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- Committer: Bazaar Package Importer
- Author(s): Roland Marcus Rutschmann
- Date: 2004-06-07 09:00:14 UTC
- Revision ID: james.westby@ubuntu.com-20040607090014-t39n52qc9zjqqqkh
Tags: upstream-0.9.6
Import upstream version 0.9.6
- files added:
- etc
- libs
- libs/dicom
- libs/ljpg
- man
- source
added
removed
man/m-intf.4
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'\" t
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.TH M-INTF 4
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.SH NAME
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m-intf - InterFile 3.3 medical image format (MedCon)
5
.SH DESCRIPTION
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.PP
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.in 0.2i
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The file consists of two parts, the administrative data in ASCII and the binary image data. It is possible to put both in one file, but we prefer to separate the data into two files. The administrative data in a file with extension `.h33' and the binary data in a file with extension `.i33'.
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.PP
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.in 0.2i
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This is a wonderful feature! Because of the separate header in ASCII you could write your own header for any raw image data you may have. I regularly use InterFile for turning unsupported formats into a supported format. Try to extract the raw image data from the unknown format and add an appropriate header with all information you know about.
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.PP
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.in 0.2i
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The basic defines for the format:
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.PP
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.in 0.2i
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.nf
18
---------------------------------------------------------------------------
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20
#define MDC_INTF_MAXKEYCHARS 256
21
22
char keystr[MDC_INTF_MAXKEYCHARS];
23
24
/* the data type */
25
#define MDC_INTF_STATIC 1
26
#define MDC_INTF_DYNAMIC 2
27
#define MDC_INTF_GATED 3
28
#define MDC_INTF_TOMOGRAPH 4
29
#define MDC_INTF_CURVE 5
30
#define MDC_INTF_ROI 6
31
32
/* the process status */
33
#define MDC_INTF_ACQUIRED 1
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#define MDC_INTF_RECONSTRUCTED 2
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/* gated spect nesting outer level */
37
#define MDC_INTF_NESTING_SPECT 1
38
#define MDC_INTF_NESTING_GATED 2
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40
typedef struct MdcInterFile_t {
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int data_type, process_status, pixel_type, gspect_nesting;
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Uint32 width, height, images_per_dimension, time_slots;
44
Uint32 data_offset, data_blocks, imagesize, number_images;
45
Uint32 energy_windows, frame_groups, time_windows, detector_heads;
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float pixel_xsize, pixel_ysize, slice_thickness, centre_centre_separation;
47
float study_duration, image_duration, image_pause, group_pause, ext_rot;
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Int8 patient_rot, patient_orient, slice_orient;
49
double version;
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51
} MDC_INTERFILE;
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---------------------------------------------------------------------------
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.fi
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.PP
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.in 0.2i
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What does the format support or not support:
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.PP
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.in 0.2i
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.nf
61
===========================================================================
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
.fi
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.PP
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.in 0.2i
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Underneath you will find a description of the format.
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.PP
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.in 0.2i
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1. ADMINISTRATIVE DATA
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.br
86
===================
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.PP
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.in 0.2i
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.IP a) 5
90
The administrative data are only composed of key-value pairs and exist in the form of ASCII text. The administrative data should be terminated with a <Ctrl-Z).
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.IP b) 5
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All administrative data are to be supplied in the form of key-value pairs in ASCII with delimiters. A `key' is the name of a parameter taking a specific `value', an example being:
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.PP
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.in 0.2i
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.ce 1
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patient name := Elvis Presley <cr><lf>
97
.IP c) 5
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The maximum permitted number of characters for a key or a value or a comment is 255 characters.
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.IP d) 5
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Neither keys nor values are to be treated as case sensitive. The characters <space> <tab> <underscore> <!> may all be treated as white space and ignored.
101
.IP e) 5
102
All relevant keys should be included in the intermediate file. A null value is permitted which will invoke the default where specified. The required keys are preceded by an exclamation mark.
103
.IP f) 5
104
A hole line or key-value pairs may have comments appended to them by preceding the comment with a semicolon <;>.
105
.IP g) 5
106
A required key ("name of data file") is included to point to the image data file, even if the binary data is in the same file of the administrative data.
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.IP h) 5
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The two alternate keys ("data starting block") or ("data offset in bytes") are used to indicate the offset of the binary data in the file as specified by the key ("name of data file"). The ("data starting block") represents the offset in number of blocks or 2048 bytes. The use of the key ("data offset in bytes") permits the offset to the binary data to be freely specified.
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.PP
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.in 0.2i
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2. IMAGE DATA
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.br
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==========
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.PP
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.in 0.2i
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.IP a) 5
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The order of the pixel data shall increment by column from left to right, and then by row, from top to bottom.
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.IP b) 5
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Image data shall be in either bit, signed or unsigned integer format, IEEE floating point format (float or double) or ASCII. When the data pixels are written in ASCII, the text line must not exceed 255 characters.
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.IP c) 5
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The default value for the key ("imagedata byte order") is BIGENDIAN, but LITTLEENDIAN is allowed. The byte order must be respected for integer and floating point numbers.
122
.IP d) 5
123
Bit data will stored in a single byte, representing 8 pixel values and ordered such that the most significant bit corresponds to the leftmost pixel.
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.PP
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.in 0.2i
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3. LIST OF KEYS - VERSION 3.3 (Updated for Gated SPECT)
127
.br
128
==========================
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.PP
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.in 0.2i
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.nf
132
!INTERFILE := <NULL>
133
;to indicate that this is an Interfile file
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135
!imaging modality := <ASCII> nucmed
136
;only nucmed is defined for the purpose of this document
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!originating system := <ASCII>
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;eg.GAMMA-11, MDS, ADAC, etc.
140
141
!version of keys := <Numeric> 3.3
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;future versions shall increment
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144
date of keys := <DateFormat> 1996:09:26
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;date of version 3.3 in date format
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147
conversion program := <ASCII>
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;name of program used
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program author := <ASCII>
151
;your chance of fame and fortune
152
153
program version := <Numeric>
154
;to keep track of conversion programs
155
156
program date := <DateFormat>
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;date of program
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!GENERAL DATA := <NULL>
160
;required but can be treated as comment
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original institution := <ASCII>
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;name of hospital etc.
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contact person := <ASCII>
166
;another chance of fame (and fortune?)
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data description := <ASCII>
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;whatever you want
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!data starting block := <Numeric> 0
172
;the value is the offset in blocks of 2048 bytes in either the
173
;administrative or the data file depending on the key value for
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;name of data file (see below)
175
| ;OR
176
!data offset in bytes:= <Numeric> 0
177
;as above but the offset may be specified freely in bytes
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!name of data file := <ASCII> <NULL>
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;<NULL> if no image data exists
181
;key is a name of the file where the data are present, either when
182
;in a separate binary data file, or when in a combined
183
;administrative/binary data file
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185
patient name := <ASCII>
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;last name, first name (recommended)
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!patient ID := <ASCII>
189
;as used in your hospital
190
191
patient dob := <DateFormat>
192
;date of birth
193
194
patient sex := <ASCIIlist> Unknown M|F|Unknown
195
;default is Unknown!
196
197
!study ID := <ASCII>
198
;as local conditions dictate
199
200
exam type := <ASCII>
201
;description of procedure as above
202
203
data compression := <ASCII> none
204
;name of algorithm if present- e.g. JPEG, etc.
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206
data encode := <ASCII> none
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;name of method of encoding if present- e.g. uuencode etc.
208
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organ := <ASCII> none
210
;ENLF: for mapping with DICOM tag (0018,0015) BodyPartExamined
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isotope := <ASCII> | <ASCII>/<ASCII> none
213
;ENLF: for mapping with DICOM radionuclide/radiopharmaceutical entries.
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dose := <Numeric> 0
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;ENLF: for mapping with DICOM tag (0018,1074) RadionuclideTotalDose [MBq]
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!GENERAL IMAGE DATA := <NULL>
219
;again required but treated as comment
220
221
!type of data := <ASCIIlist> Other
222
Static|Dynamic|Gated|Tomographic|Curve|ROI|GSPECT|Other
223
;important - this key is used for many conditionals
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225
!total number of images := <Numeric>
226
;how many images are there altogether in total in the associated
227
;data file (for all windows etc.). This overrides any other way of
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;calculating the total number of images.
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study date := <DateFormat>
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;date of the first image included in the data file
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study time := <TimeFormat>
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;time for the start of first image specified
235
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imagedata byte order := <ASCIIlist> BIGENDIAN
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BIGENDIAN|LITTLEENDIAN
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;BIGENDIAN is the default if unspecified
239
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process label := <ASCII> none
241
;ENLF: for mapping with DICOM tag (0008,103E) SeriesDescription
242
243
quantification units := +1.696265e-05
244
;ENLF: global scale factor for mediman dialect
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NUD/rescale slope := +1.696265e-05
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;ENLF: global scale factor for NUD systems
248
249
NUD/rescale intercept := +0.000000e+00
250
;ENLF: global scale intercept for NUD systems
251
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number of energy windows := <Numeric> 1
253
;defaulted to one if unspecified
254
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for ( number of energy windows, energy window)
256
{
257
energy window[<energy window>] := <ASCII>
258
;ASCII text- for example "Tc99m"
259
;this starts as "energy window [1]" and then increments to
260
;energy window[2]:= <ASCII>
261
;and then on to
262
;energy window[3]:= <ASCII>
263
;etc. etc.
264
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energy window lower level [<energy window>] := <Numeric>
266
;value of lower energy level in keV for the corresponding window
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;starts off as "energy window lower level [1]"
268
;and continues [2],[3] .. as above
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energy window upper level [<energy window>] := <Numeric>
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;value of upper energy level in keV for the corresponding window
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;starts off as "energy window upper level [1]"
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;and continues [2],[3] .. as above
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flood corrected := <ASCIIlist> Y Y|N
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;corrected if unspecified
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decay corrected := <ASCIIlist> N Y|N
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;not corrected if unspecified
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if( type of data = "Static"|"ROI")
283
{
284
!STATIC STUDY (General) := <NULL>
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;label to indicate that this is the static definition
286
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number of images/energy window := <Numeric> 1
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;number of images in THIS energy window
289
290
for ( number of images/energy window )
291
{
292
!Static Study (each frame) := <NULL>
293
;included at the beginning of the definition of
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;each new static frame
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!image number := <Numeric>
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;starting from 1 [see above]
298
;- must be specified!!
299
;starts from 1 and increments though all
300
;windows to its maximum value which equals the
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;total number of images in the file!!
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!matrix size [1] :=< Numeric>
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;matrix size across (number of columns)- previously x
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;32, 64, 128 etc. but not necessarily powers of 2
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!matrix size [2] := <Numeric>
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;matrix size down (number of rows)- previously y
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;32, 64, 128 etc. but not necessarily powers of 2
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!number format := <ASCIIlist> unsigned integer
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signed integer|unsigned integer
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|long float|short float|bit|ASCII
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;as specified
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!number of bytes per pixel := <Numeric>
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;e.g. 1|2|4.. [this key ignored for bit data]
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scaling factor (mm/pixel) [1]:= <Numeric>
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;size of pixel across- previously x
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scaling factor (mm/pixel) [2] := <Numeric>
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;size of pixel down- previously y
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image duration (sec) := <Numeric>
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;eg. 120.0 i.e. normally a float, for each image
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328
image start time := <TimeFormat>
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;time for each image
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label := <ASCII>
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;eg Anterior
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maximum pixel count := <Numeric>
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;for scaling purposes, for each image
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total counts := <Numeric>
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;either an integer or a float, for each image
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}
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;End of frame loop -Repeat for each subsequent frame
342
}
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;End of static definitions
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if( type of data = "Dynamic")
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{
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!DYNAMIC STUDY (general) := <NULL>
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;label to indicate that this is a dynamic study
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!number of frame groups := <Numeric> 1
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;defaults to 1
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for( number of frame groups, frame group number)
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{
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!Dynamic Study (each frame group) := <NULL>
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;Repeated for each group of frames as
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;indication of the start of the
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;definition of the new group
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!frame group number := <Numeric>
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;numbering starts from 1 (must be specified)
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!matrix size [1] := <Numeric>
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;matrix size across (number of columns)
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;-previously matrix size x
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;32, 64, 128 etc. but not necessarily powers of 2
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!matrix size [2] := <Numeric>
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;matrix size down (number of rows)- previously y
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;32, 64, 128 etc. but not necessarily powers of 2
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!number format := <ASCIIlist> unsigned integer
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signed integer|unsigned integer|
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long float|short float|bit|ASCII
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;as specified
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!number of bytes per pixel := <Numeric>
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;e.g. 1|2|4.. [this key ignored for bit data]
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scaling factor (mm/pixel) [1]:= <Numeric>
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;size of pixel across- previously x
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scaling factor (mm/pixel) [2] := <Numeric>
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;size of pixel down- previously y
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!number of images this frame group := <Numeric>
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;for each frame group
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;(for each energy window)
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!image duration (sec) := <Numeric>
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;eg 0.2, for each frame group
395
;(for each energy window)
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pause between images (sec) := <Numeric> 0.0
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;eg 0.0, default is 0.0
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pause between frame groups (sec) := <Numeric> 0.0
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;eg 5.0 default 0.0, time between last
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;frame group (or start of study) and this frame group
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!maximum pixel count in group := <Numeric>
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;eg 1234 (for scaling purposes)
406
;maximum pixel for all frames in this
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;group and this window!!
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}
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;Repeat for each subsequent frame group
411
}
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; End of dynamic definitions
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if( type of data = "Gated")
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{
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!GATED STUDY (general) := <NULL>
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;again a flag to indicate a gated study
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!matrix size [1] := <Numeric>
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;matrix size across (number of columns)- previously x
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;32, 64, 128 etc. but not necessarily powers of 2
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!matrix size [2] := <Numeric>
426
;matrix size down (number of rows)- previously y
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;32, 64, 128 etc. but not necessarily powers of 2
428
429
!number format := <ASCIIlist> unsigned integer
430
signed integer|unsigned integer|
431
long float|short float|bit|ASCII
432
;as specified
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!number of bytes per pixel := <Numeric>
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;e.g. 1|2|4|..> [this key ignored for bit data]
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scaling factor (mm/pixel) [1]:= <Numeric>
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;size of pixel across- previously x
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scaling factor (mm/pixel) [2] := <Numeric>
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;size of pixel down- previously y
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study duration (elapsed) sec := <Numeric>
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;eg 300, total elapsed time for whole study
445
446
number of cardiac cycles (observed) := <Numeric>
447
;total number of cycles if known, for this
448
;energy window
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450
number of time windows := <Numeric> 1
451
;defaults to 1 if unspecified- number of different
452
;sets of time intervals
453
454
for ( number of time windows, time window number)
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{
456
!Gated Study (each time window) := <NULL>
457
458
!time window number := <Numeric>
459
;starting from 1
460
461
!number of images in time window := <Numeric>
462
;eg 24
463
464
!image duration (sec) := <Numeric>
465
;eg 0.04 for each frame in THIS time window
466
467
framing method := <ASCIIlist> Forward
468
Forward|Backward|Mixed|Other
469
;default is forward
470
471
time window lower limit (sec) := <Numeric>
472
;float normally expected, for THIS time window
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time window upper limit (sec) := <Numeric>
475
;float normally expected
476
477
% R-R cycles acquired this window := <Numeric>
478
;if known
479
480
number of cardiac cycles (acquired) := <Numeric>
481
;eg 356 , if known
482
483
study duration (acquired) sec := <Numeric>
484
;total acquisition time duration for
485
;this window only (if it can be computed!!) as
486
;opposed to total acquisition time (when different)
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!maximum pixel count := <Numeric>
489
;for scaling purposes for all images in this
490
;time window (and energy window) only
491
492
R-R histogram := <ASCIIlist> N Y|N
493
;flag to indicate that one exists!!
494
495
}
496
;Repeat for each subsequent time window.
497
498
}
499
;end of gated definitions
500
501
502
if( type of data = "Tomographic")
503
{
504
505
!SPECT STUDY (general) := <NULL>
506
;flag to indicate tomographic data with no effect as such
507
508
number of detector heads := <Numeric> 1
509
;default=1 if unspecified
510
511
for ( number of detector heads )
512
{
513
514
!number of images/energy window := <Numeric>
515
;total number of images (for all heads) for
516
;THIS energy window!!
517
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!process status := Reconstructed Acquired|Reconstructed
519
;used below in conditional- MUST be defined
520
521
!matrix size [1] := <Numeric>
522
;matrix size across (number of columns)- previously x
523
;32, 64, 128 etc. but not necessarily powers of 2
524
525
!matrix size [2] := <Numeric>
526
;matrix size down (number of rows)- previously y
527
;32, 64, 128 etc. but not necessarily powers of 2
528
529
!number format := <ASCIIlist> unsigned integer
530
signed integer|unsigned integer|
531
long float|short float|bit|ASCII
532
;as specified
533
534
!number of bytes per pixel := <Numeric>
535
;e.g. 1|2|4|.. [this key ignored for bit data]
536
537
scaling factor (mm/pixel) [1]:= <Numeric>
538
;size of pixel across- previously x
539
540
scaling factor (mm/pixel) [2] := <Numeric>
541
;size of pixel down- previously y
542
543
!number of projections := <Numeric>
544
;for example- 64
545
;note this is the actual number of images per
546
;head per energy window if
547
;the data are acquired, but NOT if the data are
548
;reconstructed where the number of images is
549
;specified separately as number of slices
550
551
!extent of rotation := <Numeric>
552
;e.g 180, 360
553
554
!time per projection (sec) := <Numeric>
555
;important for Acquired data
556
557
study duration (sec) := <Numeric>
558
;eg 1280.0, for acquired data should be equal
559
;to the product of number of projections and
560
;time per projection, but could be different!!
561
562
!maximum pixel count := <Numeric>
563
;for scaling- in THIS image series( this head
564
;and this energy window)
565
566
patient orientation := <ASCIIlist> head_in
567
head_in|feet_in|other
568
569
patient rotation := <ASCIIlist> supine
570
prone|supine|other
571
572
if( process status = "acquired")
573
{
574
!SPECT STUDY (acquired data):= <NULL>
575
576
!direction of rotation := <ASCIIlist> CW CW|CCW
577
;CW = clockwise, CCW = counter clockwise
578
579
start angle := <Numeric>
580
;0 is top-dead-centre, in degrees
581
;in orientation as specified above
582
583
first projection angle in data set := <Numeric>
584
;in degrees expressed with respect to
585
;anterior- angles in direction as
586
;specified CW or CCW
587
588
acquisition mode := <ASCIIlist> stepped
589
stepped|continuous
590
591
Centre_of_rotation := <ASCIIlist> Corrected
592
Corrected|Single_value|For_every_angle
593
;default is "Corrected"
594
;"Corrected" corresponds to a null centre of rotation
595
;correction, as previous required by Interfile, that
596
;is, no centre of rotation information is to be
597
;passed. The key "Single value" indicates the
598
;conventional definition of the centre of rotation
599
;offset to be a single value specified for all angles,
600
;specified for each head given a multiple head
601
;acquisition.
602
;The key "For_every_angle" indicates that the centre
603
;of rotation offset will be specified for each head
604
;and every angle. This is not currently implemented in
605
;this Interfile definition, but will be introduced in
606
;V4.
607
;The mathematical centre of rotation is assumed to be
608
;in the exact middle of the projection for example at
609
;x= 32.5 y=32.5 for a 64x64 image where the count
610
;starts from 1. Note that the choice of coordinates
611
;does not matter, the only constraint being the
612
;assumption that all projections have a length which
613
;is an even number of pixels. The centre of rotation
614
;is specified as the offset from that position to the
615
;perpendicular dropped from a point on the axis of
616
;rotation onto the head.
617
618
if( Centre_of_rotation = "Single_value" )
619
{
620
621
!X_offset := <Numeric>
622
;x offset for all angles in mm.
623
;x_offset is the x offset between the perpendicular
624
;dropped from the centre of rotation and the dead
625
;centre of the matrix,
626
;The positive direction for the offset is considered
627
;to be that of the increasing projection index, e.g.
628
;for a projection with pixels of size 6mm, which
629
;should be centred at 32.5, an offset of +6mm
630
;indicates that the centre of rotation is at 33.5
631
;Note that since offset is specified in mm, the pixel
632
;size must be known.
633
634
635
Y_offset := <Numeric>
636
;y offset for all angles in mm
637
;y_offset is the y offset between that perpendicular
638
;dropped from the centre of rotation from that point
639
;on the axis of rotation where the y_offset is
640
;considered to be zero, and the centre of the camera's
641
;field of view. Thus y_offset is the RELATIVE shift of
642
;the y-axis with respect to some arbitrary position,
643
;normally that from the centre of the filed of view of
644
;the first at the top dead centre position. Thus for
645
;a single head, this value would normally be expected
646
;to be equal to zero.
647
648
Radius := <Numeric>
649
;radial distance to centre of rotation in mm,
650
;for this head.
651
652
653
}
654
;end of centre of rotation specification
655
656
orbit := <ASCIIlist> Circular Circular|non-circular
657
658
preprocessed := <ASCII>
659
;preprocessing method
660
661
}
662
; end of process status acquired
663
664
if( process status = "reconstructed")
665
{
666
!SPECT STUDY (reconstructed data) := <NULL>
667
668
method of reconstruction := <ASCII>
669
670
!number of slices := <Numeric>
671
;i.e. number of images in this set for this
672
;head and this energy window
673
674
number of reference frame := <Numeric> 0
675
;if unspecified the frame number
676
;originally used for defining slice positions
677
;0=default [Note- not a very useful key]
678
679
slice orientation := <ASCIIlist> Transverse
680
Transverse|Coronal|Sagittal|Other
681
;default is transverse if unspecified
682
683
slice thickness (pixels) := <Numeric> 1
684
;if unspecified 1=default
685
686
centre-centre slice separation (pixels):=<Numeric> 1
687
;e.g.1,2,3,4... as distinct from slice thickness
688
;the word centre can also be spelt as center
689
690
filter name := <ASCII>
691
;e.g. Hann, Hamming, Butterworth
692
693
filter parameters := <ASCII>
694
;Nyquist freq etc.
695
696
z-axis filter := <ASCII>
697
;method [1,2,1] etc.
698
699
attenuation correction coefficient/cm := <Numeric> 0.0
700
;default 0 means not done if unspecified
701
702
method of attenuation correction := <ASCII> none
703
704
scatter corrected := <ASCIIlist> N Y|N
705
706
method of scatter correction := <ASCII> none
707
708
oblique reconstruction := <ASCIIlist> N Y|N
709
710
oblique orientation := <ASCII>
711
;free text [Note ACR-NEMA convention preferred]
712
}
713
;end of reconstructed tomo
714
}
715
;End of tomo
716
717
718
* if( type of data = "GSPECT")
719
{
720
* !GATED SPECT STUDY (general) := <NULL>
721
;again a flag to indicate a gated SPECT study
722
;MIXTURE OF GATED & TOMO
723
724
!matrix size [1] := <Numeric>
725
;matrix size across (number of columns)- previously x
726
;32, 64, 128 etc. but not necessarily powers of 2
727
728
!matrix size [2] := <Numeric>
729
;matrix size down (number of rows)- previously y
730
;32, 64, 128 etc. but not necessarily powers of 2
731
732
!number format := <ASCIIlist> unsigned integer
733
signed integer|unsigned integer|
734
long float|short float|bit|ASCII
735
;as specified
736
737
!number of bytes per pixel := <Numeric>
738
;e.g. 1|2|4|..> [this key ignored for bit data]
739
740
!Gated SPECT nesting outer level := SPECT|Gated Gated
741
; key to indictae order of images, if SPECT is outer level
742
; order is, for every angle give each gated image, if
743
; gated is outer level, then order is, for every gated
744
; time value, vie set of tomographic images
745
746
scaling factor (mm/pixel) [1]:= <Numeric>
747
;size of pixel across- previously x
748
749
scaling factor (mm/pixel) [2] := <Numeric>
750
;size of pixel down- previously y
751
752
study duration (elapsed) sec := <Numeric>
753
;eg 300, total elapsed time for whole study
754
755
number of cardiac cycles (observed) := <Numeric>
756
;total number of cycles if known, for this
757
;energy window
758
759
number of time windows := <Numeric> 1
760
;defaults to 1 if unspecified- number of different
761
;sets of time intervals
762
763
for ( number of time windows, time window number)
764
{
765
!Gated Study (each time window) := <NULL>
766
767
!time window number := <Numeric>
768
;starting from 1
769
770
* !number of images in time window := <Numeric>
771
;eg 24 NOTE that here in gated SPECT is means images/angle
772
773
!image duration (sec) := <Numeric>
774
;eg 0.04 for each frame in THIS time window
775
776
framing method := <ASCIIlist> Forward
777
Forward|Backward|Mixed|Other
778
;default is forward
779
780
time window lower limit (sec) := <Numeric>
781
;float normally expected, for THIS time window
782
783
time window upper limit (sec) := <Numeric>
784
;float normally expected
785
786
% R-R cycles acquired this window := <Numeric>
787
;if known
788
789
number of cardiac cycles (acquired) := <Numeric>
790
;eg 356 , if known
791
792
study duration (acquired) sec := <Numeric>
793
;total acquisition time duration for
794
;this window only (if it can be computed!!) as
795
;opposed to total acquisition time (when different)
796
797
!maximum pixel count := <Numeric>
798
;for scaling purposes for all images in this
799
;time window (and energy window) only
800
801
R-R histogram := <ASCIIlist> N Y|N
802
;flag to indicate that one exists!!
803
804
}
805
;Repeat for each subsequent time window.
806
807
808
;start of tomographic keys
809
810
number of detector heads := <Numeric> 1
811
;default=1 if unspecified
812
813
for ( number of detector heads )
814
{
815
816
!number of images/energy window := <Numeric>
817
;total number of images (for all heads) for
818
;THIS energy window!!
819
820
!process status := Reconstructed Acquired|Reconstructed
821
;used below in conditional- MUST be defined
822
823
!number of projections := <Numeric>
824
;for example- 64
825
;note this is the actual number of images per
826
;head per energy window if
827
;the data are acquired, but NOT if the data are
828
;reconstructed where the number of images is
829
;specified separately as number of slices
830
831
!extent of rotation := <Numeric>
832
;e.g 180, 360
833
834
!time per projection (sec) := <Numeric>
835
;important for Acquired data
836
patient orientation := <ASCIIlist> head_in
837
head_in|feet_in|other
838
839
patient rotation := <ASCIIlist> supine
840
prone|supine|other
841
842
if( process status = "acquired")
843
{
844
!SPECT STUDY (acquired data):= <NULL>
845
846
!direction of rotation := <ASCIIlist> CW CW|CCW
847
;CW = clockwise, CCW = counter clockwise
848
849
start angle := <Numeric>
850
;0 is top-dead-centre, in degrees
851
;in orientation as specified above
852
853
first projection angle in data set := <Numeric>
854
;in degrees expressed with respect to
855
;anterior- angles in direction as
856
;specified CW or CCW
857
858
acquisition mode := <ASCIIlist> stepped
859
stepped|continuous
860
861
Centre_of_rotation := <ASCIIlist> Corrected
862
Corrected|Single_value|For_every_angle
863
;default is "Corrected"
864
;"Corrected" corresponds to a null centre of rotation
865
;correction, as previous required by Interfile, that
866
;is, no centre of rotation information is to be
867
;passed. The key "Single value" indicates the
868
;conventional definition of the centre of rotation
869
;offset to be a single value specified for all angles,
870
;specified for each head given a multiple head
871
;acquisition.
872
;The key "For_every_angle" indicates that the centre
873
;of rotation offset will be specified for each head
874
;and every angle. This is not currently implemented in
875
;this Interfile definition, but will be introduced in
876
;V4.
877
;The mathematical centre of rotation is assumed to be
878
;in the exact middle of the projection for example at
879
;x= 32.5 y=32.5 for a 64x64 image where the count
880
;starts from 1. Note that the choice of coordinates
881
;does not matter, the only constraint being the
882
;assumption that all projections have a length which
883
;is an even number of pixels. The centre of rotation
884
;is specified as the offset from that position to the
885
;perpendicular dropped from a point on the axis of
886
;rotation onto the head.
887
888
if( Centre_of_rotation = "Single_value" )
889
{
890
891
!X_offset := <Numeric>
892
;x offset for all angles in mm.
893
;x_offset is the x offset between the perpendicular
894
;dropped from the centre of rotation and the dead
895
;centre of the matrix,
896
;The positive direction for the offset is considered
897
;to be that of the increasing projection index, e.g.
898
;for a projection with pixels of size 6mm, which
899
;should be centred at 32.5, an offset of +6mm
900
;indicates that the centre of rotation is at 33.5
901
;Note that since offset is specified in mm, the pixel
902
;size must be known.
903
904
905
Y_offset := <Numeric>
906
;y offset for all angles in mm
907
;y_offset is the y offset between that perpendicular
908
;dropped from the centre of rotation from that point
909
;on the axis of rotation where the y_offset is
910
;considered to be zero, and the centre of the camera's
911
;field of view. Thus y_offset is the RELATIVE shift of
912
;the y-axis with respect to some arbitrary position,
913
;normally that from the centre of the filed of view of
914
;the first at the top dead centre position. Thus for
915
;a single head, this value would normally be expected
916
;to be equal to zero.
917
918
Radius := <Numeric>
919
;radial distance to centre of rotation in mm,
920
;for this head.
921
922
923
}
924
;end of centre of rotation specification
925
926
orbit := <ASCIIlist> Circular Circular|non-circular
927
928
preprocessed := <ASCII>
929
;preprocessing method
930
}
931
; end of process status acquired
932
933
if( process status = "reconstructed")
934
{
935
!SPECT STUDY (reconstructed data) := <NULL>
936
937
method of reconstruction := <ASCII>
938
939
!number of slices := <Numeric>
940
;i.e. number of images in this set for this
941
;head and this energy window
942
943
number of reference frame := <Numeric> 0
944
;if unspecified the frame number
945
;originally used for defining slice positions
946
;0=default [Note- not a very useful key]
947
948
slice orientation := <ASCIIlist> Transverse
949
Transverse|Coronal|Sagittal|Other
950
;default is transverse if unspecified
951
952
slice thickness (pixels) := <Numeric> 1
953
;if unspecified 1=default
954
955
centre-centre slice separation (pixels):=<Numeric> 1
956
;e.g.1,2,3,4... as distinct from slice thickness
957
;the word centre can also be spelt as center
958
959
filter name := <ASCII>
960
;e.g. Hann, Hamming, Butterworth
961
962
filter parameters := <ASCII>
963
;Nyquist freq etc.
964
965
z-axis filter := <ASCII>
966
;method [1,2,1] etc.
967
968
attenuation correction coefficient/cm := <Numeric> 0.0
969
;default 0 means not done if unspecified
970
971
method of attenuation correction := <ASCII> none
972
973
scatter corrected := <ASCIIlist> N Y|N
974
975
method of scatter correction := <ASCII> none
976
977
oblique reconstruction := <ASCIIlist> N Y|N
978
979
oblique orientation := <ASCII>
980
;free text [Note ACR-NEMA convention preferred]
981
}
982
;end of reconstructed tomo
983
}
984
;End of GATED SPECT
985
986
}
987
;end of loop for energy windows
988
989
if( type of data = "Curve")
990
{
991
!CURVE DATA := <NULL>
992
;label to indicate that this is the curve definition
993
;curves should always be kept in separate data files
994
;and not together with the administrative data
995
996
Curve_dimensions := <Numeric> 2
997
;how many dimensions- ONLY 2 is permitted in V3.3.
998
;Even if a single vector of values is required
999
;both matrix size[1] and [2] must be defined
1000
;although one of them should take the value 1.
1001
;A set of x,y values is 2 dimensional with normally
1002
;matrix size[1] or matrix size[2] equal to 2.
1003
;and the other matrix size specifying
1004
;the number of PAIRS of values present (see Fig 1).
1005
;Matrix sizes greater than 2 for BOTH dimensions are not
1006
;recommended.
1007
1008
!matrix size[1] := <Numeric>
1009
;matrix size across (number of columns)
1010
1011
!matrix size[2] := <Numeric>
1012
;matrix size down (number of rows)
1013
1014
!number format := <ASCIIlist> unsigned integer
1015
signed integer|unsigned integer|
1016
long float|short float|bit|ASCII
1017
1018
!number of bytes per pixel := <Numeric>
1019
;e.g. 1|2|4|.. [this key ignored for bit data]
1020
1021
Type_of_curve := <ASCII>
1022
;what kind of curve is it, for example time activity curve
1023
;ROI indicates that this is a list
1024
;of vectors corresponding to an ROI.
1025
1026
for( Curve_dimensions, dimension)
1027
{
1028
1029
;When matrix size[1] or matrix size[2] equals 2 (the normal
1030
;case) such that the data comprise pairs of values,
1031
;then Label[1], Units[1] etc. refers to the set of first
1032
;values for each pair, and Label[2] etc. refers the set of
1033
;second values for each pair.
1034
1035
Label[<dimension>] := <ASCII>
1036
;a text label for the corresponding axis e.g. "counts"
1037
1038
Units[<dimension>] := <ASCII>
1039
;units of measurement for the corresponding axis
1040
;e.g. "units[1]:=counts/sec"
1041
1042
Min[<dimension>] := <Numeric>
1043
;Minimum of set of values as indicated in units as defined,
1044
;optional
1045
1046
Max[<dimension>] := <Numeric>
1047
;Maximum value as above, optional
1048
1049
}
1050
;End of loop for curve dimensions
1051
1052
}
1053
!END OF INTERFILE := <NULL>
1054
.fi
1055
.PP
1056
.in 0.2i
1057
.SH FILES
1058
.PP
1059
.in 0.2i
1060
.nf
1061
/usr/local/xmedcon/source/m-intf.h The header file.
1062
/usr/local/xmedcon/source/m-intf.c The source file.
1063
.PP
1064
.in 0.2i
1065
.SH SEE ALSO
1066
.PP
1067
.in 0.2i
1068
medcon(1), xmedcon(1), xmedcon-config(1)
1069
.PP
1070
.in 0.2i
1071
m-acr(4), m-anlz(4), m-gif(5), m-inw(4), m-ecat(4)
1072
.PP
1073
.in 0.2i
1074
medcon(3)
1075
.PP
1076
.in 0.2i
1077
.SH AUTHOR
1078
.PP
1079
.in 0.2i
1080
.I (X)MedCon
1081
project was written by Erik Nolf (eNlf) for the PET-Centre at Ghent University (Belgium).
1082
.PP
1083
.in 0.2i
1084
.TS
1085
tab(=);
1086
lB l lB l.
1087
e-mail:=enlf@users.sourceforge.net=www:=http://xmedcon.sourceforge.net
1088
.TE
1089
Loggerhead is a web-based interface for Breezy
Version: 2.0.1