[Insight-users] Object map Analyze file format (.obj)

[Hans Johnson]

Elena,

There is a group at The University of Iowa that is also interested in
developing image readers for the Analyze7.5 object maps.  It should be noted
that the proposal is to develop a new image file format reader in ITK that
is separate from the existing Analyze7.5 image file reader.  If you wanted
to load both an Analyze75 image and it's object map, I would expect that you
would have to read in the ".img" file with the existing Analyze75 image
reader mechanism, and the ".obj" file with the proposed file reader (both
readers would depend on the same ".hdr" file).

You may want to contact "Imran A. Pirwani" <pirwani at cs.uiowa.edu> for
details on the work that he has already completed.

Regards,
Hans



=====================
Hans,

I am still learning the ropes with Slicer/ITK etc.  However, I think that
I know where the new files need to go; they'll go in Insight/Code/IO/
having the following 4 files:
itkRunLengthEncodedImageIO.cxx, itkRunLengthEncodedImageIO.h
itkRunLengthEncodedImageIOFactory.cxx, itkRunLengthEncodedImageFactoryIO.h

I heard that only recently Analyze changed the way they encode objectmaps
and it seems that the format is not public (at least thus far). I'll look
into it a little more and talk to Gary but the fact remains that we have
object maps that are RLE format from before.

At the moment, I am trying to gauge how well KWWidgets supports the NIREP
vision.  I am quite pleased with my evaluation thus far with regard to
the functionality that we need.  It is also nice that the Slicer framework
supports modules that people can write on their own that plug in
seamlessly with the framework.

Thanks,

-Imran.

On Wed, 7 Mar 2007, Johnson, Hans J wrote:

> Imran,
> 
> The object maps are not implemented in ITK.  I do have some code that can read
the
> object maps, and this would be a great contribution to ITK.  It is going to be
a
> little tricky because the object files require 2 files, one of which overlaps
with
> several other insufficiently regularized standards (i.e. the .hdr).
> 
> If this is early enough in the design, I would suggest looking at a few other
> options.  I could discuss this with you at some point.
> 
> Hans
> 
> 
________________________________________________________________________________
__________
> From: Imran A. Pirwani [mailto:pirwani at cs.uiowa.edu]
> Sent: Wed 3/7/2007 9:41 AM
> To: Johnson, Hans J
> Subject: Object maps
> 
> Hi Hans,
> 
> I noticed that Slicer is unable to recognize object map files that Analyze
> uses; these files are run-length encoded.  I am guessing that this is
> because the imageIO reader in ITK has not been implemented for this
> purpose.  Am I correct in my understanding?  Since this is a very useful
> (and instrumental) file format for us (and others in the community), I was
> thinking of writing one for ITK but before I did that, I wanted to find
> out if there isn't one available already.  If there is no such thing out
> there and if I were to implement it then how might one submit the code?
> 
> Thanks!
> 
> -Imran.
> 
> 
>



On 3/27/07 10:07 AM, "Vincent A. Magnotta" <vincent-magnotta at uiowa.edu>
wrote:

> Elena,
> 
> ITK does not support the Analyze Object map file format. Only the
> Analyze 7.5 image file format is supported. There appears to be a reader
> in Matlab that will support some version of the Object Map. You may be
> able to use this to load the object map and save into another format
> supported by ITK.
> 
> Vince
> 
> Matlab link:
> 
> http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=9587&
> objectType=FILE
> 
> On Mon, 2007-03-26 at 20:03 -0700, Elena Pavlovskaia wrote:
>> Hello,
>> 
>> Can anybody give me a hint on information stored in an Analyze file with an
>> extension .obj (so called Object Map file format)?
>> 
>> My primer questions are:
>> 
>> Does an .obj file have a record of the voxel size?
>> 
>> If so:
>> Is the .obj voxel size equal to the original volume voxel size?
>> (By original volume I mean the volume where the Object Map represents a
>> segmentation?
>> 
>> 
>> Thank you!
>> 
>> Elena
>> 
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