[Insight-users] GDCM version upgrade plans for ITK4?

Sun Oct 28 18:42:35 EDT 2012

You should be able to start by building GDCM external to ITK, and using
the "USE_SYSTEM_GDCM" option to see if that gets you the features you
need.  That would take a lot less time than waiting for complete
integration into ITK.

Hans

On 10/28/12 1:43 PM, "Andriy Fedorov" <fedorov at bwh.harvard.edu> wrote:

>Hans,
>
>One specific feature I am interested in is the support of DICOM
>Segmentation storage and bit-encoded PixelData, which was added in
>2.2.0 (see more details in the attached exchange with Mathieu).
>
>Looking at the release notes, 2.2.0 also includes support for
>SurfaceSegmentation. All these improvements should allow better
>support of various types of DICOM in 3D Slicer. Currently, we are
>working on implementing support for Segmentation storage in Slicer,
>and we would essentially need to duplicate the functionality available
>in GDCM.
>
>Having said that, I have not yet tested the segmentation storage
>functionality in GDCM.
>
>I cc Steve in case he has any comments as to how updated GDCM could be
>relevant for the other Slicer-related projects.
>
>
>Here's my earlier communication with Mathieu:
>
>
>---------- Forwarded message ----------
>From: Mathieu Malaterre <mathieu.malaterre at gmail.com>
>Date: Sun, Oct 28, 2012 at 1:28 PM
>Subject: Re: GDCM support of DICOM SEG PixelData read/write
>To: Andriy Fedorov <fedorov at bwh.harvard.edu>
>Cc: gdcm-developers <gdcm-developers at lists.sourceforge.net>, Johan
>Moreau <johan.moreau at gmail.com>, Steve Pieper
><pieper at bwh.harvard.edu>, David Clunie <dclunie at dclunie.com>
>
>
>Andriy,
>
>  I have not been following ITK dev in a while, so I cant say much about
>it.
>
>regards
>
>On Sun, Oct 28, 2012 at 5:52 PM, Andriy Fedorov <fedorov at bwh.harvard.edu>
>wrote:
>> Mathieu,
>>
>> This sounds very promising!
>>
>> But it looks to me ITK4 is still using gdcm 2.0.17.
>>
>> I think the only way Slicer can benefit from the new functionality is
>> if it becomes available in ITK4.
>>
>> Do you know what is the plan (if there is one) of upgrading the gdcm
>> version in ITK4?
>>
>> --
>> Andriy Fedorov, Ph.D.
>>
>> Brigham and Women's Hospital
>> Harvard Medical School
>> 75 Francis Street
>> Boston, MA 02115 USA
>> fedorov at bwh.harvard.edu
>> (617) 525-6258 (office)
>>
>>
>> On Sun, Oct 28, 2012 at 4:32 AM, Mathieu Malaterre
>> <mathieu.malaterre at gmail.com> wrote:
>>> Andriy,
>>>
>>> On Fri, Oct 26, 2012 at 9:51 PM, Andriy Fedorov
>>><fedorov at bwh.harvard.edu> wrote:
>>>> Mathieu,
>>>>
>>>> As you probably know, currently Slicer relies on ITK3/GDCM for loading
>>>> DICOM images.
>>>>
>>>> Recently, we've been working on adding support for handling DICOM
>>>> segmentation objects, which essentially are multiframe images that can
>>>> have multiple segments encoded in one DICOM object, typically using
>>>> bitset encoding for pixel data.
>>>>
>>>> Currently, we load DICOM SEGs by first identifying the source image
>>>> series, loading it using our conventional ITK3/GDCM pipeline,
>>>> resetting the content and then uncompressing the bitset pixel buffer
>>>> into the image raster. This non-GDCM part of this pipeline is
>>>> implemented in a Slicer plugin that handles DICOM SEG objects.
>>>>
>>>> This current approach is suboptimal for various reasons: we may not
>>>> have the source image series reference in the DICOM object and ideally
>>>> should use shared and per-frame functional groups sequences to
>>>> reconstruct the geometry, and also a module in Slicer is probably not
>>>> the right place to do low-level DICOM operations like encoding of the
>>>> bitset and handling of DICOM frames.
>>>>
>>>> So, my question to you is whether there are any plans to support
>>>> reading and writing of the pixel data frames stored in DICOM SEG
>>>> objects?
>>>
>>> It is included in GDCM 2.2.0:
>>> http://gdcm.sourceforge.net/html/classgdcm_1_1SegmentReader.html
>>>
>>> See:
>>>
>>>http://sourceforge.net/apps/mediawiki/gdcm/index.php?title=GDCM_Release_
>>>2.2.0
>>>
>>> A very big thanks to the IRCAD team for sponsoring this development !
>>>
>>>> When I try to read such an object with ITK4/GDCM, I have the
>>>>following error:
>>>>
>>>>    ITKv4/Modules/IO/GDCM/src/itkGDCMImageIO.cxx:391:
>>>> itk::ERROR: GDCMImageIO(0x1048f4fc0): Unhandled PixelFormat: 11
>>>>
>>>> 11 == gdcm::PixelFormat::BITSET. Looking into itkGDCMImageIO.cxx, this
>>>> pixel format is not included in the pixel types supported for
>>>> read/write.
>>>>
>>>> Is there a plan to support this pixel type and reading/writing DICOM
>>>> SEG pixel data in GDCM?
>>>
>>> I would guess you are using something before GDCM 2.2.0. Is this
>>>correct ?
>>>
>>> If you can reproduce this with 2.2.1 and or git/master, feel free to
>>> ping me again.
>>>
>>> Thanks.
>>> --
>>> Mathieu
>
>
>
>
>On Sun, Oct 28, 2012 at 2:24 PM, Johnson, Hans J <hans-johnson at uiowa.edu>
>wrote:
>> Andriy,
>>
>> 1) Matt McCormick and I recently discussed the need to do this.  I've
>>done
>> recent work on GDCM to prepare it for the update in ITKv4.
>>
>> Is there a there a specific bug fix/ feature that could help motivate
>>the
>> effort needed to accomplish updating GDCM?
>>
>> Hans
>>
>>
>>
>> On 10/28/12 12:45 PM, "Andriy Fedorov" <fedorov at bwh.harvard.edu> wrote:
>>
>>>Hi,
>>>
>>>If I am not mistaken, ITK4 is currently using GDCM version 2.0.17. The
>>>current stable release of GDCM is 2.2.1.
>>>
>>>Is there any plan for upgrading the version of GDCM used by ITK?
>>>
>>>--
>>>Andriy Fedorov, Ph.D.
>>>
>>>Brigham and Women's Hospital
>>>Harvard Medical School
>>>75 Francis Street
>>>Boston, MA 02115 USA
>>>fedorov at bwh.harvard.edu
>>>(617) 525-6258 (office)
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>>
>>
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