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For Siemens Inveon users

How to reconstruct directly from .cat file

Cobra cannot extract parameters directly from .cat files. So the first step is reconstructing a sample dataset to find geometrical setup corresponding these .cat file and scan mode (apparently this procedure has to be performed for every scan mode you use). In order to do this, please make a reconstruction of “freshly” acquired data or retroactive reconstruction. Note that Inveon system works with Cobra6 – style GUI.
Then you need to find, open, and edit Cobra .xxm file, defining the most recent parameters applied. This file is called parameter_crt.xxm; it is located in Cobra working folder. The default location of  Cobra working folder is the directory where Cobra software has been installed. The directory can also be found (re-set) using GUI. Also one might make just a global search through the disk C: looking for parameter_crt.xxm.


Once parameter_crt.xxm is found you need to edit it with WordPad. Below there is a description of changes one should make.


The following tags need care

1)  PARTAG_PROJACQUIRED, PARTAG_PROJRECON 
They should be set equal to the actual views number kept in .cat file.
How to find it . For example the actual length of .cat is 460,973,184 byte. The length of the view is 640x992x2 = 1269760 bytes (detector size is 640x992 and two bytes per pixel). How many views in cat file?
460,973,184 / 1269760 = 363.039616935483
It means that .cat file contains 363 views plus some header (Siemens did not agree to disclose the header for us).
First two views are dark and bright calibration fields (in COBRA A.K.A. offset and AirRaw). So both  PARTAG_PROJACQUIRED, PARTAG_PROJRECON  must be set to 361. Note that you cannot use another number here (for example you can not make a reconstruction from 200 projections)

2) PARTAG_INPUTLOGGEDFLOAT, OPTTAG_AIRCAL, OPTTAG_LOG, OPTTAG_OFFSET, OPTTAG_FFT, OPTTAG_PARKER.
These tags describe the signal representation and  should be set as you see below

3) PARTAG_SRCDATAPATH,OPTTAG_PRJNAMEFORMAT,PARTAG_DSTDATAPATH 
These tags define file naming and paths.
PARTAG_SRCDATAPATH, PARTAG_DSTDATAPATH  may be missing if .cat file is in the same folder along with xxm file.
OPTTAG_PRJNAMEFORMAT defines .cat file name

4) MODE_OFFLINE should be set to 1, the row MODE_INLINE = 1 must be deleted

5) BPMODETAG_USE_GPU. Please delete this row if you do not have GPU support.

6) PARTAG_CATFORMAT just must be set to 1


Example. Corrected xxm (all parameters applied by COBRA 7.3.xx ) to reconstruct directly from .cat. The parameters that need care are highlighted


----------------> Scanner Geometry
PARTAG_SRCOBJDIST    = 266.339996
PARTAG_SRCDETDIST    = 334.410004
PARTAG_SCANANGLE     = 360.000000
PARTAG_STARTANGLE    = 0.000000
PARTAG_INVERSEANGLE  = 0.000000
PARTAG_PROJACQUIRED  = 361
PARTAG_PROJRECON     = 361
PARTAG_DETSIZEU      = 640
PARTAG_DETSIZEV      = 992
PARTAG_DETOFFSETU    = 2.733017
PARTAG_DETOFFSETV    = 0.000000
PARTAG_DETPITCHU     = 0.124510
PARTAG_DETPITCHV     = 0.124510
PARTAG_DETPIVOT      = 0.000000
PARTAG_OFFSET        = 0
PARTAG_ROTATIONDIR   = 1
PARTAG_HELICAL_SPEED = 0.000000

----------------> Reconstructed Volume
PARTAG_CUBESIZEX     = 640
PARTAG_CUBESIZEY     = 640
PARTAG_CUBESIZEZ     = 992
PARTAG_CUBEPITCHX    = 0.099165
PARTAG_CUBEPITCHY    = 0.099165
PARTAG_CUBEPITCHZ    = 0.099165
PARTAG_CUBEORIGINX   = 0
PARTAG_CUBEORIGINY   = 0
PARTAG_CUBEORIGINZ   = 0

----------------> Input Data Format
PARTAG_INPUTHEADERLEN   = 0
PARTAG_INPUTLOGGEDFLOAT = 0
PARTAG_INPUTISUNSIGNED = 0
PARTAG_INPUTREQSWAP = 0
PARTAG_TRANSPOSED_PRJ = 0
PARTAG_INPUTDOWNSAMPLE_X = 1
PARTAG_INPUTDOWNSAMPLE_Y = 1
PARTAG_CROP_UP       = 0
PARTAG_CROP_DOWN     = 0
PARTAG_CROP_LEFT     = 0
PARTAG_CROP_RIGHT    = 0

----------------> Preprocessing
PARTAG_AIRLEVEL   = 32000
PARTAG_SCALEFACTOR   = 700.000000
OPTTAG_AIRCAL     = 1
OPTTAG_LOG        = 1
OPTTAG_OFFSET     = 1
OPTTAG_FFT        = 1
OPTTAG_PARKER     = 1

OPTTAG_SLVERTFILT = 1
OPTTAG_VRTSMOOTH   = 0
PARTAG_PREPROSMOOTHFACTOR   = 0
PARTAG_PREPROSMOOTHAPRTHRZ   = 0
PARTAG_PREPROSMOOTHAPRTVRT   = 0
OPTTAG_ZFILTER00 = 0
OPTTAG_ZFILTER01 = 0
OPTTAG_ZFILTER02 = 0
OPTTAG_ZFILTER03 = 0
OPTTAG_ZFILTER04 = 0
OPTTAG_ZFILTER05 = 0
OPTTAG_ZFILTER06 = 0
OPTTAG_ZFILTER07 = 0
OPTTAG_ZFILTER08 = 0
OPTTAG_ZFILTER09 = 0
OPTTAG_ZFILTER10 = 0
OPTTAG_ZFILTER11 = 0
OPTTAG_ZFILTER12 = 0
OPTTAG_ZFILTER13 = 0
OPTTAG_ZFILTER14 = 0
OPTTAG_ZFILTER15 = 0
OPTTAG_FILTERNUM   = 1
PARTAG_BHFACTOR0   = 0.000000
PARTAG_BHFACTOR1   = 0.000000
PARTAG_BHFACTOR2   = 0.000000
PARTAG_BHFACTOR3   = 0.000000
OPTTAG_DEADPIXDETECT  = 1
OPTTAG_PROTRUSIONCMODE   = 1
PARTAG_SCATTERCORRFACTOR_P0= 0.000000
PARTAG_SCATTERCORRFACTOR_P1= 1.000000

----------------> Back-Projecting Procedure
BPMODETAG_LINITRP
BPMODETAG_USE_GPU
BPMODETAG_CONEBEAM = 1
MODE_OFFLINE = 1
PARTAG_DUMPVOLBG   = 0

----------------> Extended Field of View
PARTAG_SHOWEXTRA     = 1
PARTAG_EXTRAFOVSLICE     = 0
PARTAG_HBTC = 0
PARTAG_3XVIEW     = 0
PARTAG_FASTEXTVIEW      = 0
PARTAG_STACKEDVOLQTY         = 1
PARTAG_STACKEDVOLMODE        = 0
PARTAG_STACKEDVOLOVERLAP  = 33
PARTAG_STACKEDVOLDIRECTION= 1
PARTAG_STACKEDVOLADJUSTFACTOR= 100
PARTAG_STACKEDVOLSEAMLOCATION= 0
PARTAG_PROJ_RECON0           = 360
PARTAG_PROJ_RECON1           = 0
PARTAG_PROJ_RECON2           = 0
PARTAG_PROJ_RECON3           = 0
PARTAG_PROJ_RECON4           = 0
PARTAG_PROJ_RECON5           = 0
PARTAG_PROJ_RECON6           = 0
PARTAG_PROJ_RECON7           = 0
PARTAG_PROJ_RECON8           = 0
PARTAG_PROJ_RECON9           = 0
PARTAG_PROJ_RECON10          = 0
PARTAG_PROJ_RECON11          = 0
PARTAG_PRJ_STARTFROM_3X   = 0
PARTAG_PRJ_RECON_FORWARD_3X   = 180
PARTAG_DET_OFFSET_U_3XEXT = 0.000000
PARTAG_DET_OFFSET_V_3XEXT = -1111111.000000
PARTAG_ANGULARCORRECTION_3X = 0.000000

----------------> Post-Reconstruction Corrections
PARTAG_POSTPROFACTOR     = 0
PARTAG_INTERCUBESIZE = 0
PARTAG_SLICE_AUTOWATER   = 0000
PARTAG_DERINGON   = 0000
PARTAG_DERINGAPERTUREX   = 0010
PARTAG_DERINGTHRESHOLD   = 0040

----------------> Iterative Correction Algorithms
OPTTAG_CFA = 0
SAMARATAG_HIGHCONTRASTLEVEL   = 0
SAMARATAG_LOWCONTRASTLEVEL   = 0
SAMARATAG_HIDENSLEVEL           = 0
SAMARATAG_TOOTHDENSLEVEL      = 0
SAMARATAG_SMALLDETAILSIZE     = 0
OPTTAG_TOMOSYN                 = 0000
PARTAG_FP_GPU                 = 0000

----------------> Volumetric Data Format
OPTTAG_SLICESCALE    = 1.475400
OPTTAG_GAMMASLICESCALE   = 1.000000
PARTAG_MINUS1000     = 0
PARTAG_SLICEOFFSETVALUE     = -1000
PARTAG_DICOM     = 0
PARTAG_NEGATIVE_DENIED     = 0
PARTAG_SLICEFLIPX   = 0
PARTAG_SLICEFLIPY   = 0
PARTAG_SLICEFLIPZ   = 0

----------------> Naming and Folders
PARTAG_PRJSTARTFROM = 0
PARTAG_UNIFSLICELOCATION   = 1
PARTAG_SRCDATAPATH   = C:\CT_DATA\NIH\NIH MIF Test Data\09_12_03_1627\CTscan_[2009-12-03-12h-04m-41s]
OPTTAG_PRJNAMEFORMAT   = 09_12_03_1627_v1.cat
PARTAG_DSTDATAPATH   = C:\CT_DATA\NIH\NIH MIF Test Data\09_12_03_1627\CTscan_[2009-12-03-12h-04m-41s]

OPTTAG_SLCNAMEFORMAT   = %04i.slice

----------------> System
OPTTAG_3DBUFFERSIZE   = -1
OPTTAG_ENGINEQTY   = 1

----------------> Special COBRA Use
PARTAG_CATFORMAT = 1


Example. Original xxm (all parameters applied by COBRA 7.3.xx ) from Inveon system. The parameters that need care are highlighted

----------------> Scanner Geometry
PARTAG_SRCOBJDIST    = 266.339996
PARTAG_SRCDETDIST    = 334.410004
PARTAG_SCANANGLE     = 360.000000
PARTAG_STARTANGLE    = 0.000000
PARTAG_INVERSEANGLE  = 0.000000
PARTAG_PROJACQUIRED  = 360
PARTAG_PROJRECON     = 359

PARTAG_DETSIZEU      = 640
PARTAG_DETSIZEV      = 992
PARTAG_DETOFFSETU    = 2.733017
PARTAG_DETOFFSETV    = 0.000000
PARTAG_DETPITCHU     = 0.124510
PARTAG_DETPITCHV     = 0.124510
PARTAG_DETPIVOT      = 0.000000
PARTAG_OFFSET        = 0
PARTAG_ROTATIONDIR   = 1
PARTAG_HELICAL_SPEED = 0.000000

----------------> Reconstructed Volume
PARTAG_CUBESIZEX     = 640
PARTAG_CUBESIZEY     = 640
PARTAG_CUBESIZEZ     = 992
PARTAG_CUBEPITCHX    = 0.099165
PARTAG_CUBEPITCHY    = 0.099165
PARTAG_CUBEPITCHZ    = 0.099165
PARTAG_CUBEORIGINX   = 0
PARTAG_CUBEORIGINY   = 0
PARTAG_CUBEORIGINZ   = 0

----------------> Input Data Format
PARTAG_INPUTHEADERLEN   = 0
PARTAG_INPUTLOGGEDFLOAT = 1
PARTAG_INPUTISUNSIGNED = 0
PARTAG_INPUTREQSWAP = 0
PARTAG_TRANSPOSED_PRJ = 0
PARTAG_INPUTDOWNSAMPLE_X = 1
PARTAG_INPUTDOWNSAMPLE_Y = 1
PARTAG_CROP_UP       = 0
PARTAG_CROP_DOWN     = 0
PARTAG_CROP_LEFT     = 0
PARTAG_CROP_RIGHT    = 0

----------------> Preprocessing
PARTAG_AIRLEVEL   = 32000
PARTAG_SCALEFACTOR   = 700.000000
OPTTAG_AIRCAL      = 0
OPTTAG_LOG            = 0
OPTTAG_OFFSET     = 0
OPTTAG_FFT             = 1
OPTTAG_PARKER    = 0

OPTTAG_SLVERTFILT = 1
OPTTAG_VRTSMOOTH   = 0
PARTAG_PREPROSMOOTHFACTOR   = 0
PARTAG_PREPROSMOOTHAPRTHRZ   = 0
PARTAG_PREPROSMOOTHAPRTVRT   = 0
OPTTAG_ZFILTER00 = 0
OPTTAG_ZFILTER01 = 0
OPTTAG_ZFILTER02 = 0
OPTTAG_ZFILTER03 = 0
OPTTAG_ZFILTER04 = 0
OPTTAG_ZFILTER05 = 0
OPTTAG_ZFILTER06 = 0
OPTTAG_ZFILTER07 = 0
OPTTAG_ZFILTER08 = 0
OPTTAG_ZFILTER09 = 0
OPTTAG_ZFILTER10 = 0
OPTTAG_ZFILTER11 = 0
OPTTAG_ZFILTER12 = 0
OPTTAG_ZFILTER13 = 0
OPTTAG_ZFILTER14 = 0
OPTTAG_ZFILTER15 = 0
OPTTAG_FILTERNUM   = 1
PARTAG_BHFACTOR0   = 0.000000
PARTAG_BHFACTOR1   = 0.000000
PARTAG_BHFACTOR2   = 0.000000
PARTAG_BHFACTOR3   = 0.000000
OPTTAG_DEADPIXDETECT  = 1
OPTTAG_PROTRUSIONCMODE   = 1
PARTAG_SCATTERCORRFACTOR_P0= 0.000000
PARTAG_SCATTERCORRFACTOR_P1= 1.000000

----------------> Back-Projecting Procedure
BPMODETAG_LINITRP
BPMODETAG_CONEBEAM = 1
MODE_INLINE = 1
PARTAG_DUMPVOLBG   = 0

----------------> Extended Field of View
PARTAG_SHOWEXTRA     = 0
PARTAG_EXTRAFOVSLICE     = 0
PARTAG_HBTC = 0
PARTAG_3XVIEW     = 0
PARTAG_FASTEXTVIEW      = 0
PARTAG_STACKEDVOLQTY         = 1
PARTAG_STACKEDVOLMODE        = 0
PARTAG_STACKEDVOLOVERLAP  = 33
PARTAG_STACKEDVOLDIRECTION= 1
PARTAG_STACKEDVOLADJUSTFACTOR= 100
PARTAG_STACKEDVOLSEAMLOCATION= 0
PARTAG_PROJ_RECON0           = 360
PARTAG_PROJ_RECON1           = 0
PARTAG_PROJ_RECON2           = 0
PARTAG_PROJ_RECON3           = 0
PARTAG_PROJ_RECON4           = 0
PARTAG_PROJ_RECON5           = 0
PARTAG_PROJ_RECON6           = 0
PARTAG_PROJ_RECON7           = 0
PARTAG_PROJ_RECON8           = 0
PARTAG_PROJ_RECON9           = 0
PARTAG_PROJ_RECON10          = 0
PARTAG_PROJ_RECON11          = 0
PARTAG_PRJ_STARTFROM_3X   = 0
PARTAG_PRJ_RECON_FORWARD_3X   = 180
PARTAG_DET_OFFSET_U_3XEXT = 0.000000
PARTAG_DET_OFFSET_V_3XEXT = -1111111.000000
PARTAG_ANGULARCORRECTION_3X = 0.000000

----------------> Post-Reconstruction Corrections
PARTAG_POSTPROFACTOR     = 0
PARTAG_INTERCUBESIZE = 0
PARTAG_SLICE_AUTOWATER   = 0000
PARTAG_DERINGON   = 0000
PARTAG_DERINGAPERTUREX   = 0010
PARTAG_DERINGTHRESHOLD   = 0040

----------------> Iterative Correction Algorithms
OPTTAG_CFA = 0
SAMARATAG_HIGHCONTRASTLEVEL   = 0
SAMARATAG_LOWCONTRASTLEVEL   = 0
SAMARATAG_HIDENSLEVEL           = 0
SAMARATAG_TOOTHDENSLEVEL      = 0
SAMARATAG_SMALLDETAILSIZE     = 0
OPTTAG_TOMOSYN                 = 0000
PARTAG_FP_GPU                 = 0000

----------------> Volumetric Data Format
OPTTAG_SLICESCALE    = 1.475400
OPTTAG_GAMMASLICESCALE   = 1.000000
PARTAG_MINUS1000     = 0
PARTAG_SLICEOFFSETVALUE     = -1000
PARTAG_DICOM     = 0
PARTAG_NEGATIVE_DENIED     = 0
PARTAG_SLICEFLIPX   = 0
PARTAG_SLICEFLIPY   = 0
PARTAG_SLICEFLIPZ   = 0

----------------> Naming and Folders
PARTAG_PRJSTARTFROM = 0
PARTAG_UNIFSLICELOCATION   = 1
PARTAG_SRCDATAPATH   = c:\data
OPTTAG_PRJNAMEFORMAT   = raw.%04i
PARTAG_DSTDATAPATH   = c:\images
OPTTAG_SLCNAMEFORMAT   = %04i.slice

----------------> System
OPTTAG_3DBUFFERSIZE   = -1
OPTTAG_ENGINEQTY   = 1

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