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Re: [Stir-users] conversion of real images to STIR Interfile
|
From: <aga...@bi...> - 2012-09-15 17:52:36
|
Hi Kris
please ignore the previous email. I have fixed the problem.
thanks a lot
tasos
> Hi Kris
> thanks for your advices. I changed the .h33 file manually according to the
> template of the .hv and now my file works.
>
> The only problem is that the reconstructed image has different size with
> the initial. I have found a discussion in the mailing list under the title
> "FBP3DRP output image dimensions", but I think this is different from my
> case (I use data from Biograph 6).
>
> Actually when I do list_image_info for both initial and reconstructed
> images I got the following:
>
> tasos@Tasos-Notebook:~/STIR/TASOS/Patient_Data_AA/test$ list_image_info
> PETimages_AA.h33 (This is the initial image)
>
> WARNING: interfile parsing: setting origin to (z=0,y=5.27521,x=5.27521)
>
> Origin in mm {z,y,x} :{0, 5.27521, 5.27521}
> Voxel-size in mm {z,y,x}:{2, 4.0628, 4.0628}
> Min_indices {z,y,x} :{0, -84, -84}
> Max_indices {z,y,x} :{343, 83, 83}
> Number of voxels {z,y,x}:{344, 168, 168}
> Physical coordinate of first index in mm {z,y,x} :{0, -336, -336}
> Physical coordinate of last index in mm {z,y,x} :{686, 342.488, 342.488}
> Physical coordinate of first edge in mm {z,y,x} :{-1, -338.031, -338.031}
> Physical coordinate of last edge in mm {z,y,x} :{687, 344.519, 344.519}
> Image min: 0
> Image max: 83543.5
> Image sum: 4.12364e+09
>
> and
>
> tasos@Tasos-Notebook:~/STIR/TASOS/Patient_Data_AA/test$ list_image_info
> OSMAPOSL_AA_NAC_1iter_4.hv (this is the reconstructed image)
>
> Origin in mm {z,y,x} :{0, 0, 0}
> Voxel-size in mm {z,y,x}:{2, 2, 2}
> Min_indices {z,y,x} :{0, -168, -168}
> Max_indices {z,y,x} :{80, 168, 168}
> Number of voxels {z,y,x}:{81, 337, 337}
> Physical coordinate of first index in mm {z,y,x} :{0, -336, -336}
> Physical coordinate of last index in mm {z,y,x} :{160, 336, 336}
> Physical coordinate of first edge in mm {z,y,x} :{-1, -337, -337}
> Physical coordinate of last edge in mm {z,y,x} :{161, 337, 337}
> Image min: 0
> Image max: 6982.32
> Image sum: 2.52619e+09
>
> I am wondering why for the initial image I got this warning message:
> WARNING: interfile parsing: setting origin to (z=0,y=5.27521,x=5.27521)
>
> When I check the origin of this image in Amide the origin seems to be
> (0,0,0). I found that this can be changed, changing the "first pixel
> offset" parameters, but I am afraid that I make a mistake somwhere...
> Any help?
> thank you very much
>
>> Hi Taso
>>
>> A clue is given by
>>
>> WARNING: KeyParser: the list corresponding to the keyword "matrix size"
>> has to be resized to size 1. This might mean you have a problem in the
>> keyword values
>>
>> you forgot the " number of dimensions" keyword. Below are some other
>> corrections.
>>
>> number of dimensions := 3
>> !matrix size [1] := 274
>> !matrix size [2] := 274
>> % use this instead of "total number of images"
>> !matrix size [3]:= 344
>> % not sure if STIR will undertand the 2.5e+0 notation. If not, edit and
>> just
>> use 2.5
>> scaling factor (mm/pixel) [1] := +2.500000e+000
>> scaling factor (mm/pixel) [2] := +2.500000e+000
>> % use this instead of " slice thickness (pixels)"
>> scaling factor (mm/pixel) [3] := +2.500000e+000
>>
>> % STIR will interpret this as relative to where the header is (I think).
>> Far
>> better to put
>> % your header in the same location as the data-file, and use no path
>> here.
>> !name of data file := tasos/STIR/TASOS/Patient_Data_AA/tasos_test.i33
>>
>> If that still doesn't work, have a look at any output of STIR and check
>> keywords there.
>>
>> Kris
>>
>>>
>>> Please have a look of the header:
>>>
>>> !INTERFILE :=
>>> !imaging modality := nucmed
>>> !originating system := (X)MedCon
>>> date of keys := 1996:09:24
>>> conversion program := (X)MedCon
>>> program author := Erik Nolf
>>> program version := 0.10.7
>>> program date := 2010:09:15
>>> ;
>>> !GENERAL DATA :=
>>> original institution := NucMed
>>> !data offset in bytes[1] := 0
>>> !name of data file := tasos/STIR/TASOS/Patient_Data_AA/tasos_test.i33
>>> patient name := A^A
>>> !patient ID := XXXX
>>> patient dob := XXXX:XX:XX
>>> patient sex := female
>>> !study ID := Unknown
>>> exam type := Unknown
>>> data compression := none
>>> data encode := none
>>> organ := Unknown
>>> isotope := Unknown
>>> dose := 257.738
>>> NUD/Patient Weight [kg] := 56.00
>>> NUD/imaging modality := PT
>>> NUD/activity := 257.738
>>> NUD/activity start time := 00:00:00
>>> NUD/isotope half life [hours] := 0.000000
>>> ;
>>> !GENERAL IMAGE DATA :=
>>> !type of data := PET
>>> !total number of images := 344
>>> study date := 0000:00:00
>>> study time := 00:00:00
>>> imagedata byte order := LITTLEENDIAN
>>> process label := Unknown
>>> ;
>>> quantification units := +1.000000e+000
>>> NUD/rescale slope := +1.000000e+000
>>> NUD/rescale intercept := +0.000000e+000
>>> ;
>>> number of energy windows := 1
>>> ;
>>> energy window [1] :=
>>> energy window lower level [1] :=
>>> energy window upper level [1] :=
>>> flood corrected := N
>>> decay corrected := N
>>> ;
>>> ;!SPECT STUDY (general) :=
>>> ;number of detector heads := 1
>>> ;
>>> !number of images/energy window := 344
>>> !process status := Reconstructed
>>> !matrix size [1] := 274
>>> !matrix size [2] := 274
>>> !number format := short float
>>> !number of bytes per pixel := 4
>>> scaling factor (mm/pixel) [1] := +2.500000e+000
>>> scaling factor (mm/pixel) [2] := +2.500000e+000
>>> !number of projections := 344
>>> !extent of rotation :=
>>> !time per projection (sec) := 0.5232558
>>> study duration (sec) := 180
>>> !maximum pixel count := +8.354347e+004
>>> patient orientation := head_in
>>> patient rotation := supine
>>> ;
>>> !PET STUDY (reconstructed data) :=
>>> method of reconstruction := Unknown
>>> !number of slices := 344
>>> number of reference frame := 0
>>> slice orientation := Transverse
>>> slice thickness (pixels) := +1.000000e+000
>>> centre-centre slice separation (pixels) := +1.000000e+000
>>> filter name := Unknown
>>> filter parameters := Cutoff
>>> method of attenuation correction := measured
>>> scatter corrected := N
>>> oblique reconstruction := N
>>> !END OF INTERFILE :=
>>>
>>> Using this header with list_image_info utility, the result is:
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: imaging modality
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: version of keys
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: date of keys
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: conversion program
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: program author
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: program version
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: program date
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: original institution
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: patient name
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: patient id
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: patient dob
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: patient sex
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: study id
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: exam type
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: data compression
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: data encode
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: organ
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: isotope
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: dose
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: nud/patient weight
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: nud/imaging modality
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: nud/activity
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: nud/activity start
>>> time
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: nud/isotope half life
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: total number of
>>> images
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: study date
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: study time
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: process label
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: nud/rescale slope
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: nud/rescale intercept
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: number of energy
>>> windows
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: energy window
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: energy window lower
>>> level
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: energy window upper
>>> level
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: flood corrected
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: decay corrected
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: number of
>>> images/energy
>>> window
>>>
>>>
>>> WARNING: KeyParser: the list corresponding to the keyword "matrix size"
>>> has to be resized to size 1. This might mean you have a problem in the
>>> keyword values.
>>>
>>>
>>> WARNING: KeyParser: the list corresponding to the keyword "matrix size"
>>> has to be resized to size 2. This might mean you have a problem in the
>>> keyword values.
>>>
>>> KeyParser warning : value of keyword "number format" is "short float"
>>> should have been one of:
>>> bit
>>> ascii
>>> signed integer
>>> unsigned integer
>>> float
>>>
>>>
>>> WARNING: KeyParser: the list corresponding to the keyword "scaling
>>> factor
>>> (mm/pixel)" has to be resized to size 1. This might mean you have a
>>> problem in the keyword values.
>>>
>>>
>>> WARNING: KeyParser: the list corresponding to the keyword "scaling
>>> factor
>>> (mm/pixel)" has to be resized to size 2. This might mean you have a
>>> problem in the keyword values.
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: number of
>>> projections
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: extent of rotation
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: time per projection
>>> (sec)
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: study duration (sec)
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: patient rotation
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: pet study
>>> (reconstructed
>>> data)
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: method of
>>> reconstruction
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: number of slices
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: number of reference
>>> frame
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: slice orientation
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: slice thickness
>>> (pixels)
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: centre-centre slice
>>> separation (pixels)
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: filter name
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: filter parameters
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: method of
>>> attenuation
>>> correction
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: scatter corrected
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: oblique
>>> reconstruction
>>>
>>>
>>> WARNING: Interfile internal error: 'number_format_index' out of range
>>>
>>> Segmentation fault (core dumped)
>>>
>>>
>>> the manip_image utility:
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: imaging modality
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: version of keys
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: date of keys
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: conversion program
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: program author
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: program version
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: program date
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: original institution
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: patient name
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: patient id
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: patient dob
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: patient sex
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: study id
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: exam type
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: data compression
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: data encode
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: organ
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: isotope
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: dose
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: nud/patient weight
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: nud/imaging modality
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: nud/activity
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: nud/activity start
>>> time
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: nud/isotope half life
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: total number of
>>> images
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: study date
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: study time
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: process label
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: nud/rescale slope
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: nud/rescale intercept
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: number of energy
>>> windows
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: energy window
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: energy window lower
>>> level
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: energy window upper
>>> level
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: flood corrected
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: decay corrected
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: number of
>>> images/energy
>>> window
>>>
>>>
>>> WARNING: KeyParser: the list corresponding to the keyword "matrix size"
>>> has to be resized to size 1. This might mean you have a problem in the
>>> keyword values.
>>>
>>>
>>> WARNING: KeyParser: the list corresponding to the keyword "matrix size"
>>> has to be resized to size 2. This might mean you have a problem in the
>>> keyword values.
>>>
>>> KeyParser warning : value of keyword "number format" is "short float"
>>> should have been one of:
>>> bit
>>> ascii
>>> signed integer
>>> unsigned integer
>>> float
>>>
>>>
>>> WARNING: KeyParser: the list corresponding to the keyword "scaling
>>> factor
>>> (mm/pixel)" has to be resized to size 1. This might mean you have a
>>> problem in the keyword values.
>>>
>>>
>>> WARNING: KeyParser: the list corresponding to the keyword "scaling
>>> factor
>>> (mm/pixel)" has to be resized to size 2. This might mean you have a
>>> problem in the keyword values.
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: number of
>>> projections
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: extent of rotation
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: time per projection
>>> (sec)
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: study duration (sec)
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: patient rotation
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: pet study
>>> (reconstructed
>>> data)
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: method of
>>> reconstruction
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: number of slices
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: number of reference
>>> frame
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: slice orientation
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: slice thickness
>>> (pixels)
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: centre-centre slice
>>> separation (pixels)
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: filter name
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: filter parameters
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: method of
>>> attenuation
>>> correction
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: scatter corrected
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: oblique
>>> reconstruction
>>>
>>>
>>> WARNING: Interfile internal error: 'number_format_index' out of range
>>>
>>> Segmentation fault (core dumped)
>>>
>>>
>>> and the fwdtest:
>>>
>>> Maximum absolute segment number to process: [0,2 D:2]: 2
>>> Output will be written to output_fwd and its Interfile header
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: imaging modality
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: version of keys
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: date of keys
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: conversion program
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: program author
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: program version
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: program date
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: original institution
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: patient name
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: patient id
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: patient dob
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: patient sex
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: study id
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: exam type
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: data compression
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: data encode
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: organ
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: isotope
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: dose
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: nud/patient weight
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: nud/imaging modality
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: nud/activity
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: nud/activity start
>>> time
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: nud/isotope half life
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: total number of
>>> images
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: study date
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: study time
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: process label
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: nud/rescale slope
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: nud/rescale intercept
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: number of energy
>>> windows
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: energy window
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: energy window lower
>>> level
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: energy window upper
>>> level
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: flood corrected
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: decay corrected
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: number of
>>> images/energy
>>> window
>>>
>>>
>>> WARNING: KeyParser: the list corresponding to the keyword "matrix size"
>>> has to be resized to size 1. This might mean you have a problem in the
>>> keyword values.
>>>
>>>
>>> WARNING: KeyParser: the list corresponding to the keyword "matrix size"
>>> has to be resized to size 2. This might mean you have a problem in the
>>> keyword values.
>>>
>>> KeyParser warning : value of keyword "number format" is "short float"
>>> should have been one of:
>>> bit
>>> ascii
>>> signed integer
>>> unsigned integer
>>> float
>>>
>>>
>>> WARNING: KeyParser: the list corresponding to the keyword "scaling
>>> factor
>>> (mm/pixel)" has to be resized to size 1. This might mean you have a
>>> problem in the keyword values.
>>>
>>>
>>> WARNING: KeyParser: the list corresponding to the keyword "scaling
>>> factor
>>> (mm/pixel)" has to be resized to size 2. This might mean you have a
>>> problem in the keyword values.
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: number of
>>> projections
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: extent of rotation
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: time per projection
>>> (sec)
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: study duration (sec)
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: patient rotation
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: pet study
>>> (reconstructed
>>> data)
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: method of
>>> reconstruction
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: number of slices
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: number of reference
>>> frame
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: slice orientation
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: slice thickness
>>> (pixels)
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: centre-centre slice
>>> separation (pixels)
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: filter name
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: filter parameters
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: method of
>>> attenuation
>>> correction
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: scatter corrected
>>>
>>>
>>> WARNING: KeyParser warning: unrecognized keyword: oblique
>>> reconstruction
>>>
>>>
>>> WARNING: Interfile internal error: 'number_format_index' out of range
>>>
>>> Segmentation fault (core dumped)
>>>
>>> >From all the above warnings, I've tried to fix some but the final
>>> error
>>> message (Segmentation fault) remains. That's why I attach the original
>>> warnings.
>>>
>>> What do you believe?
>>> Thank you very much
>>> Tasos
>>>
>>> > Hi Tasos
>>> >
>>> > What does your new header look like? What does any STIR utility (e.g.
>>> > list_image_info, manip_image, or indeed fwdtest) say when you try to
>>> use
>>> > your new header?
>>> >
>>> > Kris
>>> >
>>> > PS: my Ubuntu-AMIDE does have dcmtk. Maybe you need to install the
>>> dcmtk
>>> > package separately (or first)?
>>> >
>>> >> -----Original Message-----
>>> >> From: sti...@li... [mailto:stir-users-
>>> >> bo...@li...] On Behalf Of aga...@bi...
>>> >> Sent: 08 September 2012 08:03
>>> >> To: sti...@li...
>>> >> Subject: [Stir-users] conversion of real images to STIR Interfile
>>> >>
>>> >> Hi STIR users,
>>> >>
>>> >> I have access to real PET/CT images from a Siemens Biograph 6
>>> scanner
>>> >> and
>>> >> I would like to convert these images in STIR interfile. I've tried
>> using
>>> >> AMIDE but without success. The steps I followed were:
>>> >>
>>> >> 1. Using AMIDE (in Windows 7), I opened the images (File| Import
>>> File|
>>> >> DICOM via dcmtk) and then I saved them (File| Export Data Set|
>>> Export
>>> >> Format (Interfile 3.3)) and the images were stored as an .h33 file.
>>> >>
>>> >> 2. Following the guidelines given by Charalambos Tsoumpas (Mailing
>> List,
>>> >> Email Title: Conversion: Interfile 3.3 to Extended Interfile,
>> 2012-06-23
>>> >> 20:29) I changed some lines in the header file and I re-saved. The
>>> >> format
>>> >> (.h33) was the same.
>>> >>
>>> >> 3. I tried to open the .h33 file with AMIDE (in Ubuntu) but I got
>>> the
>>> >> following error messages:
>>> >> i. AMIDE_WARNING: Can't read file /media/Data/STIR/Real Patient's
>>> Data
>>> >> Aug
>>> >> 12/AA_test_Interfile.h33 with libmdc/(X)MedCon, and
>>> >> ii. AMIDE_WARNING: Could not import data sets from file
>>> >> /media/Data/STIR/Real Patient's Data Aug 12/AA_test_Interfile.h33
>>> >>
>>> >> 4. I also tried to fwd project my data using this .h33 file but
>>> without
>>> >> success.
>>> >>
>>> >> 5. I tried to repeat the steps 1 and 2 using AMIDE in Ubuntu but
>>> AMIDE
>>> >> is
>>> >> unable to open all the slice images. This happens because the choice
>>> >> (File| Import File| DICOM via dcmtk) doesn't exist and AMIDE opens
>>> only
>>> >> one slice.
>>> >>
>>> >> Do you have any suggestion? I will appreciate any help.
>>> >> Thanks in advance
>>> >> Tasos
>>> >>
>>> >>
>>> >>
>>> >
>> ----------------------------------------------------------------------------
>>> > --
>>> >> Live Security Virtual Conference
>>> >> Exclusive live event will cover all the ways today's security and
>>> >> threat landscape has changed and how IT managers can respond.
>>> >> Discussions
>>> >> will include endpoint security, mobile security and the latest in
>>> >> malware
>>> >> threats.
>>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>> >> _______________________________________________
>>> >> Stir-users mailing list
>>> >> Sti...@li...
>>> >> https://lists.sourceforge.net/lists/listinfo/stir-users
>>> >
>>> >
>>>
>>>
>>>
>>>
>> ----------------------------------------------------------------------------
>> --
>>> Live Security Virtual Conference
>>> Exclusive live event will cover all the ways today's security and
>>> threat landscape has changed and how IT managers can respond.
>>> Discussions
>>> will include endpoint security, mobile security and the latest in
>>> malware
>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>> _______________________________________________
>>> Stir-users mailing list
>>> Sti...@li...
>>> https://lists.sourceforge.net/lists/listinfo/stir-users
>>
>>
>
>
>
|
