[Insight-users] any MRI data

[Luis Ibanez]

Hi Jose,

Thanks for pointing this out.

We were able to reporduce the problem that you reported.

The soure of the problem seems to be the slice

                    126_37_22.img

that has a size different from all other slices. This slice
has file size = 108544 bytes, while all the  others have
131072 bytes as file size.

You may want to remove this slice from the set by simply
editing the MetaImage header and replacing 22 with 21.

Note that you must do this in two places:

     1) DimSize
     2) ElementDataFile



We are checking with the IBSR project to find out why this
slice is smaller than the others.



   Regards,


     Luis



-----------------------
jose santamaria wrote:

> Hi Luis,
> 
>   I only have found one problem trying to generate the
> .hdr header file for the last 126_37.mhd scan, with the
> following output
> 
> 126_37.img> ../ImageReadWrite 126_37.mhd 126_37.hdr
> MetaImage: M_ReadElements: data not read completely
>    ideal = 131072 : actual = 0
> 
> It was the only problem that I had.
> 
> Luis, thanks for your encouraged supports.
> 
> Sincerely,
> 
> Jose
> 
> 
> El dom, 19 de 12 de 2004 a las 16:56, Luis Ibanez escribió:
> 
>>Hi Jose,
>>
>>
>>Please read the code of the example:
>>
>>    Insight/Examples/IO/ImageReadWrite.cxx
>>
>>you will notice that you don't need to hardcode the
>>filename of the input or output images.  The filenames
>>are taken from the command line. Thats the purpose of
>>line 134-135:
>>
>>
>>      const char * inputFilename  = argv[1];
>>      const char * outputFilename = argv[2];
>>
>>
>>
>>
>>
>>The only thing that you have to do in the code
>>is to select the correct pixel type and dimension
>>for this images. Which in this case is:
>>
>>      PixelType  =  signed short
>>      Dimension  =  3
>>
>>
>>Just change lines  87-88 from
>>
>>   typedef unsigned short      PixelType;
>>   const   unsigned int        Dimension = 2;
>>
>>into
>>
>>   typedef signed short        PixelType;
>>   const   unsigned int        Dimension = 3;
>>
>>then recompile the program.
>>
>>
>>
>>
>>
>>After you have an executable, then you simply invoke
>>this executable from the command line (a MS-DOS console,
>>or a Unix shell) with filenames for each one of the
>>images.
>>
>>
>>Like:
>>
>>   ImageReadWrite.exe   126_1.mhd       126_1.hdr
>>   ImageReadWrite.exe   126_10.mhd      126_10.hdr
>>   ImageReadWrite.exe   126_13.mhd      126_13.hdr
>>   ImageReadWrite.exe   126_21.mhd      126_21.hdr
>>   ImageReadWrite.exe   126_26.mhd      126_26.hdr
>>   ImageReadWrite.exe   126_31.mhd      126_31.hdr
>>   ImageReadWrite.exe   126_37.mhd      126_37.hdr
>>
>>Note that the extension ".exe" is only needed if you are
>>doing this on MS-Windows.  On Unix systems the executable
>>will not have any extension.
>>
>>The extension ".mhd" will be for the input images
>>and the extension ".hdr" will be for the output
>>images in Analyze format.
>>
>>
>>
>>
>>In order to understand this program you *MUST* read
>>the IO chapter from the ITK Software Guide
>>
>>        http://www.itk.org/ItkSoftwareGuide.pdf
>>
>>
>>
>>Please let us know if you encounter any problems,
>>
>>
>>    Thanks
>>
>>
>>      Luis
>>
>>
>>
>>-----------------------
>>jose santamaria wrote:
>>
>>>Hi Luis,
>>>
>>>  firstly of all, thanks a lot. I have downloaded 
>>>
>>>SingleWithTumorMetaImageHeaders.tgz 
>>>
>>>and added each .mhd metaimage file inside its 
>>>corresponding 126_*/ folder.
>>>
>>>I have built the Insight/Examples/IO/ImageReadWrite.cxx
>>>example but I have not yet probed it. My doubt is if
>>>to convert each scan images to the Analyze format I must
>>>to do as follow:
>>>
>>>1) Loading given scan by its .mhd header file with
>>>    
>>>reader->SetFileName( headerfilename.mhd );
>>>
>>>2) Once loaded it and instantiated the itk::ImageFileWriter class,
>>>should I use the itkAnalyzeImageIO class to convert the loaded 
>>>volume to the Analyze format? I do not understand very much
>>>how to do this.
>>>
>>>Kind regards Luis.
>>>
>>>Jose.
>>>
>>>El vie, 17 de 12 de 2004 a las 22:18, Luis Ibanez escribió:
>>>
>>>
>>>>Hi Jose,
>>>>
>>>>You will find MRI data for the same patient over time at
>>>>the IBSR (Internet Brain Segmentation Repository) project
>>>>
>>>>       http://www.cma.mgh.harvard.edu/ibsr/
>>>>
>>>>You can download this data for free. Just need to register
>>>>with them, and make sure that they give them credit on any
>>>>potential publication.
>>>>
>>>>Note that the images they provide are in files with extension
>>>>.img, but are not in Analyze format. These images are in .raw
>>>>format. You should create MetaImage headers for them, and you
>>>>can use simple ITK code for converting them to Analyze format.
>>>>
>>>>For example you can use the program
>>>>
>>>>     Insight/Examples/IO/ImageReadWrite.cxx
>>>>
>>>>
>>>>Regards,
>>>>
>>>>
>>>>    Luis
>>>>
>>>>
>>>>---------------------
>>>>jose santamaria wrote:
>>>>
>>>>
>>>>
>>>>>Hi,
>>>>>
>>>>>  I will be pleasure with anyone who could send me two brain MRI 
>>>>>data in the Analyse file format (.hdr + .img) from the same patient 
>>>>>but in two different times. I need it for registering.
>>>>>
>>>>>Thanks at all,
>>>>>
>>>>>Bye, jose.
>>>>>
>>>>>_______________________________________________
>>>>>Insight-users mailing list
>>>>>Insight-users at itk.org
>>>>>http://www.itk.org/mailman/listinfo/insight-users
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>>
> 
> 
>