[Insight-users] Problem writing to Analyze file format

[Oleksandr Dzyubak]

Hi Luis,

the ImageViewer and SNAP from ITK works fine.  Thanks.
The other ones, ParaView and Slicer, do not accept the Analyze format
with complains below.

A reader for "/home/dzyubak/SquareBinary201_out.hdr" could not be found.

Do those softs really support the Analyze format or I am doing something 
wrong?
It looks like I have to stick with the type float since my users would 
prefer using ImageJ.

Thanks,

Alex

Luis Ibanez wrote:
>
> Hi Alex,
>
> You can instantiate the Distance map filters in ITK
> using images of pixel type float as the output image type.
>
> Note that you can also use the ImageViewer application
> available in InsightApplications.
>
> You will find a binary at:
> http://public.kitware.com/pub/itk/InsightApplicationsBin/
>
> Other suitable viewers are:
>
>   * SNAP
>   * Slicer
>   * ParaView
>
>
>    Regards,
>
>       Luis
>
>
> ---------------------------
> Oleksandr Dzyubak wrote:
>> Daniele,
>>
>> Thanks a lot for pointing me out to those documents.
>> Now the things became a bit clear.
>>
>> One question though.
>> Some ITK filters (distance map, for example) work with a type double.
>> If I save the result in the Analyze format and
>> try to see the output using the ImageJ (also from NIH) viewer,
>> it always shows some garbage but it is OK if the float type used.
>>
>> Does it mean that I have to use a float type in those filters?
>>
>> Thanks,
>>
>> Alex
>>
>> Daniele Domenichelli wrote:
>>
>>> Oleksandr Dzyubak wrote:
>>>  
>>>
>>>> The only problem is that the Analyze75 header does not have a tag with
>>>> that info, right?
>>>>     
>>>
>>>
>>> No, analyze has a tag "orient" (1 byte) but it has only 6 valid values
>>>
>>>           0         transverse unflipped
>>>           1         coronal unflipped
>>>           2         sagittal unflipped
>>>           3         transverse flipped
>>>           4         coronal flipped
>>>           5         sagittal flipped
>>>
>>> Nifti uses quaternion for orientation. See nifti header if you are
>>> interested:
>>>
>>>      http://nifti.nimh.nih.gov/pub/dist/src/niftilib/nifti1.h
>>>
>>>
>>>
>>>  
>>>
>>>> The Analyze75 header size is 348 vs 352 for NifTI. Does it mean that
>>>> those extra bites can hold all the directional info in case of the 
>>>> NIfTI
>>>> format and well treated by the ITK filters?
>>>>     
>>>
>>>
>>> No bytes from 349 to 352 are used for extensions.
>>> Nifti header in not necessarily 352 bytes, it can contain extensions 
>>> for
>>> example to contain dicom tags (see nifti header for details)
>>> Nifti stores informations about orientations of the image in bytes that
>>> were not used in Analyze
>>>
>>>
>>>  
>>>
>>>> The question is since the Analyze image format has "poor 
>>>> performance" in
>>>> a sense
>>>> of the directional info, how does it affect the final results after 
>>>> ITK
>>>> filters have been used
>>>> on those images? Do any "info corruptions/changes" squeeze in
>>>> automatically into
>>>> the image info tags afterwards since it might be implemented in a 
>>>> filter
>>>> by some defaults?
>>>>     
>>>
>>>
>>> I think that the only thing you should take care of when using analyze
>>> files is that you can't write them in any direction, so you may need to
>>> reorient the image.
>>>
>>> I'm not sure about this anyway, because I mostly use nifti, maybe
>>> someone else on the mailing list who uses analyze can tell you 
>>> something
>>> more...
>>>
>>>
>>> Regards,
>>> Daniele
>>>   
>>
>>
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