Re: raw images

Posted by Mauro Maiorca on Dec 10, 2012; 7:16am
URL: http://imagej.273.s1.nabble.com/raw-images-tp5001066p5001086.html

Hi Lisa,

you might also consider the MetaIO file format, see
http://www.itk.org/Wiki/ITK/MetaIO/Documentation.
MetaIO files have a raw file and a header file (mhd) which can be
editable with any text editor. In ImageJ you can import/save MetaIO
files using this plugin:
http://www.kangli.org/code/MetaImage_Reader_Writer.html

The advantage of using MetaIO is that it is a widely recognized
format: you can read/write/process/convert MetaIO files using the gdcm
libraries, and many stand-alone programs including itk-snap, paraview,
slicer3d, etc. etc.

The major drawback of using MetaIO files instead of DICOMs is that you
might loose track of some information in the dicom header, for example
most of the patient's information. However, you definitely have most
of the info you might need for image processing/rendering, including
pixel spacing, pixel type, slice thickness, anatomical orientation,
etc etc.

cheers,
Mauro


On Mon, Dec 10, 2012 at 4:17 PM, Lisa Dean <[hidden email]> wrote:

> Thank you Wayne, Richard. I didn't know about the part where information
> can be saved as a text file. Definitely helpful. And thank you for the
> additional detail Richard, it seems I'll have to create macros because I do
> have a lot of images.
>
> Yes Jim, I'd been starting to ponder that approach myself. However, I think
> I'll first give a try to the raw images and text files, since information
> in the text files can be read using any text editor unlike that of the .hdr
> file. But, thank you for the input.
>
>
> Lisa
>
>
> On 8 December 2012 20:52, Richard VanMetter <[hidden email]> wrote:
>
>> Hi Lisa -
>>
>> I think that ImageJ can easily provide the two files you would like to
>> obtain from each DICOM file.
>>
>> 1. Open your DICOM image in ImageJ.
>> 2. Save a raw data file as follows: select menu option ">File>Save As" and
>> then select "Raw Data...". The raw image data from your DICOM image will be
>> saved in a file with the same name, but with the extension ".raw". This
>> DOES NOT include any of the header information, but only the pixel data.
>> 3. Save the DICOM header as follows: select menu option ">Image>Show
>> Info". This will open and "info" window that shows you all the DICOM header
>> information along with some additional image information, like the number
>> of bits per pixel, and the width, height and depth of your image file.
>> 4. Select ">File>Save As" from the menu on the info window and save this
>> information in a file (it will be an ascii text file readable in any text
>> editor). The default file name for this text file is "Info-(image
>> name).txt". You may change it if you wish.
>> 5. Close all windows by selecting ">File>Close All" from the ImageJ menu.
>>
>> If you have many images, you can automate this process by recording a
>> macro. If you plan to work with images in the future, learning how to
>> create ImageJ macros will be a useful skill. I would refer you to resources
>> for learning the macro language on the ImageJ Developer Resources page "
>> http://imagej.nih.gov/ij/developer/index.html". You can also get to this
>> page from within ImageJ by selecting ">Help>Dev. Resources..." from the
>> menu.
>>
>> Richard VanMetter
>>
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>>
>
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