if2e7 2.2.0 © 2005 by Turku PET Centre
SYNTAX:
./if2e7
[--version] [-v] [-m] [-x] [-t scanner]
[-a [anonyName]] [-d dd mm yyyy] [-f f1,..,fn] [-i isotope]
[-c calibfactor] [-s slicesensfile] [-u units]
[-r startplane endplane] [-p pixel x0 y0] [-w startframe endframe]
[-o outfile] interfile_image
The program converts interfile images to ECAT7 format.
The Output images are quantified if there is calibration information available.
-a [anonyName] anonymous. Erases patient information from the output image
(patient name, ID and birth date). <anonyName> will be
placed in the 'patient name' filed, if specified.
-c calibfactor factor which scales counts/s to Bq/ml
-d dd mm yyyy date of scan. Obsolete as it can be taken from the header.
The date must be in the format dd mm yyyy, e.g. '-d 31 1 1999'
-f f1,..,fn framing information. Obsolete as it can be taken from the header.
Frame length of frame 1 to n in sec, numbers are sperated by ','.
Example: '-f 120,300,300' for 3 frames with 2min, 5min and 5min
-i isotope Obsolete as it can be taken from the header.
<isotope> can be 'C-11', 'O-15', 'F-18' 'Ga-68' or 'Ge-68'
-m multiplies matrix pixel values with <calibFactor>.
Obsolete as image tools (MEDx, Vinci, YaIT) and the conversion
program to Analyse format do the calibration internally.
-p pixel x0 y0 reduces the size of the ECAT7 image. This is useful for
studies, where the outer parts of a plane contain only '0's.
The new image centre will be at pixel (<x0>/<y0>). The pixel size
is unchanged. <pixel> is the x-y-dimension of the ECAT7 image.
Example: '-p 64 128 128' for a 64x64 image cut out of the
centre of a 256x256 image.
-r start end reduces the number of slices in the ECAT7 image. This is
useful for studies where most planes contain only '0's.
<start> is the number of the first plane to take <end> the
number of the last. (First plane is plane 0)
Example: '-r 0 9' for the first 10 slices only
-s filename reads the slice sensitivity values from file <filename>.
The file has to be an ASCII file with lines 'keyword := value'.
'calibration factor' and 'efficient factor for plane x', where
'x' are integers (i.e. plane numbers, starting with plane 0),
are the only relevant keywords. ';' marks a comment line.
Example for a slice sensitivity file:
; This is a slice sensitivity file, 3D OSEM, 5 iter, 14 subs
; calibration factor in (Bq/ml)/(counts/s)
calibration factor := 6.52630e+06
; plane := value
efficient factor for plane 0 := 0.985115
efficient factor for plane 1 := 1.01314
-t scanner sets defaults for several scanner specific fields like plane
separation, bin size, number of planes etc. and determines
the kind of interfile format. Options for <scanner> are 'HRRT'.
If not specified it is taken form the image file name extension;
'.i' for HRRT.
-u units data units in the calibrated ECAT7 image.
Options for <units> are 'Bq/ml', 'kBq/ml' (default) and 'MBq/ml'
-v verbose mode. Prints useful information to screen.
--version print build information and exit(0).
-w start end reduces the number of frames in the ECAT7 image. This is
useful if one needs only a part of a dynamic study.
<start> is the number of the first frame to take <end> the
number of the last. (First frame is frame 1)
Example: '-w 1 3' for the first 3 frames only
-x supress all corrections (also decay and duration)
Explicit command line switches override the values from the header.
The interfile_image filename is expected to consist of several fields
separated by '_'. The last '.' is the beginning of the file name extension.
HRRT-image filenames have the form RB9999_bla_framex_bla.i. The first field is
expected to be the study name. Dynamic studies must contain a field 'framex'.
The extension for the header is '.i.hdr' (e.g. RB9999_bla_framex_bla.i.hdr).
It is enough to specify one image (frame) in the command line as the programm
looks for all other frames (e.g. RB9999_bla_framex_bla.i).
./if2e7
[--version] [-v] [-m] [-x] [-t scanner]
[-a [anonyName]] [-d dd mm yyyy] [-f f1,..,fn] [-i isotope]
[-c calibfactor] [-s slicesensfile] [-u units]
[-r startplane endplane] [-p pixel x0 y0] [-w startframe endframe]
[-o outfile] interfile_image