[Fwd: Re: [Dcmlib] GetPatSliceOrient(gdcm::File &h) (BIS)]

[Luca Picello]

Hi JP,

I believe I wrote my code exactly as you suggest to do.
And I believe it happens exactly what you describe (images are ignored).
Here we can open another parenthesis on how to choose the right slices 
to build the volume ;-)
the anonimized dataset can be downloaded at 
http://www.surgisystems.com/ST1.zip [about 40 megabytes]

cya,
Luca



Jean-Pierre ROUX wrote:

>> Hello everybody.
>> I see you are playing with orientation....
>> I have some new datasets to test...
>> Some are total-body and I can see something strange (to me at least):
>> in the same dicomdir images are oriented differently.
>> thus, the reader return only few slices when I have many and many of 
>> them....
>> does it suggest to you something?
>
>
> Hi, Luca.
> How do you use vtkgdcmreader?
> -->The 'usual' way (passing info to build the file names) considers 
> the orientation of the *first* image and discards any image with a 
> different orientation, considering it's a bugged image (?!?)
> (This feature was written a ling time ago ...)
>
> -->You may now pass a CoherentFileList (result of gdcm::SerieHelper 
> -that may build more than one SerieHelper-)
> Normaly (?), within a CoherentFileList (same "Serie Instance UID"), 
> you should have the same orientation.
>
> (note : this is not 100% true, since for MR studies, a single serie 
> may hold all the 'scout views', with 2 or 3 diferrent orientations 
> -but never anybody will try use scout view as 'slices' to make a volume-)
>
> If this new feature doesn't help you, could you upload your images 
> somewhere, so we can have a look at them.
> (use
> AnonymizeNoLoad dirin=yourSinglePatientImageDirectory
> to anomymize the whole directory)
>
> Thx
>
> JP
>
>
>
>
>>
>> luca
>>
>>
>>
>> Mathieu Malaterre wrote:
>>
>>> Mathieu Malaterre wrote:
>>>
>>>> Jean-Pierre Roux wrote:
>>>>
>>>>> Jean-Pierre Roux wrote:
>>>>>
>>>>>> Mathieu Malaterre wrote:
>>>>>>
>>>>>>
>>>>>> I had a look a Xmedcon's code a few years ago.
>>>>>> I gave it up, since they use :
>>>>>> Patient Orientation (0020,0020),  (Optional Tag for MR, CT,, etc)
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --> Sorry : actually they use PatientPosition (0x0010,0x5100)
>>>>> assumed to be equal to "HF" or "FF".
>>>>>
>>>>> In *all* the images I have, it "HFS " or "FFS "  (S for supine 
>>>>> -the guy is lying on his back- , You can also have P, for Prone).
>>>>>
>>>>>
>>>>> Moreover, on MR, you can have *any* value -1< <+1 for the cosines  :
>>>>>
>>>>> ImageOrientationPatient (0x0020,0x0037)= [ 
>>>>> -0.002378\0.999985\0.004852\0.030516\0.004923\-0.999522]
>>>>>
>>>>> an other image shows me :
>>>>>
>>>>> ImageOrientationPatient (0x0020,0x0037)= 
>>>>> [0.569486\0.822001\0.000000\-0.000000\0.000000\-1.000000 ]
>>>>>
>>>>> JP
>>>>>
>>>>>
>>>>>> and the suppose the only values for cosines inside "Image 
>>>>>> Orientation (Patient)" (0020,0037) are -1, 0, +1 !
>>>>>>
>>>>>> Have a look  at :
>>>>>> http://www.dclunie.com/medical-image-faq/html/part2.html#DICOMOrientation 
>>>>>>
>>>>>>
>>>>>> It *computes* the "Patient Orientation" from "Image Orientation 
>>>>>> (Patient)" ...
>>>>>>
>>>>>> gdcm uses David Clunie's code in the method :
>>>>>> std::string Orientation::GetOrientation ( File *f )
>>>>>
>>>>>
>>>>
>>>>
>>>> I have to say I am clueless. How exactly does this thing works. For 
>>>> instance, SIEMENS_Sonata-16-MONO2-Value_Multiplicity.dcm
>>>>
>>>> I get:
>>>> V 0018|5100 [CS]                       [Patient Position] [HFS ]
>>>>
>>>>
>>>> but gdcm returns:
>>>> Orientation [LHP\PF]
>>>>
>>>> What does LHP stand for ? How about PF ?
>>>
>>>
>>>
>>> Ok forget that mail, I have a strong headache and I don't understand 
>>> what I am saying anymore (Position != Orientation). I'll play with 
>>> Orientation a little more after resting.
>>>
>>> sorry for the noise
>>> Mathieu
>>> _______________________________________________
>>> Dcmlib mailing list
>>> Dcmlib at creatis.insa-lyon.fr
>>> http://www.creatis.insa-lyon.fr/mailman/listinfo/dcmlib
>>> .
>>>
>>
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>
>
>   Jean-Pierre ROUX
>   CREATIS - CNRS UMR 5515, INSERM U 630
>   Laboratoire de Radiologie Experimentale
>   Hopital Cardiologique
>   28 Avenue du Doyen LEPINE
>   B.P. Lyon-Montchat
>   69394 Lyon Cedex 03
>
>   Tel      : (+33) 04 72 35 74 12
>   Fax      : (+33) 04 72 68 49 16
>   URL      : http://www.creatis.univ-lyon1.fr
>   e-mail   : jpr at creatis.univ-lyon1.fr
>                                    .
>