Diffusion MRI Matlab scripts - Revision history

Jadrian Miles: Updated directory path to $G from old /map/gfx0

2015-08-26T15:46:00Z

Updated directory path to $G from old /map/gfx0

← Older revision		Revision as of 15:46, 26 August 2015
Line 1:		Line 1:
	There are many Matlab scripts in <tt>~~[file:~~///~~map/gfx0/common0/diffusion/Interface/bin/data /map/gfx0/common0/diffusion/Interface/bin/data]~~</tt> that are useful for manipulating [[diffusion MRI]] data. These generally fall into two groups: those used in the [[diffusion processing pipeline]] for non-interactive conversion to the VRL in-house [[MRIimage]] format, and those used interactively to inspect and troubleshoot data.		There are many Matlab scripts in <tt>$G/project/brain/pipeline</tt> that are useful for manipulating [[diffusion MRI]] data. These generally fall into two groups: those used in the [[diffusion processing pipeline]] for non-interactive conversion to the VRL in-house [[MRIimage]] format, and those used interactively to inspect and troubleshoot data.

	For non-interactive applications, the utility program <tt>matlabLauncher.py</tt> can be used to call a Matlab function with specific arguments from the command line.		For non-interactive applications, the utility program <tt>matlabLauncher.py</tt> can be used to call a Matlab function with specific arguments from the command line.

Jadrian Miles at 00:03, 13 October 2009

2009-10-13T00:03:41Z

← Older revision		Revision as of 00:03, 13 October 2009
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	** <tt>strjoin.m</tt> --- join a cell array of strings together into a single string, separated by some delimiter		** <tt>strjoin.m</tt> --- join a cell array of strings together into a single string, separated by some delimiter
	** <tt>strsplit.m</tt> --- split a single string containing some delimiter into a cell array of delimited strings		** <tt>strsplit.m</tt> --- split a single string containing some delimiter into a cell array of delimited strings

			=== 3rd Party Scripts ===
			* [http://www.mathworks.com/matlabcentral/fileexchange/8797 Tools for NIfTI and ANALYZE images]

	[[Category:Diffusion MRI]][[Category:Software]]		[[Category:Diffusion MRI]][[Category:Software]]

Jadrian Miles at 22:41, 6 July 2009

2009-07-06T22:41:56Z

← Older revision		Revision as of 22:41, 6 July 2009
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	** <tt>processMosaics.m</tt> --- convert from a directory full of [[DICOM]] Mosaic files		** <tt>processMosaics.m</tt> --- convert from a directory full of [[DICOM]] Mosaic files
	* '''Read''' images in various formats from disk and create Matlab structures from them		* '''Read''' images in various formats from disk and create Matlab structures from them
	** <tt>readMriImage.m</tt> --- read a ~~single~~ [[MRIimage]]		** <tt>readMriImage.m</tt> --- read a directory of [[MRIimage]] volumes
	** <tt>readMriImageVolume.m</tt> --- read ~~an entire volume~~ of [[MRIimage]]s		** <tt>readMriImageVolume.m</tt> --- read a single of [[MRIimage]] volume
	** <tt>readDicomDir.m</tt> --- read a directory of [[DICOM]] images		** <tt>readDicomDir.m</tt> --- read a directory of [[DICOM]] images
	** <tt>stackFromPattern.m</tt> --- read an arbitrary collection of [[DICOM]] images matching a pattern		** <tt>stackFromPattern.m</tt> --- read an arbitrary collection of [[DICOM]] images matching a pattern

Jadrian Miles: Diffusion MRI Matlab Scripts moved to Diffusion MRI Matlab scripts: Article titles only get capitalized for initial words and proper nouns

2009-07-06T22:34:41Z

Diffusion MRI Matlab Scripts moved to Diffusion MRI Matlab scripts: Article titles only get capitalized for initial words and proper nouns

← Older revision	Revision as of 22:34, 6 July 2009
(No difference)

Jadrian Miles: New page: There are many Matlab scripts in `[file:///map/gfx0/common0/diffusion/Interface/bin/data /map/gfx0/common0/diffusion/Interface/bin/data]` that are useful for manipulating [[diffusio...

2009-07-06T22:33:29Z

New page: There are many Matlab scripts in <tt>[file:///map/gfx0/common0/diffusion/Interface/bin/data /map/gfx0/common0/diffusion/Interface/bin/data]</tt> that are useful for manipulating [[diffusio...

New page

There are many Matlab scripts in <tt>[file:///map/gfx0/common0/diffusion/Interface/bin/data /map/gfx0/common0/diffusion/Interface/bin/data]</tt> that are useful for manipulating [[diffusion MRI]] data. These generally fall into two groups: those used in the [[diffusion processing pipeline]] for non-interactive conversion to the VRL in-house [[MRIimage]] format, and those used interactively to inspect and troubleshoot data.

For non-interactive applications, the utility program <tt>matlabLauncher.py</tt> can be used to call a Matlab function with specific arguments from the command line.

* '''Batch Convert''' several files of a given type to [[MRIimage]]
** <tt>processDicoms.m</tt> --- convert from a directory full of single-slice [[DICOM]]s
** <tt>processMosaics.m</tt> --- convert from a directory full of [[DICOM]] Mosaic files
* '''Read''' images in various formats from disk and create Matlab structures from them
** <tt>readMriImage.m</tt> --- read a single [[MRIimage]]
** <tt>readMriImageVolume.m</tt> --- read an entire volume of [[MRIimage]]s
** <tt>readDicomDir.m</tt> --- read a directory of [[DICOM]] images
** <tt>stackFromPattern.m</tt> --- read an arbitrary collection of [[DICOM]] images matching a pattern
** <tt>splitMosaic.m</tt> --- read a single [[DICOM]] mosaic file
** <tt>splitMosaicList.m</tt> --- run <tt>splitMosaic</tt> on each of a list of files
** <tt>readTubegenLineFile.m</tt> --- read a <tt>[[tubegen]]</tt> <tt>.data</tt> or <tt>.nocr</tt> file
* '''Write''' Matlab structures to disk in various formats
** <tt>writeVolumes.m</tt> --- write a collection of Matlab data volumes to [[MRIimage]] and/or [[DICOM]] files
** <tt>writeTubegenLineFile.m</tt> --- write a cell array of three-column Matlab arrays to a <tt>[[tubegen]]</tt> <tt>.nocr</tt> file
* '''Inspect''' and troubleshoot data interactively
** <tt>viewSlice.m</tt> --- show a single 2-D slice of an array with a realistic gamma-corrected monochrome colormap
** <tt>stackToVideo.m</tt> --- show 2-D slices of an array as a video, sweeping the viewing slice along the Z axis
** <tt>makeMriAtlas.m</tt> --- read MRIimage data, generate a mosaic for each volume, and write the mosaics to disk as PNGs
** <tt>stackToMosaic.m</tt> --- flatten an array to 2-D by assembling slices into a tiled 2-D matrix (view the output with <tt>viewSlice</tt>)
** <tt>viewDicomDir.m</tt> --- show all 2-D [[DICOM]] images in a directory as a video
* '''Utility''' functions used in the above
** <tt>getDicomIdentifiers.m</tt> --- get the b-value and gradient ID from the [[DICOM]] header (assuming the Siemens file naming scheme)
** <tt>patternToFileList.m</tt> --- generate a cell array of full paths to non-directory files matching a simple (not regex) path pattern
** <tt>copyType.m</tt> --- change the type (''e.g.'' <tt>uint16</tt> or <tt>double</tt>) of one object to match that of another object
** <tt>searchUpward.m</tt> --- find a file whose name matches a given regular expression in the deepest directory above a specified path
** <tt>strjoin.m</tt> --- join a cell array of strings together into a single string, separated by some delimiter
** <tt>strsplit.m</tt> --- split a single string containing some delimiter into a cell array of delimited strings

[[Category:Diffusion MRI]][[Category:Software]]

Diffusion MRI Matlab scripts - Revision history

Jadrian Miles: Updated directory path to $G from old /map/gfx0

Jadrian Miles at 00:03, 13 October 2009

Jadrian Miles at 22:41, 6 July 2009

Jadrian Miles: Diffusion MRI Matlab Scripts moved to Diffusion MRI Matlab scripts: Article titles only get capitalized for initial words and proper nouns

Jadrian Miles: New page: There are many Matlab scripts in [file:///map/gfx0/common0/diffusion/Interface/bin/data /map/gfx0/common0/diffusion/Interface/bin/data] that are useful for manipulating [[diffusio...

Jadrian Miles: New page: There are many Matlab scripts in `[file:///map/gfx0/common0/diffusion/Interface/bin/data /map/gfx0/common0/diffusion/Interface/bin/data]` that are useful for manipulating [[diffusio...