Diffusion MRI Matlab scripts

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

3rd Party Scripts

• Tools for NIfTI and ANALYZE images