[Insight-developers] NIfTI orientation issue

[Bill Lorensen]

The meta data dictionary is not currently passed through the pipeline.
We are investigating the best approach.


On Tue, Oct 27, 2009 at 11:36 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
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://kitware.com/products/protraining.html
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://www.itk.org/mailman/listinfo/insight-developers
>>>
>>>
>>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.html
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://www.itk.org/mailman/listinfo/insight-developers
>