[Insight-developers] NIfTI orientation issue

Tue Oct 27 14:20:40 EDT 2009

I opened a bug report regarding the NIfTI case:
http://www.itk.org/Bug/view.php?id=9784
Thanks,

Mathieu

On 2009-10-27, at 12:01 PM, Bill Lorensen wrote:

> Currently (almost 100% of the time) the meta data dictionary is only
> populated and accessed in IO classes (I checked this morning). And,
> the writers and readers of a given filetype seem to use it correctly.
> That is they copy file format specific information from the input to
> the output. So I think it is serving a purpose in its current use.
>
> But, as several have noted, it is not propagated through the pipeline.
> I think it should be and I'm investigating the solution that Jim
> Miller suggested in this bug report:
> http://public.kitware.com/Bug/view.php?id=4625
>
> Please stand by,
>
> Bill
>
> On Tue, Oct 27, 2009 at 11:53 AM, kent williams
> <norman-k-williams at uiowa.edu> wrote:
>> Unfortunately, the MetaData idea has not been consistently  
>> implemented, and
>> understanding why it's there, and why in particular there is  
>> support for it
>> in the NIfTI reader/writer means understanding the history.
>>
>> Hans Johnson did the original addition of Metadata before there was  
>> any sort
>> of orientation information stored as part of an image. The first  
>> reason for
>> it being included was to add a way to store orientation as 'out of  
>> band'
>> data with images.
>>
>> Now, obviously, having a general metadata infrastructure was  
>> valuable from
>> the standpoint of, e.g. keeping DICOM tags with an image.
>>
>> But for the Metadata infrastructure to be consistently implemented,  
>> it would
>> have to be propogated down pipelines, but it has never been  
>> consistently
>> implemented.  And it raises issues that aren't easy to definitively  
>> settle,
>> like what to do when a particular filter makes changes in its  
>> output that
>> might conflict with the metadata.
>>
>> Once ITK added orientation information to Images, it made storing
>> orientation in the metadata obsolete; and in fact it never was  
>> globally
>> implemented, so it could never be depended on anyway.
>>
>> It would be nice if we did a comprehensive review of how metadata is
>> actually used, and what it would require to ensure that it's  
>> propogation was
>> consistent.  But as always, we're all prioritizing available time and
>> Metadata keeps getting pushed down.  ITK enhancement and  
>> maintainence, at
>> least at organizations not directly funded for ITK work, is driven  
>> by the
>> needs of actually funded research.
>>
>> On 10/27/09 10:36 AM, "Mathieu Coursolle" <mathieu at rogue- 
>> research.com>
>> wrote:
>>
>>> Hi,
>>>
>>> I am not sure I understand that issue... Is the metadata currently
>>> copied in the pipeline ?
>>> I also noticed that the metadata in the itkNiftiImageIO has  
>>> predefined
>>> keys starting with ITK_.
>>> Is that a standard to follow if I had the metadata from the NIfTI
>>> header ? I think that the GDCM reader
>>> just uses the DICOM tags as the keys.
>>>
>>> Thanks,
>>>
>>> Mathieu
>>>
>>> On 2009-10-27, at 11:22 AM, Luis Ibanez wrote:
>>>
>>>> Mathieu,
>>>>
>>>> No objection from my corner...
>>>>
>>>> But, please note the related thread regarding the subsequent
>>>> passing of the MetaDataDictionary through the pipeline:
>>>> http://www.itk.org/pipermail/insight-users/2009-October/033423.html
>>>>
>>>>
>>>>    Regards,
>>>>
>>>>            Luis
>>>>
>>>>
>>>> -------------------------------------------------------------
>>>> On Tue, Oct 27, 2009 at 9:26 AM, Mathieu Coursolle
>>>> <mathieu at rogue-research.com> wrote:
>>>>> Hi,
>>>>> On the same topic, the itkNiftiImageIO has a function called
>>>>> DumpNiftiHeader
>>>>> used to output
>>>>> the header information.
>>>>> Any objection on all this header information being added to the
>>>>> metadata
>>>>> dictionary ?
>>>>> Thanks,
>>>>> Mathieu
>>>>> On 2009-10-26, at 1:59 PM, Mathieu Coursolle wrote:
>>>>>
>>>>> Hi ITK developers,
>>>>> I am using the itkNiftiImageIO to load NIfTI image data. The NIfTI
>>>>> file
>>>>> format defines 2 different methods to map voxels
>>>>> to physical coordinates. One of those methods is using a  
>>>>> quaternion
>>>>> and is
>>>>> defined when the qform_code > 0. The other
>>>>> method is using a linear transform and is defined when the
>>>>> sform_code > 0.
>>>>> Looking at the code which sets the orientation based on the NIfTI
>>>>> header, it
>>>>> seems to prioritize the qform over the sform.
>>>>> (See void NiftiImageIO:: SetImageIOOrientationFromNIfTI(unsigned
>>>>> short int
>>>>> dims))
>>>>> However, there are some cases where I would need both the qform  
>>>>> and
>>>>> the
>>>>> sform transforms once the data is loaded.
>>>>> I guess one option would be to add them as part of the metadata ?
>>>>> Could we do something like:
>>>>> EncapsulateMetaData<std::vector<std::vector<double>
>>>>>>> (this->GetMetaDataDictionary(),"qform", myQForm);
>>>>> EncapsulateMetaData<std::vector<std::vector<double>
>>>>>>> (this->GetMetaDataDictionary(),"sform", mySForm);
>>>>> Any other suggestions ?
>>>>> Thanks,
>>>>> Mathieu
>>>>> _________________________
>>>>> Mathieu Coursolle, ing.jr., M.Ing.
>>>>> Rogue Research Inc.
>>>>> www.rogue-research.com
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
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>>>>
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