Re: [Stir-users] which sinogram format is created by siemens scanner (ECAT 962)?

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Dear Thomas,

It just looks like a truncated file. There is a sinogram header in there but the data tag seems to be truncated. This is causing the DICOM parse error because which produces an EOF error on the first pass..

Based on the sinogram header I can see from "cat Recovery.ptd", you files should be about 120Mb in size. 336*336*559*2/(1024*1024)

On 01/04/2012, at 6:14 AM, thomas layer wrote:

> dear all, sorry for sending two mails just containing an attachment!
> i try to send my text now without attachment hoping this works.
> 
> i used gdcmraw -i Recovery.ptd -t 0029,1010 -o binarydata which gave the output
> 
> Failed to read: Recovery.ptd
> 
> also using gdcm from inside an ipython shell does not support the format as it is with the vtkDICOM packages.
> 
> after searching the mailing list for ecat8 i employed ifheaders_for_ecat7 resulting in:
> 
> WARNING: FactoryRegistry:: overwriting previous value of key in registry.
>     key: None
> Warning: improper or missing value for isotopem) in the main header
> Recovery_SINO.ptd: Invalid argument
> 
> for me this looks like there is no problem with the dicom part of the header but with the interfile entries. therefore i have cut the last lines of the sinogram data which seems for me to be header information and attached to the last two empty mails hoping somebody could have a quick look into it.
> 
> thanks and kind regards, thomas.
> 
> -------- Original-Nachricht --------
> Datum: Fri, 30 Mar 2012 10:18:30 +0100
> Von: "Kris Thielemans" <kr...@as...>
> An: "\'Robert Barnett\'" <rba...@un...>
> CC: "\'thomas layer\'" <tho...@gm...>
> Betreff: RE: [Stir-users] which sinogram format is created by siemens	scanner (ECAT 962)?
> 
> 
> I'm reluctant to put non-public info on the STIR wiki. So I had a quick look
> at this,.
> 
> The Siemens dicom conformance statement
> <http://www.medical.siemens.com/siemens/en_GLOBAL/rg_marcom_FBAs/files/broch
> ures/DICOM/nm/DICOMConformanceStatement2011A.pdf>
> only mentions
> (7FE1,xx10) SIEMENS CSA NON-IMAGE CSA Data (p174) which is "Binary data as
> byte stream." (p185)
> (0029,xx10) SIEMENS CSA HEADER (Manufacturer Model dependent information).
> (p175)
> P185 has a bit more information on other CSA related fields.
> 
> So I guess you could say something on the wiki like "Empirical evidence
> shows that", quoting the conformance statement above (but adding a nice
> caveat). What do you think?
> 
> I guess that gdcmdump will indeed dump these attributes, but probably only
> for MRI. Might be worth a try though.
> http://gdcm.sourceforge.net/html/gdcmdump.html
> 
> Could one of you try that first? If it works, great. If it doesn't, a
> possible solution would be to use
> 
> gdcmraw -i file -0029,1010 -o binarydata
> 
> but that's obviously more explicit.
> 
> Kris
> 
> PS: by the way, I did like your last sentence...
> 
>> -----Original Message-----
>> From: Robert Barnett [mailto:rba...@un...]
>> Sent: 30 March 2012 08:41
>> To: kr...@as...
>> Cc: thomas layer
>> Subject: Re: [Stir-users] which sinogram format is created by siemens
>> scanner (ECAT 962)?
>> 
>> 
>> No, sorry I do not know of any published format, however it does seems to
>> be a common format across Siemens MR/CT and PET.
>> 
>> I noticed that recent versions of gdcmdump had an option for dumping the
>> Siemens data, but I hadn't bothered to test it out.
>> 
>> Perhaps I could add something in the wiki pointing users to the gdcm
>> package? That shouldn't cause a stir.
>> 
>> Robbie
>> 
>> On 30/03/2012, at 6:14 PM, Kris Thielemans wrote:
>> 
>>> Hi Robbie
>>> 
>>> Do you know if this info is published somewhere by Siemens? E.g. in
> their
>>> dicom conformance statement. If so,  we could put it on the wiki or so.
>>> 
>>> I'm guessing that your java code just dumps the content of the tag? Then
>> we
>>> could use gdcmdump or equivalent for those that don't have java.
>>> 
>>>> -----Original Message-----
>>>> From: sti...@li... [mailto:stir-users-
>>>> bo...@li...] On Behalf Of Robert Barnett
>>>> Sent: 30 March 2012 07:27
>>>> To: thomas layer
>>>> Cc: Stir Users
>>>> Subject: Re: [Stir-users] which sinogram format is created by siemens
>>>> scanner (ECAT 962)?
>>>> 
>>>> 
>>>> Sounds like the file you have is a DICOM file with the interfile header
>>> and
>>>> data encapsulated in the DICOM tags.
>>>> 
>>>> The SOP Class UID should be 1.3.12.2.1107.5.9.1but I am not sure what
> it
>>>> would be on your system.
>>>> The interfile data is stored in the dicom tag: 0x7FE11010
>>>> The interfile header is stored in the dicom tag: 0x00291010
>>>> 
>>>> I have some java code to read (and write) these kind of files. Once
> you've
>>>> extracted these files, you'll need to change the interfile header into
> one
>>> that
>>>> is understood by STIR.
>>>> 
>>>> Robbie
>>>> 
>>>> On 30/03/2012, at 12:18 PM, thomas layer wrote:
>>>> 
>>>>> dear Stir users!
>>>>> 
>>>>> i want to reconstruct a PET sinogram yielded from a Siemens Biograph
> 64
>>>> True Point scanner which i think is of type ECAT 962.
>>>>> i expected that the output format will be of ECAT7 type but instead i
>>> got a
>>>> file ending with .ptd. a check with "is_ecat7_file" says no.
>>>>> looking into the file with a hex editor shows a header on the last
> lines
>>>> looking like a combination of dicom header interrupted by a interfile
>>> header.
>>>>> deleting the dicom part and cutting out the interfile part making a
>>> header
>>>> file also screwed up.
>>>>> is somebody having experience with siemens output data processing
>> with
>>>> stir?
>>>>> 
>>>>> thanks and kind regards, thomas
>>>>> --
>>>>> NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone!
>>>>> Jetzt informieren:
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>>>>> 
>>>>> 
>>> 
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> 
> 
> 
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