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linrecon

Section: User Commands (1)
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NAME

linrecon - Runs a linear transformation in each voxel.

SYNOPSIS

linrecon <data file> <scheme file> <matrix file>

DESCRIPTION

Reads a linear transformation from the matrix file assuming the imaging scheme specified in the scheme file. Performs the linear transformation on the data in every voxel and outputs the result to the standard output. The ouput in every voxel is actually [exit code, ln(S(0)), p1, ..., pR] where p1, ..., pR are the parameters of the reconstruction. Possible exit codes are:

0. No problems.

6. Bad data replaced by substitution of zero, see modelfit(1).

The matrix must be R by (N+M), where N+M is the number of measurements and R is the number of parameters of the reconstruction. The matrix file contains binary double-precision floats. The matrix elements are stored row by row.

If the first command line argument is - the program reads data from the standard input.

EXAMPLES

Fit the diffusion tensor to the data in SubjectA.Bfloat using linear regression to the log measurements:

$ # Create the DT fitting matrix
$ dtmx -schemefile A.scheme > A_DTMX.Bdouble
$ # Run it over each voxel
$ linrecon SubjectA.Bfloat A.scheme A_DTMX.Bdouble -log > DiffTensorA.Bdouble

The above is equivalent to:

$ dtfit SubjectA.Bfloat A.scheme > DiffTensorA.Bdouble

To save a matrix from matlab in the right format, follow this example:

>> % The matrix has size 755x54. 755 reconstruction parameters and 54
>> % normalized measurements.
>> size(rbfkernel)

ans =

755 54

>> fid=fopen('/tmp/Q_BallBMX7_Matrix.Bdouble', 'w', 'b');
>> fwrite(fid, rbfkernel', 'double');
>> fclose(fid);

Then run

$ linrecon SubjectA.Bfloat A.scheme /tmp/Q_BallBMX7_Matrix.Bdouble -normalize > /tmp/QBALL_A.Bdouble

The matrix Q_BallBMX7_Matrix.Bdouble is for Q-Ball reconstruction, which uses the normalized measurements, hence the -normalize flag.

OPTIONS

-normalize: Tells the program to normalize the measurements and discard the zero measurements before the linear transform.
-log: Tells the program to transform the log measurements rather than the measurements themselves.

AUTHORS

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

BUGS

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

Linrecon