DICOM - Revision history

Jadrian Miles: /* Useful Links */

2011-03-03T12:16:05Z

Useful Links

← Older revision		Revision as of 12:16, 3 March 2011
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	== Useful Links ==		== Useful Links ==
	* [http://medical.nema.org The DICOM standards committee]		* [http://medical.nema.org The DICOM standards committee]
			* [http://www.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI Vendor-specific DICOM header entries for DWI]

	[[Category:Diffusion MRI]][[Category:File Formats]]		[[Category:Diffusion MRI]][[Category:File Formats]]

Jadrian Miles at 22:35, 6 July 2009

2009-07-06T22:35:49Z

← Older revision		Revision as of 22:35, 6 July 2009
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	=== Mosaic ===		=== Mosaic ===
	An unusual storage strategy for DICOM-formatted medical images is the so-called "mosaic" scheme, in which a three-dimensional voxel volume is represented as a two-dimensional flat image. The volume is divided up into X-Y slices which are then arranged in 2D like a tile floor, with Z increasing left to right, top to bottom. You can spot one of these by visual inspection or if the header shows an image size much larger than a single slice---a single slice is usually 128x128 or 256x256 voxels, while a mosaic file may be much larger than that, depending on the Z resolution of the volume.		An unusual storage strategy for DICOM-formatted medical images is the so-called "mosaic" scheme, in which a three-dimensional voxel volume is represented as a two-dimensional flat image. The volume is divided up into X-Y slices which are then arranged in 2D like a tile floor, with Z increasing left to right, top to bottom. You can spot one of these by visual inspection or if the header shows an image size much larger than a single slice---a single slice is usually 128x128 or 256x256 voxels, while a mosaic file may be much larger than that, depending on the Z resolution of the volume. There are [[Diffusion MRI Matlab Scripts\|Matlab scripts]] available that automatically split the slices in a Mosaic image, assemble them into a single volume, and write them out in the desired format.

	~~==== Code ====~~
	~~The following scripts to handle DICOM mosaic files can be found in <tt>~~[~~file:///map/gfx0/common0/diffusion/Interface/bin/data/ /map/gfx0/common0/diffusion/Interface/bin/data/]</tt>:~~
	* <tt>processMosaics.m</tt> --- split all mosaic files matching a given pattern into DICOM and [~~[MRIimage~~]] ~~files~~
	* <tt>splitMosaic.m</tt> --- split a ~~single mosaic file~~ into a ~~Matlab data array~~
	~~All of these can be launched non-interactively with <tt>matlabLauncher.py</tt>~~.

	== Handling DICOMs ==		== Handling DICOMs ==
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	Matlab has [http://www.mathworks.com/company/newsletters/digest/nov02/dicom.html extensive built-in support] for DICOM header and image data I/O with the [http://www.mathworks.com/access/helpdesk/help/toolbox/images/dicominfo.html <code>dicominfo</code>], [http://www.mathworks.com/access/helpdesk/help/toolbox/images/dicomread.html <code>dicomread</code>], and [http://www.mathworks.com/access/helpdesk/help/toolbox/images/dicomwrite.html <code>dicomwrite</code>] functions. This is nice for quickly creating DICOM processing scripts to be run manually, but Matlab is relatively slow and difficult to call from non-interactive scripts. Therefore it's encouraged to port Matlab code into another language (preferably C++ or Python) for inclusion in the [[diffusion processing pipeline]].		Matlab has [http://www.mathworks.com/company/newsletters/digest/nov02/dicom.html extensive built-in support] for DICOM header and image data I/O with the [http://www.mathworks.com/access/helpdesk/help/toolbox/images/dicominfo.html <code>dicominfo</code>], [http://www.mathworks.com/access/helpdesk/help/toolbox/images/dicomread.html <code>dicomread</code>], and [http://www.mathworks.com/access/helpdesk/help/toolbox/images/dicomwrite.html <code>dicomwrite</code>] functions. This is nice for quickly creating DICOM processing scripts to be run manually, but Matlab is relatively slow and difficult to call from non-interactive scripts. Therefore it's encouraged to port Matlab code into another language (preferably C++ or Python) for inclusion in the [[diffusion processing pipeline]].

	~~<tt>/map/gfx0/common0/diffusion/Interface/bin/data/matlabLauncher.py</tt> is available to call~~ Matlab ~~functions non-interactively from~~ the ~~command line~~, ~~which makes it possible~~ to ~~include them in~~ the ~~pipeline but does not mitigate speed issues~~.		Despite the shortcomings of including Matlab scripts in the pipeline, flexibility and ease of development have led to its use for handling the diverse storage strategies associated with DICOM data. Check out the list of [[diffusion MRI Matlab scripts]] for useful code that's already been written.

	=== Python ===		=== Python ===

Jadrian Miles: /* Code */

2009-07-06T16:31:29Z

Code

← Older revision		Revision as of 16:31, 6 July 2009
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	* <tt>processMosaics.m</tt> --- split all mosaic files matching a given pattern into DICOM and [[MRIimage]] files		* <tt>processMosaics.m</tt> --- split all mosaic files matching a given pattern into DICOM and [[MRIimage]] files
	* <tt>splitMosaic.m</tt> --- split a single mosaic file into a Matlab data array		* <tt>splitMosaic.m</tt> --- split a single mosaic file into a Matlab data array
	* <tt>writeMosaicSlices.m</tt> --- write a collection of Matlab data volumes to DICOM and [[MRIimage]] files
	All of these can be launched non-interactively with <tt>matlabLauncher.py</tt>.		All of these can be launched non-interactively with <tt>matlabLauncher.py</tt>.

Jadrian Miles: /* Python */

2009-07-06T15:39:16Z

Python

← Older revision		Revision as of 15:39, 6 July 2009
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	=== Python ===		=== Python ===
	~~A few Python libraries for handling DICOMs exist; these might be worth looking into:~~
	* [http://code.google.com/p/pydicom/ pydicom] --- a pure Python DICOM library		* [http://code.google.com/p/pydicom/ pydicom] --- a pure Python DICOM library
	* [http://dicomlib.swri.ca/pydicomlib.html pydicomlib] --- a Python wrapper around dicomlib, below		* [http://dicomlib.swri.ca/pydicomlib.html pydicomlib] --- a Python wrapper around dicomlib, below

Jadrian Miles: /* Matlab */

2009-07-06T15:38:47Z

Matlab

← Older revision		Revision as of 15:38, 6 July 2009
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	=== Matlab ===		=== Matlab ===
	Matlab has [http://www.mathworks.com/company/newsletters/digest/nov02/dicom.html extensive built-in support] for DICOM header and image data I/O with the [http://www.mathworks.com/access/helpdesk/help/toolbox/images/dicominfo.html <code>dicominfo</code>], [http://www.mathworks.com/access/helpdesk/help/toolbox/images/dicomread.html <code>dicomread</code>], and [http://www.mathworks.com/access/helpdesk/help/toolbox/images/dicomwrite.html <code>dicomwrite</code>] functions. This is nice for quickly creating DICOM processing scripts to be run manually, but Matlab is relatively slow and difficult to call from non-interactive scripts. Therefore it's encouraged to port Matlab code into another language (preferably C++ or Python) for inclusion in the [[diffusion processing pipeline]].		Matlab has [http://www.mathworks.com/company/newsletters/digest/nov02/dicom.html extensive built-in support] for DICOM header and image data I/O with the [http://www.mathworks.com/access/helpdesk/help/toolbox/images/dicominfo.html <code>dicominfo</code>], [http://www.mathworks.com/access/helpdesk/help/toolbox/images/dicomread.html <code>dicomread</code>], and [http://www.mathworks.com/access/helpdesk/help/toolbox/images/dicomwrite.html <code>dicomwrite</code>] functions. This is nice for quickly creating DICOM processing scripts to be run manually, but Matlab is relatively slow and difficult to call from non-interactive scripts. Therefore it's encouraged to port Matlab code into another language (preferably C++ or Python) for inclusion in the [[diffusion processing pipeline]].

			<tt>/map/gfx0/common0/diffusion/Interface/bin/data/matlabLauncher.py</tt> is available to call Matlab functions non-interactively from the command line, which makes it possible to include them in the pipeline but does not mitigate speed issues.

	=== Python ===		=== Python ===

Jadrian Miles at 02:38, 2 July 2009

2009-07-02T02:38:18Z

@@ Line 37: / Line 37: @@
 All of these can be launched non-interactively with <tt>matlabLauncher.py</tt>.
-== Matlab ==
+== Handling DICOMs ==
 Matlab has [http://www.mathworks.com/company/newsletters/digest/nov02/dicom.html extensive built-in support] for DICOM header and image data I/O with the [http://www.mathworks.com/access/helpdesk/help/toolbox/images/dicominfo.html <code>dicominfo</code>], [http://www.mathworks.com/access/helpdesk/help/toolbox/images/dicomread.html <code>dicomread</code>], and [http://www.mathworks.com/access/helpdesk/help/toolbox/images/dicomwrite.html <code>dicomwrite</code>] functions.  This is nice for quickly creating DICOM processing scripts to be run manually, but Matlab is relatively slow and difficult to call from non-interactive scripts.  Therefore it's encouraged to port Matlab code into another language (preferably C++ or Python) for inclusion in the [[diffusion processing pipeline]].
 == Useful Links ==
-* [http://dicom.offis.de/dcmtk DCMTK --- the DICOM toolkit library]
+* [http://medical.nema.org The DICOM standards committee]
 [[Category:Diffusion MRI]][[Category:File Formats]]

Jadrian Miles: /* Volumes as DICOMs */

2009-07-02T01:24:48Z

Volumes as DICOMs

← Older revision		Revision as of 01:24, 2 July 2009
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	== Volumes as DICOMs ==		== Volumes as DICOMs ==
	A single DICOM file stores only one 2-D image, and so various strategies exist for storing and transferring volumes and collections of volumes as DICOM images. Most commonly, you'll just get a directory full of dozens (if not hundreds or thousands) of <tt>.ima</tt> or <tt>.dcm</tt> files, each one storing a single slice. Some other strategies crop up from time to time, though, to represent a whole volume or a collection of volumes as a single file. If you have reason to believe that your data should be in DICOM format but ~~it seems~~ a little funky, it might be stored as a tarball or in "mosaic" format. Here are a couple clues that indicate you should consider these possibilities:		A single DICOM file stores only one 2-D image, and so various strategies exist for storing and transferring volumes and collections of volumes as DICOM images. Most commonly, you'll just get a directory full of dozens (if not hundreds or thousands) of <tt>.ima</tt> or <tt>.dcm</tt> files, each one storing a single slice. Some other strategies crop up from time to time, though, to represent a whole volume or a collection of volumes as a single file. If you have reason to believe that your data should be in DICOM format but they seem a little funky, they might be stored as a tarball or in "mosaic" format. Here are a couple clues that indicate you should consider these possibilities:
	* Matlab or Medcon claims that your file is not a DICOM		* Matlab or Medcon claims that your file is not a DICOM
	* the file size is much larger than you'd expect for a single slice (which should be on the order of 100kB)		* the file size is much larger than you'd expect for a single slice (which should be on the order of 100kB)

Jadrian Miles: /* Volumes as DICOMs */

2009-07-02T01:23:51Z

Volumes as DICOMs

← Older revision		Revision as of 01:23, 2 July 2009
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	== Volumes as DICOMs ==		== Volumes as DICOMs ==
	A single DICOM file stores only one 2-D image, and so various strategies exist for storing and transferring volumes and collections of volumes as DICOM images. Most commonly, you'll just get a directory full of dozens (if not hundreds) of <tt>.ima</tt> or <tt>.dcm</tt> files, each one storing a single slice. Some other strategies crop up from time to time, though, to represent a whole volume or a collection of volumes as a single file. If you have reason to believe that your data should be in DICOM format but it seems a little funky, it might be stored as a tarball or in "mosaic" format. Here are a couple clues that indicate you should consider these possibilities:		A single DICOM file stores only one 2-D image, and so various strategies exist for storing and transferring volumes and collections of volumes as DICOM images. Most commonly, you'll just get a directory full of dozens (if not hundreds or thousands) of <tt>.ima</tt> or <tt>.dcm</tt> files, each one storing a single slice. Some other strategies crop up from time to time, though, to represent a whole volume or a collection of volumes as a single file. If you have reason to believe that your data should be in DICOM format but it seems a little funky, it might be stored as a tarball or in "mosaic" format. Here are a couple clues that indicate you should consider these possibilities:
	* Matlab or Medcon claims that your file is not a DICOM		* Matlab or Medcon claims that your file is not a DICOM
	* the file size is much larger than you'd expect for a single slice (which should be on the order of 100kB)		* the file size is much larger than you'd expect for a single slice (which should be on the order of 100kB)

Jadrian Miles at 23:50, 1 July 2009

2009-07-01T23:50:39Z

← Older revision		Revision as of 23:50, 1 July 2009
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	Files ending in <tt>'''.ima'''</tt> or <tt>'''.dcm'''</tt> are in the [http://medical.nema.org/ DICOM] [[Diffusion MRI\|medical image]] ~~format~~. It is a widely used format that enjoyed great popularity but, in the [[diffusion MRI]] community at least, has been mostly superseded by [[NIfTI]].		Files ending in <tt>'''.ima'''</tt> or <tt>'''.dcm'''</tt> are in the [http://medical.nema.org/ DICOM] [[Diffusion MRI#File Formats \|medical image format]]. It is a widely used format that enjoyed great popularity but, in the [[diffusion MRI]] community at least, has been mostly superseded by [[NIfTI]].

	== ~~Matlab~~ ==		You can confirm that you're dealing with DICOM data by running the following two commands:
	~~Matlab has [http://www~~.~~mathworks~~.~~com~~/~~company~~/~~newsletters/digest/nov02/dicom~~.~~html extensive built-~~in ~~support]~~ for DICOM header ~~and image data I/O with~~ the ~~[http:~~/~~/www~~.~~mathworks.com~~/~~access/helpdesk/help/toolbox/images/dicominfo~~.~~html~~ <~~code~~>~~dicominfo~~</~~code~~>], ~~[http://www~~.~~mathworks.com~~/~~access/helpdesk/help/toolbox/images/dicomread.html~~ <~~code~~>~~dicomread~~</~~code~~>], ~~and [http://www~~.~~mathworks.com/access/helpdesk/help/toolbox/~~images/~~dicomwrite.html~~ <~~code~~>~~dicomwrite~~</~~code~~>] functions. This is nice for quickly creating DICOM processing scripts to be run manually, but Matlab is relatively slow and difficult to call from non-interactive scripts. Therefore it's encouraged to port Matlab code into another language (preferably C++ or Python) for inclusion in the ~~[[diffusion processing pipeline]].~~		<pre>
			strings <SUSPECTED_DICOM_FILE> \| grep -i "dicom"
			strings <SUSPECTED_DICOM_FILE> \| grep -i "dcim"
			</pre>
			If you get output, that means that the DICOM magic string shows up somewhere in the file. Another good indication that you're dealing with some sort of DICOM data is that your collaborator told you so.

			== Volumes as DICOMs ==
			A single DICOM file stores only one 2-D image, and so various strategies exist for storing and transferring volumes and collections of volumes as DICOM images. Most commonly, you'll just get a directory full of dozens (if not hundreds) of <tt>.ima</tt> or <tt>.dcm</tt> files, each one storing a single slice. Some other strategies crop up from time to time, though, to represent a whole volume or a collection of volumes as a single file. If you have reason to believe that your data should be in DICOM format but it seems a little funky, it might be stored as a tarball or in "mosaic" format. Here are a couple clues that indicate you should consider these possibilities:
			* Matlab or Medcon claims that your file is not a DICOM
			* the file size is much larger than you'd expect for a single slice (which should be on the order of 100kB)
			* the number of files is much lower than you'd expect for a collection of slices (hundreds or maybe even thousands)
			* the DICOM header reports an unusually large slice resolution (> 256x256)

			=== Tar ===
			Sometimes many DICOM files (or even a whole directory structure of different files) are concatenated together into a single file using the Unix <tt>tar</tt> utility. If your presumed DICOM file seems a little funky, it might actually be a "tarball" (as the result of a <tt>tar</tt> concatenation is called) of DICOMs. Here's how to check:
			<pre>tar -tf <SUSPECTED_DICOM_FILE></pre>
			If you get non-error output, especially a list of <tt>.dcm</tt> or <tt>.ima</tt> filenames, then you're dealing with a tarball of DICOMs. Extract the original images as follows:
			<pre>tar -xf <SUSPECTED_DICOM_FILE></pre>

			The tarball may also have been compressed after concatenation; in which case you would need the <tt>-z</tt> option in the above commands:
			<pre>
			tar -tzf <SUSPECTED_DICOM_FILE>
			tar -xzf <SUSPECTED_DICOM_FILE>
			</pre>

	== Mosaic ==		=== Mosaic ===
	~~One~~ unusual storage strategy for DICOM-formatted medical images is the so-called "mosaic" scheme, in which a three-dimensional voxel volume is represented as a two-dimensional flat image. The volume is divided up into X-Y slices which are then arranged in 2D like a tile floor, with Z increasing left to right, top to bottom.		An unusual storage strategy for DICOM-formatted medical images is the so-called "mosaic" scheme, in which a three-dimensional voxel volume is represented as a two-dimensional flat image. The volume is divided up into X-Y slices which are then arranged in 2D like a tile floor, with Z increasing left to right, top to bottom. You can spot one of these by visual inspection or if the header shows an image size much larger than a single slice---a single slice is usually 128x128 or 256x256 voxels, while a mosaic file may be much larger than that, depending on the Z resolution of the volume.

	=== Code ===		==== Code ====
	The following scripts to handle DICOM mosaic files can be found in <tt>[file:///map/gfx0/common0/diffusion/Interface/bin/data/ /map/gfx0/common0/diffusion/Interface/bin/data/]</tt>:		The following scripts to handle DICOM mosaic files can be found in <tt>[file:///map/gfx0/common0/diffusion/Interface/bin/data/ /map/gfx0/common0/diffusion/Interface/bin/data/]</tt>:
	* <tt>processMosaics.m</tt> --- split all mosaic files matching a given pattern into DICOM and [[MRIimage]] files		* <tt>processMosaics.m</tt> --- split all mosaic files matching a given pattern into DICOM and [[MRIimage]] files
Line 13:		Line 36:
	* <tt>writeMosaicSlices.m</tt> --- write a collection of Matlab data volumes to DICOM and [[MRIimage]] files		* <tt>writeMosaicSlices.m</tt> --- write a collection of Matlab data volumes to DICOM and [[MRIimage]] files
	All of these can be launched non-interactively with <tt>matlabLauncher.py</tt>.		All of these can be launched non-interactively with <tt>matlabLauncher.py</tt>.

			== Matlab ==
			Matlab has [http://www.mathworks.com/company/newsletters/digest/nov02/dicom.html extensive built-in support] for DICOM header and image data I/O with the [http://www.mathworks.com/access/helpdesk/help/toolbox/images/dicominfo.html <code>dicominfo</code>], [http://www.mathworks.com/access/helpdesk/help/toolbox/images/dicomread.html <code>dicomread</code>], and [http://www.mathworks.com/access/helpdesk/help/toolbox/images/dicomwrite.html <code>dicomwrite</code>] functions. This is nice for quickly creating DICOM processing scripts to be run manually, but Matlab is relatively slow and difficult to call from non-interactive scripts. Therefore it's encouraged to port Matlab code into another language (preferably C++ or Python) for inclusion in the [[diffusion processing pipeline]].

	== Useful Links ==		== Useful Links ==

Jadrian Miles at 13:46, 13 March 2009

2009-03-13T13:46:12Z

← Older revision		Revision as of 13:46, 13 March 2009
Line 1:		Line 1:
	Files ending in <tt>'''.ima'''</tt> of <tt>'''.dcm'''</tt> are in the [http://medical.nema.org/ DICOM] [[Diffusion MRI\|medical image]] format. It is a widely used format that enjoyed great popularity but, in the [[diffusion MRI]] community at least, has been mostly superseded by [[NIfTI]].		Files ending in <tt>'''.ima'''</tt> or <tt>'''.dcm'''</tt> are in the [http://medical.nema.org/ DICOM] [[Diffusion MRI\|medical image]] format. It is a widely used format that enjoyed great popularity but, in the [[diffusion MRI]] community at least, has been mostly superseded by [[NIfTI]].

	== Matlab ==		== Matlab ==