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Restore

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restore

Section: User Commands (1)
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NAME

restore - Fits the diffusion tensor to diffusion MRI measurements robustly using the RESTORE algorithm by Chang et al MRM 53 2005.

 

SYNOPSIS

restore <data file> <scheme file> <noise std> [<outlier map file>] [options]

 

DESCRIPTION

Operation is similar to dtfit. The RESTORE algorithm requires an estimate of the
standard deviation of the background noise in the measurements, which it assumes is uniform across the image.

The exitcodes indicate the number of measurements that the RESTORE algorithm decided were outliers. The following exitcodes appear:

 -1: background voxel, no fitting performed.
  0: no outliers, no problems.
  2: non-linear fitting did not converge.
 1000 or greater: (exitcode - 1000) outliers ignored.

restore will optionally output an outlier map to indicate which measurements the algorithm classified as outliers. The outlier map is a voxel-order binary file containing a byte for each measurement with b > 0. Thus each voxel contains a byte for each non-zero wavenumber in the scheme file with the same ordering. If the byte is zero, the measurement was not an outlier and contributed to the fitted diffusion tensor; if the byte is one, the measurement is an outlier.

restore is a wrapper for modelfit (see modelfit(1)), which provides more command line options if required. The command

 restore <data file> <scheme file> <noise std> [<outlier map file>]

is equivalent to

 modelfit -inputfile <data file> -inversion -2 -schemefile <scheme file> 
          -sigma <noise std> -outliermap <outlier map file>

To read data from stdin, do

 cat <data file> | restore - <scheme file> <noise std>

See datastats(1) for help on how to compute sigma.

 

EXAMPLES

Fit the diffusion tensor to the data in SubjectA.Bfloat in which the background noise standard deviation is 35 using RESTORE:

restore SubjectA.Bfloat A.scheme 35.0 > DiffTensorA.Bdouble

Equivalently:

cat SubjectA.Bfloat | restore - A.scheme 35.0 > DiffTensorA.Bfloat

 

AUTHORS

Daniel Alexander <camino@cs.ucl.ac.uk>

 

SEE ALSO

modelfit(1), twotenfit(1), threetenfit(1), fa(1), trd(1), shfit(1), shanis(1), dtfit(1)

 

BUGS

The restore algorithm can get stuck in noisy background voxels. Remove background, for example, by adding a -bgthresh X option where X is the b=0 intensity below which voxels are background.

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Index

NAME

SYNOPSIS

DESCRIPTION

EXAMPLES

AUTHORS

SEE ALSO

BUGS

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Time: 02:07:11 GMT, December 04, 2017