[Insight-users] Problem writing to Analyze file format

[Luis Ibanez]

Hi Alex,

1) Slicer should be able to read Analyze files.
    What error did you get from Slicer ?

2) ParaView: It doesn't really support Analyze. (My Mistake)


   Regards,


      Luis


----------------------------
Oleksandr Dzyubak wrote:
> 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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>>>
> 
>