[Stir-users] Image Reconstruction with OSMAPOSL

[anvariz <an...@ra...>]

Dear all stir users

I want to reconstruct my images with the following parameters with OSMAPOSL
and I use parameters bellow, but I get these warnings before starting to compute
sensitivity.
In both states of determining and not determining the  interfile output file
format parameters these warnings appear.
Is this parameter file suitable?

I appreciate very much any help.




WARNING: KeyParser warning: unrecognized keyword: output file format


WARNING: KeyParser warning: unrecognized keyword: interfile output file format
parameters


WARNING: KeyParser warning: unrecognized keyword: end interfile output file
format parameters


WARNING: KeyParser warning: unrecognized keyword: prior type


WARNING: Determined voxel size by dividing default_bin_size (3.375) by zoom

WARNING: WARNING: ProjMatrixByBinUsingRayTracing used for pixel size (in x,y)
that is larger than the bin size.
Backprojecting with this matrix might have artefacts at views 0 and 90 degrees.

    !INTERFILE  :=
    name of data file := static.v
    !GENERAL DATA :=
    !GENERAL IMAGE DATA :=
    !type of data := PET
    imagedata byte order := LITTLEENDIAN
    !PET STUDY (General) :=
    !PET data type := Image
    process status := Reconstructed
    !number format := float
    !number of bytes per pixel := 4
    number of dimensions := 3
    matrix axis label [1] := x
    !matrix size [1] := 256
    scaling factor (mm/pixel) [1] :=3.125
    matrix axis label [2] := y
    !matrix size [2] := 256
    scaling factor (mm/pixel) [2] := 3.125
    matrix axis label [3] := z
    !matrix size [3] := 125
    scaling factor (mm/pixel) [3] := 3.375
    number of time frames := 1
    image scaling factor[1] := 1
    data offset in bytes[1] := 0
    quantification units := 1
    !END OF INTERFILE :=

   OSMAPOSLParameters :=
  ;lines starting with semicolons are comments
   objective function type:= \
  PoissonLogLikelihoodWithLinearModelForMeanAndProjData
  PoissonLogLikelihoodWithLinearModelForMeanAndProjData Parameters:=
  ; input, sensitivity and prior parameters here
  input file := atn-c-s-sino.hs
 ; sensitivity related keywords
   sensitivity filename:=
   time frame definition filename:=
   time frame number:= 1
   recompute sensitivity := 1
   ; keywords for specifying the prior information
   prior type := None

   ; use -1 to use the maximum available
   maximum absolute segment number to process :=3
   zero end planes of segment 0 := 0
   ;keywords that specify the projectors to be used
   Projector pair type := Matrix
   Projector Pair Using Matrix Parameters :=
   Matrix type := Ray Tracing
     Ray Tracing Matrix Parameters:=
   number of rays in tangential direction to trace for each bin := 4
   End Ray Tracing Matrix Parameters:=
   End Projector Pair Using Matrix Parameters :=
   ; background (e.g. randoms)
    additive sinogram := 0

   ; next keywords can be used to specify image size, but will be removed
    zoom := 1.08
    ; use --1 for default sizes that cover the whole field of view
    XY output image size (in pixels) := 256
    end PoissonLogLikelihoodWithLinearModelForMeanAndProjData Parameters:=

   ; set output file format, if omitted a default value will be used
   Output file format := Interfile
   Interfile Output File Format Parameters :=
   ; byte order := little-endian
   ;number format := float
   ;number of bytes per pixel :=4
    End Interfile Output File Format Parameters :=
    enforce initial positivity condition:=0
    number of subsets:= 4
    number of subiterations:= 20
    start at subiteration number:=1
    output filename prefix := recon-atn-c-s
    save estimates at subiteration intervals:= 20
    ;uniformly randomise subset order:= 1
    ; keywords for preventing too drastic (multiplicative) updates
    ; below just set to their default values
    maximum relative change := 3.40282e+38
    minimum relative change := 0
    ; enabling this will write the multiplicative update images
    ; every sub-iteration
    ;write update image := 0
    inter-update filter subiteration interval := 0
    inter-update filter type := None
    inter-iteration filter subiteration interval := 20
    inter-iteration filter type := Separable Cartesian Metz
    Separable Cartesian Metz Filter Parameters :=
    x-dir filter FWHM (in mm) := 7.0
    y-dir filter FWHM (in mm) := 7.0
    z-dir filter FWHM (in mm) := 7.0
    x-dir filter Metz power := 0.0
    y-dir filter Metz power := 0.0
    z-dir filter Metz power := 0.0
    END Separable Cartesian Metz Filter Parameters :=
    post-filter type := None
    prior type := None
    END :=
    END :=











Thanks in advance
---
Zahra

--
Tehran University of Medical Sciences


--
Tehran University of Medical Sciences


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