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Hi list users,
Could I have some help on the following problem please. I have some DICOM images. I want to perform certain operations on them. My program works better with raw images rather than DICOM so I converted these DICOM series to a raw image using Image J. I know that raw is just a string of binary. But, since the raw image I obtain contains both the image and the header information from the DICOM series, I am confused as to how I may (i.e. how my program will) be able to distinguish the image from the header, like, for eg:- how many bytes will be alloted to the header and what all information will be present in the header(all the information from the DICOM or only certain significant information?) and also whether the header is followed by the image or vice-versa. If I read the raw image using Image J's raw image reader I see that the original series is reproduced. How can I achieve this? Essentially I want to read in the input raw image and separate the header and the image into 2 different files. Thanks a lot people Lisa -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi list users,
I work with ndpi files from hamamatzu nanozoomer I have problem with the new version of loci Bio format (4.4.4) this is not the right colors the 4.4.2 version work correctely Is it a bug in loci_tool.jar ? thanks marc lartaud -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by Lisa Dean
Hi Lisa - I think the easiest way to get your result is to use one of the publicly available DICOM to Analyze filters. Analyze files come with a separate header, and a raw data file, with .hdr and .img extensions, respectively. Google "DICOM to Analyze" to get a little more information.
- Jim On Dec 7, 2012, at 1:23 AM, Lisa Dean wrote: > Hi list users, > > Could I have some help on the following problem please. > > I have some DICOM images. I want to perform certain operations on them. My > program works better with raw images rather than DICOM so I converted these > DICOM series to a raw image using Image J. > > I know that raw is just a string of binary. But, since the raw image I obtain > contains both the image and the header information from the DICOM series, > I am confused as to how I may (i.e. how my program will) be able to distinguish > the image from the header, like, for eg:- how many bytes will be alloted to > the header and what all information will be present in the header(all the > information from the DICOM or only certain significant information?) and > also whether the header is followed by the image or vice-versa. > > If I read the raw image using Image J's raw image reader I see that > the original > series is reproduced. How can I achieve this? Essentially I want to read in > the input raw image and separate the header and the image into 2 different > files. > > Thanks a lot people > Lisa > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html ... [show rest of quote] -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by Lisa Dean
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 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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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 > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > ... [show rest of quote] -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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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 >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html ... [show rest of quote] -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by lartaud marc
Hi Marc,
> I work with ndpi files from hamamatzu nanozoomer > I have problem with the new version of loci Bio format (4.4.4) > this is not the right colors > the 4.4.2 version work correctely > Is it a bug in loci_tool.jar ? The latest version of Bio-Formats is 4.4.5. Do you see a problem with that version as well? If so, it would be very helpful if you could send one .ndpi file that shows the problem, as well as listing the options selected in the "Bio-Formats Import Options" window. Regards, -Melissa On Fri, Dec 07, 2012 at 09:28:33AM +0100, lartaud marc wrote: > Hi list users, > I work with ndpi files from hamamatzu nanozoomer > I have problem with the new version of loci Bio format (4.4.4) > this is not the right colors > the 4.4.2 version work correctely > Is it a bug in loci_tool.jar ? > thanks > marc lartaud > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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