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