[Insight-users] Problem writing to Analyze file format

[Oleksandr Dzyubak]

Hi Luis,

The viewer crashes with the error below.

*********Begin Error*******

dzyubak at debian: /Slicer33$ ./Slicer3 SquareBinary201_out.hdr
Starting Slicer: /home/dzyubak/Viewers/Slicer33
*** glibc detected *** malloc(): memory corruption: 0x0b6f1dd8 ***

child killed: SIGABRT

CHILDKILLED 9331 SIGABRT SIGABRT
dzyubak at debian: /Slicer33$

*******End Error******

Regards,
Alex

Luis Ibanez wrote:
>
> 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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>>>>
>>
>>