[Insight-users] Writing Analyze file and specifying header properties

Tue Apr 3 18:10:48 EDT 2012

There is not a way to set the analyze header values when writing.  The
reason is that Analyze only supports 3 orientations, and that is
insufficient to properly describe the data.

You should use the FlipImage filter to re-arrange your data into one of
the acceptable Analyze data organizations, and then write that out.

Hans

--
Hans J. Johnson, Ph.D.
hans-johnson at uiowa.edu
Assistant Professor of Psychiatry
University of Iowa Carver College of Medicine
W278 GH, 200 Hawkins Drive

Iowa City, Iowa 52242
Phone:  319-353-8587

-----Original Message-----
From: Sara Rolfe <smrolfe at u.washington.edu>
Date: Tue, 3 Apr 2012 14:45:52 -0700
To: Hans Johnson <hans-johnson at uiowa.edu>
Cc: Kent Williams <nkwmailinglists at gmail.com>, "insight-users at itk.org
Users" <insight-users at itk.org>
Subject: Re: [Insight-users] Writing Analyze file and specifying header
properties

Thanks for your response.  I am working with a 3D image, but it is
stored as a series of 2D BMPs.  It's the final 3D file that I need to
write in Analyze file format.

I understand that I can simply mirror my image to get the output I
need and that this will be specific to my application.  However, I
also need to set the Analyze header fields to the correct values, and
this is what I'm not seeing how to do.  I would expect that there's a
way to change the default values when writing a new Analyze image.

Thanks,
Sara

On Apr 3, 2012, at 2:17 PM, Johnson, Hans J wrote:

> The Analyze file format was never intended for 2D images.  The
> meaning of
> "CORONAL" "TRANSVERSE" in the Analyze file format are insufficient to
> properly describe physical space orientation.
>
> In a 3D image there are 8 different possible definitions of
> "CORONAL", and
> each would give a different physical space representation.  There is
> no
> good default, so it must be left up to the user to make their own
> problem
> specific solution.
>
> Hans
> --
> Hans J. Johnson, Ph.D.
> hans-johnson at uiowa.edu
> Assistant Professor of Psychiatry
> University of Iowa Carver College of Medicine
> W278 GH, 200 Hawkins Drive
>
> Iowa City, Iowa 52242
> Phone:  319-353-8587
>
>
>
>
>
>
>
> -----Original Message-----
> From: Sara Rolfe <smrolfe at u.washington.edu>
> Date: Tue, 3 Apr 2012 14:09:30 -0700
> To: Kent Williams <nkwmailinglists at gmail.com>
> Cc: "insight-users at itk.org Users" <insight-users at itk.org>
> Subject: Re: [Insight-users] Writing Analyze file and specifying
> header
> properties
>
> It seems like it would be easiest to manually reverse the pixel rows,
> but I'm not clear on how this would change the orientation in the
> image information.  Isn't this necessary to change the Analyze header
> orientation option to "CORONAL" instead of "TRANSVERSE", or am I
> missing something?
>
> If I use the OrientImageFilter on the reconstructed 3D volume I
> thought AnalyzeImageIO would get the new orientation from this image.
> Is this correct?  It is true that I'm not sure how to choose the
> correct orientation to get the output I need.
>
> I am wondering if there is an easier way to accomplish this.  Other
> image readers allow a stack of BMPs to be read into a 3D volume and
> let the user to input the orientation (eg Transverse or Coronal) and
> voxel resolution.  It seems strange that the ITK forces the user to
> use the default orientation (Transverse) and resolution.
>
> Thanks,
> Sara
>
> On Apr 3, 2012, at 1:48 PM, Kent Williams wrote:
>
>> The OrientImageFilter is 3D only.  The easiest thing for you to do if
>> your images are showing up left/right swapped when converted to
>> Analyze would be to manually reverse the pixel rows.
>>
>> I assume you're going from BMP->itk::Image<pixType,2>. If you're
>> assembling a bunch of BMP files into a 3D Volume, then the
>> OrientImageFilter might be the thing to use.  But for that to work
>> properly you'd have to know what the orientation for the image you're
>> constructing is.
>>
>> On Tue, Apr 3, 2012 at 3:16 PM, Sara Rolfe
>> <smrolfe at u.washington.edu> wrote:
>>> Hi Kent,
>>>
>>> Thanks, that makes sense.  Unfortunately I am stuck using the
>>> Analyze
>>> format.
>>>
>>> Would I use the Orientation image filter that Saurabh mentioned to
>>> change
>>> the direction cosines?
>>>
>>> Thanks,
>>> Sara
>>>
>>>
>>> On Apr 3, 2012, at 10:45 AM, Kent Williams wrote:
>>>
>>>> When you read in the BMP file, the image orientation defaults to
>>>> identity.  You can change the Direction cosines for the image to
>>>> reflect what you want for the output image.  The ImageIO object
>>>> that
>>>> does the actual writing uses the orientation/spacing/origin
>>>> information contained in the image that you're writing.
>>>>
>>>> I guess there's a reason you're using Analyze format, but I'd
>>>> recommend against it, as it's very limited, especially when it
>>>> comes
>>>> to correct representation of orientation.
>>>>
>>>> On Mon, Apr 2, 2012 at 5:43 PM, Sara Rolfe
>>>> <smrolfe at u.washington.edu>
>>>> wrote:
>>>>>
>>>>> Hello,
>>>>>
>>>>> I would like to read a file of bmp images and write them as a
>>>>> 3DAnalyze
>>>>> image.  I have implemented this using the ImageSeriesReader.
>>>>> However,
>>>>> when
>>>>> the output is written as an Analyze volume, the default values for
>>>>> orientation and voxel resolution are incorrect.  This causes the
>>>>> output
>>>>> image to be mirrored.  I've not been able to find an explanation
>>>>> of how
>>>>> to
>>>>> set these properties and would appreciate help figuring this out.
>>>>>
>>>>> Thanks,
>>>>> Sara
>>>>>
>>>>>
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>
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