Content-type: text/html Manpage of fsl2scheme

fsl2scheme

Section: User Commands (1)
Index Return to Main Contents

 

NAME

fsl2scheme - converts b-vectors and b-values from FSL format to a Camino scheme file.

 

SYNOPSIS

fsl2scheme -bvecfile <bvecs> -bvalfile <bvals> -diffusiontime <secs>
 -bscale <factor> [-flipx] [-flipy] [-flipz] [-usegradmod]

 

DESCRIPTION

This program reads gradient directions and b-values in FSL format and creates a Camino scheme file.

The output is a BVECTOR scheme file:


 VERSION: BVECTOR
 g_x g_y g_z b
 ...
 g_x g_y g_z b

Note that the diffusion time is not stored here, only the b-values. One gradient vector [g_x, g_y, g_z] is stored for each measurement, along with a b-value. These vectors will be normalized to unity automatically for b > 0 measurements. If b = 0, the gradient direction may be [0 0 0].

The b-values are scaled by default, to give units of s / m^2. The program assumes that the b-values in FSL format are in units of s / mm^2, and scales by 10^6 to give s / m^2. The scaling can be set to some other value with -bscale.

The b-values may additionally be scaled by the gradient direction magnitude. Some scanners will factor the gradient magnitude into the b-value. If the gradient directions have magnitude |g| = sqrt(g_x^2 + g_y^2 + g_z^2), and the nominal b-value is beta, then the actual b-value is beta * |g|^2. To follow this convention, use the -usegradmod option. The gradient directions will still be normalized to unity in the output, and the b-value will be scaled appropriately.

These scheme files do not restrict the position of b=0 scans in the scheme, so there is no need to re-order your data.

 

EXAMPLES


   fsl2scheme -bvecfile bvecs -bvalfile bvals -diffusiontime 0.04 -version 0 > A.scheme

Create a version 2 scheme file, keeping b in native units.


   fsl2scheme -bvecfile bvecs -bvalfile bvals -bscale 1 > A.scheme2

Create a scheme file for a scan that is repeated twice


   fsl2scheme -bvecfile bvecs -bvalfile bvals -bscale 1 -numscans 2 > A.scheme

 

OPTIONS

-bvecfile <bvecs>
The file containing the b-vectors. This is a text file of format


 x(1) x(2)... x(N+M)
 y(1) y(2) ... y(N+M)
 z(1) z(2) ... z(N+M)

where the gradient direction for measurement (i) is [x(i), y(i), z(i)], and there are M unweighted and N diffusion-weighted measurements.

-bvalfile <bvals>
The file containing the b-values. This is a text file of format

b(1) b(2) ... b(N+M)

where there are M unweighted (b = 0) and N diffusion-weighted measurements.

-bscale <factor>
Scaling factor to convert the b-values into different units. Default is 10^6.

-flipx
Negate the x component of all the vectors.

-flipy
Negate the y component of all the vectors.

-flipz
Negate the z component of all the vectors.

-interleave
Interleave repeated scans. Only used with -numscans. If this is selected, the output will be interleaved, so you will have measurement 0 repeated numScans times, then measurement 1, etc.

-numscans <number>
Output all measurements number times, used when combining multiple scans from the same imaging session. The default behaviour is to repeat the entire block of measurements, like you'd get from copying and pasting the scheme number times. If -interleave is specified, then identical measurements are grouped together.

-usegradmod
Use the gradient magnitude to scale b. This option has no effect if your gradient directions have unit magnitude. It should only be used if your scanner does not normalize the gradient directions.

 

AUTHORS

Philip Cook <camino@cs.ucl.ac.uk>

 

SEE ALSO

camino(1)

 

BUGS


 

Index

NAME
SYNOPSIS
DESCRIPTION
EXAMPLES
OPTIONS
AUTHORS
SEE ALSO
BUGS

This document was created by man2html, using the manual pages.
Time: 02:06:54 GMT, December 10, 2011