[Insight-users] Re: Volume Data Headsq in ITK VTK Example

[alqatarneh at netscape.net]

Thanks Karthik and Luis,

I am asking about the HEADSQ datsset format because I would like to use my own images (a Patient images) instead of the HEADSQ images in the exampl: InsightApplications/vtkITK/Scripts/DemoMutual.tcl.

Please note that:
1. The HEADSQ dataset I am referring to is in:
ftp://public.kitware.com/pub/vtk/VTKTextbook/FullHead.tgz
2. Example works perfectly only with ths HEADSQ dataset that has connectivity bit set ( Example reads data without any header file).
3. The example can not read the Headsq Quarter dataset.

My question is:
How is it possible to convert my patient to similar format to the HEADSQ format, so that I can run the example on my own data instead of the HEADSQ patient?

I truly appreciate your help and support.

Regards,
Sharef


Karthik Krishnan <Karthik.Krishnan at kitware.com> wrote:

>Hi Sharef:
>
>Try using
>
>vtkImageReader *reader = vtkImageReader::New();
>
>reader->SetDataMask(0x7fff);
>
>Thanks
>Regards
>karthik
>
>
>alqatarneh at netscape.net wrote:
>
>>Hello Luis and all again,
>>
>>Thank you Luis for your fast reply.
>>I agree that Google is a good search engine but it did not help me much in this case.
>>I found the link that you directed me to and many other links but that was not the dataset that I was referring to.
>>
>>Maybe I did not make myself clear..
>>There are 2 different Headsq datasets in ITK (Quarter, Half).
>>There is also one more dataset of HEADSQ Images (headsq.1, headsq.2,.... headsq.94) that is used to demonstarte the example:(InsightApplications/vtkITK/Scripts/DemoMutual.tcl).
>>
>>That dataset I downloaded from:
>>ftp://public.kitware.com/pub/vtk/VTKTextbook/FullHead.tgz
>>
>>To my understanding it has different format from the Headsq Quarter and Half format. 
>>The ReadMe of this HEADSQ dataset says: "Warning: this dataset has a connectivity bit set (unlike the half and quarter resolution cases). Set the data mask in vtkVolume16Source to mask out the high-order bit."
>>
>>Am I wrong? is the format of this dataset similar to the Quarter and Half datasets?
>>If it is different from the others , can you tell me how I can convert my images to the same format as the HEADSQ Image format, and add the connectivity bit set " As mentioned above: this dataset has a connectivity bit set "?
>>
>>
>>Kind regards,
>>Sharef
>>Luis Ibanez <luis.ibanez at kitware.com> wrote:
>>
>>  
>>
>>>Hi Sharef,
>>>
>>>
>>>         Google is an amazing tool.
>>>
>>>If you type:
>>>
>>>
>>>              "headsq itk"
>>>
>>>
>>>The third link is the following email of the ITK users list
>>>http://public.kitware.com/pipermail/insight-users/2003-May/003894.html
>>>
>>>Where you will find the MetaImage header that allows you to read
>>>the headsq dataset with an itk::ImageFileReader.
>>>
>>>filename="quarter.mhd":
>>>
>>>
>>>NDims = 3
>>>DimSize = 64 64 93
>>>ElementSpacing = 1 1 1
>>>Position = 0 0 0
>>>ElementByteOrderMSB = False
>>>ElementType = MET_USHORT
>>>ElementDataFile = quarter.%d 1 93 1
>>>
>>>
>>>
>>>
>>>Note that the actual demo that you are looking at is an early
>>>experiment where ITK filters where wrapped inside VTK filters.
>>>In that situation, the reading of the image is done with VTK
>>>filters.
>>>
>>>
>>>I would suggest you to use the MetaImage header attached and
>>>look at the ITK registration applications such as
>>>
>>>
>>>    InsightApplications/
>>>         LandmarkInitializedMutualInformationRegistration
>>>
>>>
>>>Once you load an image in ITK you can save it in any
>>>of the formats listed on the FAQ
>>>
>>>http://www.itk.org/Wiki/ITK_FAQ#What_3D_file_formats_can_ITK_import_and_export.3F
>>>
>>>
>>>
>>>
>>>  Regards,
>>>
>>>
>>>     Luis
>>>
>>>
>>>
>>>----------------------------------
>>>alqatarneh at netscape.net wrote:
>>>
>>>    
>>>
>>>>Hi Luis, Hi all,
>>>>
>>>>There is a dataset of HEADSQ Images (headsq.1, headsq.2,.... headsq.94)
>>>>
>>>>that is used to demonstarte the example (InsightApplications/vtkITK/Scripts/DemoMutual.tcl).
>>>>
>>>>I understand that the format of such data is different from the Quarter and Half Headsq data as pointed out in the ReadMe:
>>>>"Warning: this dataset has a connectivity bit set (unlike the half and
>>>>quarter resolution cases). Set the data mask in vtkVolume16Source to
>>>>mask out the high-order bit."
>>>>
>>>>Can someone tell me how to produce similar format to the HEADSQ.n format from my own images?
>>>>
>>>>I searched quite alot but I found most info available is mostly about the Headsq Quarter dataset.
>>>>
>>>>Thank you very much in advance!
>>>>
>>>>Regards,
>>>>Sharef
>>>>
>>>>
>>>>      
>>>>
>>>
>>>
>>>    
>>>
>>
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>>  
>>
>
>

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