ct | file / import() list dim() debug export() delete steps() read display num() write inspect eqvpathlength() slice() swap window() ctstates() ctref() singlect create4DCT() actstate() newrefstate()
<file>.CTX
data file together with
a text <file>.HED
header file.
<file>
is
taken as a prefix.
<file>
is used as a patient name.
cadslices
imports a bunch of CT data slices
in Lyon's
CADPlan
format.
cadslicesxy
does the same, but for an early
version with x running as lines and y running as columns.
All slice files need to be specified, wild cards are supported.
isogray
imports a bunch of CT data slices
in IsoGray
format. Only their stem name may be given, and only the files
<file>m*.hdr
,
<file>p*.hdr
,
<file>m*.sca
,
<file>p*.sca
will be considered.
cadslices
gd
<prefix>ct.gd
,
<prefix>ct.um<yyyyyy>.gd
,
<yyyyyy>
is the slice coordinate (centre) in micrometers.
<prefix>
is either given by file
or, if omitted, derived from either the patient name or, if omitted,
from the original input file name.
ctnum.gd
<prefix>ctnum.gd
,
<file>.ctx
, <file>.hed
,
<patient-id>000.ctx
, <patient-id>000.hed
,
*
may be used to specify the lower/upper limit, respectively.
<interval>
might be
* <slice-number> <low-slice>,<high-slice> *,<high-slice> <low-slice>,*where
*
stands for "all" or the lower/upper limit, respectively.
<nx,ny,nz>
specifies a
list of three numbers denoting the number of voxels in the three dimensions.
<dx,dy,dz>
specifies a
list of three numbers denoting the voxel sizes (in mm) in the three dimensions.
Note that the file parameter must also be given
in order to assign a patient name.
<hf>
can be interpreted
as a reasonable Hounsfield number (hf
>=-1000) it will be assumed as a
constant value for all CT voxels.
Otherwise <hf>
is assumed to be the name of
a user-supplied executable (plug-in) which calculates the Hounsfield
numbers.
<len>
can be interpreted
as a reasonable equivalent path length (len
>0) it will be assumed as a
constant value for all CT voxels.
Otherwise <len>
is assumed to be the name of
a user-supplied executable (plug-in) which calculates the
equivalent path lengths.
ct OTTOT3000 / readReads CT data (files
OTTOT3000.CTX
and OTTOT3000.HED
) for patient "OTTOT3".
ct xxxxxx /dim(8,4,2) steps(1,1,1) num(17)Creates a CT data cube with size 8x4x2, a voxel size of 1 mm in either direction and a constant Hounsfield number of 17.
ct 'CADPLAN/250603007*.txt' /import(cadslices)Imports
CADplan
CT slices stored in directory CADPLAN
ct "ISOGRAY/80325" /import(isogray)Imports
IsoGray
CT slices
80325m*.hdr
,
80325p*.hdr
,
80325m*.sca
,
80325p*.sca
stored in directory ISOGRAY
ct "/TESTDATA/CT/anonymous4812_RIG" /read ctstates(10) ctref(6)It's the classic read command with the two additional parameters,
/ctstates()
specifying the total number of states,
and
/ctref()
specifying the reference state.
"/TESTDATA/CT/anonymous4812_RIG_00.ctx"
,"/TESTDATA/CT/anonymous4812_RIG_01.ctx"
,"/TESTDATA/CT/anonymous4812_RIG_09.ctx"
,ct "/TESTDATA/CT/A" /readThen a transformation is needed to convert the 3D into a 4D CT, e.g.:
trafo "/TESTDATA/anonymous4812" /readwill read
/TESTDATA/anonymous4812.trf
. ct /create4d /actstate(2) /newrefstate(6)creates a sequence of 3D CTs in the current working directory. Note that the parameters
/actstate()
and /newrefstate()
are necessary in addition to /create4d