known
488 number of cardiac cycles (acquired) := <Numeric>
490 ;eg 356 , if known
491 study duration (acquired) sec := <Numeric>
493 ;total acquisition time duration for
494 ;this window only (if it can be computed!!) as
495 ;opposed to total acquisition time (when different)
496 !maximum pixel count := <Numeric>
498 ;for scaling purposes for all images in this
499 ;time window (and energy window) only
500 R-R histogram := <ASCIIlist> N Y|N
502 ;flag to indicate that one exists!!
503 }
505 ;Repeat for each subsequent time window.
506 }
508 ;end of gated definitions
509 if( type of data = "Tomographic")
512 {
513 !SPECT STUDY (general) := <NULL>
515 ;flag to indicate tomographic data with no effect as such
516 number of detector heads := <Numeric> 1
518 ;default=1 if unspecified
519 for ( number of detector heads )
521 {
522 !number of images/energy window := <Numeric>
524 ;total number of images (for all heads) for
525 ;THIS energy window!!
526 !process status := Reconstructed Acquired|Reconstructed
528 ;used below in conditional- MUST be defined
529 !matrix size [1] := <Numeric>
531 ;matrix size across (number of columns)- previously x
532 ;32, 64, 128 etc. but not necessarily powers of 2
533 !matrix size [2] := <Numeric>
535 ;matrix size down (number of rows)- previously y
536 ;32, 64, 128 etc. but not necessarily powers of 2
537 !number format := <ASCIIlist> unsigned integer
539 signed integer|unsigned integer|
540 long float|short float|bit|ASCII
541 ;as specified
542 !number of bytes per pixel := <Numeric>
544 ;e.g. 1|2|4|.. [this key ignored for bit data]
545 scaling factor (mm/pixel) [1]:= <Numeric>
547 ;size of pixel across- previously x
548 scaling factor (mm/pixel) [2] := <Numeric>
550 ;size of pixel down- previously y
551 !number of projections := <Numeric>
553 ;for example- 64
554 ;note this is the actual number of images per
555 ;head per energy window if
556 ;the data are acquired, but NOT if the data are
557 ;reconstructed where the number of images is
558 ;specified separately as number of slices
559 !extent of rotation := <Numeric>
561 ;e.g 180, 360
562 !time per projection (sec) := <Numeric>
564 ;important for Acquired data
565 study duration (sec) := <Numeric>
567 ;eg 1280.0, for acquired data should be equal
568 ;to the product of number of projections and
569 ;time per projection, but could be different!!
570 !maximum pixel count := <Numeric>
572 ;for scaling- in THIS image series( this head
573 ;and this energy window)
574 patient orientation := <ASCIIlist> head_in
576 head_in|feet_in|other
577 patient rotation := <ASCIIlist> supine
579 prone|supine|other
580 if( process status = "acquired")
582 {
583 !SPECT STUDY (acquired data):= <NULL>
584 !direction of rotation := <ASCIIlist> CW CW|CCW
586 ;CW = clockwise, CCW = counter clockwise
587 start angle := <Numeric>
589 ;0 is top-dead-centre, in degrees
590 ;in orientation as specified above
591 first projection angle in data set := <Numeric>
593 ;in degrees expressed with respect to
594 ;anterior- angles in direction as
595 ;specified CW or CCW
596 acquisition mode := <ASCIIlist> stepped
598 stepped|continuous
599 Centre_of_rotation := <ASCIIlist> Corrected
601 Corrected|Single_value|For_every_angle
602 ;default is "Corrected"
603 ;"Corrected" corresponds to a null centre of rotation
604 ;correction, as previous required by Interfile, that
605 ;is, no centre of rotation information is to be
606 ;passed. The key "Single value" indicates the
607 ;conventional definition of the centre of rotation
608 ;offset to be a single value specified for all angles,
609 ;specified for each head given a multiple head
610 ;acquisition.
611 ;The key "For_every_angle" indicates that the centre
612 ;of rotation offset will be specified for each head
613 ;and every angle. This is not currently implemented in
614 ;this Interfile definition, but will be introduced in
615 ;V4.
616 ;The mathematical centre of rotation is assumed to be
617 ;in the exact middle of the projection for example at
618 ;x= 32.5 y=32.5 for a 64x64 image where the count
619 ;starts from 1. Note that the choice of coordinates
620 ;does not matter, the only constraint being the
621 ;assumption that all projections have a length which
622 ;is an even number of pixels. The centre of rotation
623 ;is specified as the offset from that position to the
624 ;perpendicular dropped from a point on the axis of
625 ;rotation onto the head.
626 if( Centre_of_rotation = "Single_value" )
628 {
629 !X_offset := <Numeric>
631 ;x offset for all angles in mm.
632 ;x_offset is the x offset between the perpendicular
633 ;dropped from the centre of rotation and the dead
634 ;centre of the matrix,
635 ;The positive direction for the offset is considered
636 ;to be that of the increasing projection index, e.g.
637 ;for a projection with pixels of size 6mm, which
638 ;should be centred at 32.5, an offset of +6mm
639 ;indicates that the centre of rotation is at 33.5
640 ;Note that since offset is specified in mm, the pixel
641 ;size must be known.
642 Y_offset := <Numeric>
645 ;y offset for all angles in mm
646 ;y_offset is the y offset between that perpendicular
647 ;dropped from the centre of rotation from that point
648 ;on the axis of rotation where the y_offset is
649 ;considered to be zero, and the centre of the camera's
650 ;field of view. Thus y_offset is the RELATIVE shift of
651 ;the y-axis with respect to some arbitrary position,
652 ;normally that from the centre of the filed of view of
653 ;the first at the top dead centre position. Thus for
654 ;a single head, this value would normally be expected
655 ;to be equal to zero.
656 Radius := <Numeric>
658 ;radial distance to centre of rotation in mm,
659 ;for this head.
660 }
663 ;end of centre of rotation specification
664 orbit := <ASCIIlist> Circular Circular|non-circular
666 preprocessed := <ASCII>
668 ;preprocessing method
669 }
671 ; end of process status acquired
672 if( process status = "reconstructed")
674 {
675 !SPECT STUDY (reconstructed data) := <NULL>
676 method of reconstruction := <ASCII>
678 !number of slices := <Numeric>
680 ;i.e. number of images in this set for this
681 ;head and this energy window
682 number of reference frame := <Numeric> 0
684 ;if unspecified the frame number
685 ;originally used for defining slice positions
686 ;0=default [Note- not a very useful key]
687 slice orientation := <ASCIIlist> Transverse
689 Transverse|Coronal|Sagittal|Other
690 ;default is transverse if unspecified
691 slice thickness (pixels) := <Numeric> 1
693 ;if unspecified 1=default
694 centre-centre slice separation (pixels):=<Numeric> 1
696 ;e.g.1,2,3,4... as distinct from slice thickness
697 ;the word centre can also be spelt as center
698 filter name := <ASCII>
700 ;e.g. Hann, Hamming, Butterworth
701 filter parameters := <ASCII>
703 ;Nyquist freq etc.
704 z-axis filter := <ASCII>
706 ;method [1,2,1] etc.
707 attenuation correction coefficient/cm := <Numeric> 0.0
709 ;default 0 means not done if unspecified
710 method of attenuation correction := <ASCII> none
712 scatter corrected := <ASCIIlist> N Y|N
714 method of scatter correction := <ASCII> none
716 oblique reconstruction := <ASCIIlist> N Y|N
718 oblique orientation := <ASCII>
720 ;free text [Note ACR-NEMA convention preferred]
721 }
722 ;end of reconstructed tomo
723 }
724 ;End of tomo
725 * if( type of data = "GSPECT")
728 {
729 * !GATED SPECT STUDY (general) := <NULL>
730 ;again a flag to indicate a gated SPECT study
731 ;MIXTURE OF GATED & TOMO
732 !matrix size [1] := <Numeric>
734 ;matrix size across (number of columns)- previously x
735 ;32, 64, 128 etc. but not necessarily powers of 2
736 !matrix size [2] := <Numeric>
738 ;matrix size down (number of rows)- previously y
739 ;32, 64, 128 etc. but not necessarily powers of 2
740 !number format := <ASCIIlist> unsigned integer
742 signed integer|unsigned integer|
743 long float|short float|bit|ASCII
744 ;as specified
745 !number of bytes per pixel := <Numeric>
747 ;e.g. 1|2|4|..> [this key ignored for bit data]
748 !Gated SPECT nesting outer level := SPECT|Gated Gated
750 ; key to indictae order of images, if SPECT is outer level
751 ; order is, for every angle give each gated image, if
752 ; gated is outer level, then order is, for every gated
753 ; time value, vie set of tomographic images
754 scaling factor (mm/pixel) [1]:= <Numeric>
756 ;size of pixel across- previously x
757 scaling factor (mm/pixel) [2] := <Numeric>
759 ;size of pixel down- previously y
760 study duration (elapsed) sec := <Numeric>
762 ;eg 300, total elapsed time for whole study
763 number of cardiac cycles (observed) := <Numeric>
765 ;total number of cycles if known, for this
766 ;energy window
767 number of time windows := <Numeric> 1
769 ;defaults to 1 if unspecified- number of different
770 ;sets of time intervals
771 for ( number of time windows, time window number)
773 {
774 !Gated Study (each time window) := <NULL>
775 !time window number := <Numeric>
777 ;starting from 1
778 * !number of images in time window := <Numeric>
780 ;eg 24 NOTE that here in gated SPECT is means images/angle
781 !image duration (sec) := <Numeric>
783 ;eg 0.04 for each frame in THIS time window
784 framing method := <ASCIIlist> Forward
786 Forward|Backward|Mixed|Other
787 ;default is forward
788 time window lower limit (sec) := <Numeric>
790 ;float normally expected, for THIS time window
791 time window upper limit (sec) := <Numeric>
793 ;float normally expected
794 % R-R cycles acquired this window := <Numeric>
796 ;if known
797 number of cardiac cycles (acquired) := <Numeric>
799 ;eg 356 , if known
800 study duration (acquired) sec := <Numeric>
802 ;total acquisition time duration for
803 ;this window only (if it can be computed!!) as
804 ;opposed to total acquisition time (when different)
805 !maximum pixel count := <Numeric>
807 ;for scaling purposes for all images in this
808 ;time window (and energy window) only
809 R-R histogram := <ASCIIlist> N Y|N
811 ;flag to indicate that one exists!!
812 }
814 ;Repeat for each subsequent time window.
815 ;start of tomographic keys
818 number of detector heads := <Numeric> 1
820 ;default=1 if unspecified
821 for ( number of detector heads )
823 {
824 !number of images/energy window := <Numeric>
826 ;total number of images (for all heads) for
827 ;THIS energy window!!
828 !process status := Reconstructed Acquired|Reconstructed
830 ;used below in conditional- MUST be defined
831 !number of projections := <Numeric>
833 ;for example- 64
834 ;note this is the actual number of images per
835 ;head per energy window if
836 ;the data are acquired, but NOT if the data are
837 ;reconstructed where the number of images is
838 ;specified separately as number of slices
839 !extent of rotation := <Numeric>
841 ;e.g 180, 360
842 !time per projection (sec) := <Numeric>
844 ;important for Acquired data
845 patient orientation := <ASCIIlist> head_in
846 head_in|feet_in|other
847 patient rotation := <ASCIIlist> supine
849 prone|supine|other
850 if( process status = "acquired")
852 {
853 !SPECT STUDY (acquired data):= <NULL>
854 !direction of rotation := <ASCIIlist> CW CW|CCW
856 ;CW = clockwise, CCW = counter clockwise
857 start angle := <Numeric>
859 ;0 is top-dead-centre, in degrees
860 ;in orientation as specified above
861 first projection angle in data set := <Numeric>
863 ;in degrees expressed with respect to
864 ;anterior- angles in direction as
865 ;specified CW or CCW
866 acquisition mode := <ASCIIlist> stepped
868 stepped|continuous
869 Centre_of_rotation := <ASCIIlist> Corrected
871 Corrected|Single_value|For_every_angle
872 ;default is "Corrected"
873 ;"Corrected" corresponds to a null centre of rotation
874 ;correction, as previous required by Interfile, that
875 ;is, no centre of rotation information is to be
876 ;passed. The key "Single value" indicates the
877 ;conventional definition of the centre of rotation
878 ;offset to be a single value specified for all angles,
879 ;specified for each head given a multiple head
880 ;acquisition.
881 ;The key "For_every_angle" indicates that the centre
882 ;of rotation offset will be specified for each head
883 ;and every angle. This is not currently implemented in
884 ;this Interfile definition, but will be introduced in
885 ;V4.
886 ;The mathematical centre of rotation is assumed to be
887 ;in the exact middle of the projection for example at
888 ;x= 32.5 y=32.5 for a 64x64 image where the count
889 ;starts from 1. Note that the choice of coordinates
890 ;does not matter, the only constraint being the
891 ;assumption that all projections have a length which
892 ;is an even number of pixels. The centre of rotation
893 ;is specified as the offset from that position to the
894 ;perpendicular dropped from a point on the axis of
895 ;rotation onto the head.
896 if( Centre_of_rotation = "Single_value" )
898 {
899 !X_offset := <Numeric>
901 ;x offset for all angles in mm.
902 ;x_offset is the x offset between the perpendicular
903 ;dropped from the centre of rotation and the dead
904 ;centre of the matrix,
905 ;The positive direction for the offset is considered
906 ;to be that of the increasing projection index, e.g.
907 ;for a projection with pixels of size 6mm, which
908 ;should be centred at 32.5, an offset of +6mm
909 ;indicates that the centre of rotation is at 33.5
910 ;Note that since offset is specified in mm, the pixel
911 ;size must be known.
912 Y_offset := <Numeric>
915 ;y offset for all angles in mm
916 ;y_offset is the y offset between that perpendicular
917 ;dropped from the centre of rotation from that point
918 ;on the axis of rotation where the y_offset is
919 ;considered to be zero, and the centre of the camera's
920 ;field of view. Thus y_offset is the RELATIVE shift of
921 ;the y-axis with respect to some arbitrary position,
922 ;normally that from the centre of the filed of view of
923 ;the first at the top dead centre position. Thus for
924 ;a single head, this value would normally be expected
925 ;to be equal to zero.
926 Radius := <Numeric>
928 ;radial distance to centre of rotation in mm,
929 ;for this head.
930 }
933 ;end of centre of rotation specification
934 orbit := <ASCIIlist> Circular Circular|non-circular
936 preprocessed := <ASCII>
938 ;preprocessing method
939 }
940 ; end of process status acquired
941 if( process status = "reconstructed")
943 {
944 !SPECT STUDY (reconstructed data) := <NULL>
945 method of reconstruction := <ASCII>
947 !number of slices := <Numeric>
949 ;i.e. number of images in this set for this
950 ;head and this energy window
951 number of reference frame := <Numeric> 0
953 ;if unspecified the frame number
954 ;originally used for defining slice positions
955 ;0=default [Note- not a very useful key]
956 slice orientation := <ASCIIlist> Transverse
958 Transverse|Coronal|Sagittal|Other
959 ;default is transverse if unspecified
960 slice thickness (pixels) := <Numeric> 1
962 ;if unspecified 1=default
963 centre-centre slice separation (pixels):=<Numeric> 1
965 ;e.g.1,2,3,4... as distinct from slice thickness
966 ;the word centre can also be spelt as center
967 filter name := <ASCII>
969 ;e.g. Hann, Hamming, Butterworth
970 filter parameters := <ASCII>
972 ;Nyquist freq etc.
973 z-axis filter := <ASCII>
975 ;method [1,2,1] etc.
976 attenuation correction coefficient/cm := <Numeric> 0.0
978 ;default 0 means not done if unspecified
979 method of attenuation correction := <ASCII> none
981 scatter corrected := <ASCIIlist> N Y|N
983 method of scatter correction := <ASCII> none
985 oblique reconstruction := <ASCIIlist> N Y|N
987 oblique orientation := <ASCII>
989 ;free text [Note ACR-NEMA convention preferred]
990 }
991 ;end of reconstructed tomo
992 }
993 ;End of GATED SPECT
994 }
996 ;end of loop for energy windows
997 if( type of data = "Curve")
999 {
1000 !CURVE DATA := <NULL>
1001 ;label to indicate that this is the curve definition
1002 ;curves should always be kept in separate data files
1003 ;and not together with the administrative data
1004 Curve_dimensions := <Numeric> 2
1006 ;how many dimensions- ONLY 2 is permitted in V3.3.
1007 ;Even if a single vector of values is required
1008 ;both matrix size[1] and [2] must be defined
1009 ;although one of them should take the value 1.
1010 ;A set of x,y values is 2 dimensional with normally
1011 ;matrix size[1] or matrix size[2] equal to 2.
1012 ;and the other matrix size specifying
1013 ;the number of PAIRS of values present (see Fig 1).
1014 ;Matrix sizes greater than 2 for BOTH dimensions are not
1015 ;recommended.
1016 !matrix size[1] := <Numeric>
1018 ;matrix size across (number of columns)
1019 !matrix size[2] := <Numeric>
1021 ;matrix size down (number of rows)
1022 !number format := <ASCIIlist> unsigned integer
1024 signed integer|unsigned integer|
1025 long float|short float|bit|ASCII
1026 !number of bytes per pixel := <Numeric>
1028 ;e.g. 1|2|4|.. [this key ignored for bit data]
1029 Type_of_curve := <ASCII>
1031 ;what kind of curve is it, for example time activity curve
1032 ;ROI indicates that this is a list
1033 ;of vectors corresponding to an ROI.
1034 for( Curve_dimensions, dimension)
1036 {
1037 ;When matrix size[1] or matrix size[2] equals 2 (the normal
1039 ;case) such that the data comprise pairs of values,
1040 ;then Label[1], Units[1] etc. refers to the set of first
1041 ;values for each pair, and Label[2] etc. refers the set of
1042 ;second values for each pair.
1043 Label[<dimension>] := <ASCII>
1045 ;a text label for the corresponding axis e.g. "counts"
1046 Units[<dimension>] := <ASCII>
1048 ;units of measurement for the corresponding axis
1049 ;e.g. "units[1]:=counts/sec"
1050 Min[<dimension>] := <Numeric>
1052 ;Minimum of set of values as indicated in units as defined,
1053 ;optional
1054 Max[<dimension>] := <Numeric>
1056 ;Maximum value as above, optional
1057 }
1059 ;End of loop for curve dimensions
1060 }
1062 !END OF INTERFILE := <NULL>
1063
1065 /usr/local/xmedcon/source/m-intf.h The header file.
1066 /usr/local/xmedcon/source/m-intf.c The source file.
1067
1069 medcon(1), xmedcon(1), xmedcon-config(1)
1070 m-acr(4), m-anlz(4), m-gif(5), m-inw(4), m-ecat(4)
1072 medcon(3)
1074
1076 (X)MedCon project was originally written by Erik Nolf (eNlf) for the former
1077 PET-Centre at Ghent University (Belgium).
1078 e-mail: enlf-at-users.sourceforge.net www: http://xmedcon.sourceforge.net
1080 M-INTF(4)