mbalign - Aligns the diffusion-weighted images within a single acquisition.
SYNOPSIS
mbalign
[options]
DESCRIPTION
Reads DWI in voxel-order data from the standard input, fits the DT model using RESOTRE,
synthetizes reference from the model, and aligns each measurement of input to its
synthetic reference. Finally, it gives the output as voxel-order big-endian data file.
This program requires an installation of FSL, as it uses FLIRT for alignment. By default
the program uses a 3D affine registration to align each image, although you can tell it
to use 3D rotations. Occasionally FLIRT fails when trying to compute 3D affine
registrations. When it does, the program computes a 3D rigid transformation instead, just
for that DWI. If that fails too, the output file contains a copy of the input image
volume for that measurement.
OPTIONS
mbalign processes options in command line order.
(1) Required options:
-inputfile < input voxel-order file>
The input file must have BIG-ENDIAN ordering.
-schemefile < Scheme file name>
-datadims < X Y Z>
Specifies the number of voxels in each dimension.
-voxeldims < x y z>
Specifies the voxel sizes in each dimension, in millimetres.
-sigma < noise standard deviation>
The approximate noise standard deviation, sigma. A suggested value is sqrt(E(M^2)/2),
where M is the signal in background and E denotes expectation over an ROI. A camino
program called datastats works it out for you. See datastats(1), modelfit(1).
(2) Optional options:
-outputfile < output voxel-order file>
Default outfile is derived from input file name, but user can specify the file name
including the directory.
-datatype < data type for input and output files>
Specifies the same data type for the input and output file. The data type can be any of
the following strings: "char", "short", "int", "long", "float" or "double". By default,
the input type is "float".
-bgmask < mask file>
The data type of mask file should be "short". See modelfit(1).
The program creates quite a lot of temporary files, which are stored in this directory.
Deault name is derived from input file name, current date time, and is a subdirectory of
"/tmp". But if "/tmp" is small, specifying an alternative location is necessary. User
needs a separate directory for each data set when running "mbalgin" multiple processes
concurrently. By default, the program removes the directory containing all the temporary
files, but user can tell it to keep it all by adding -keepjunk.
-fsldir < FSL directory>
Specifies the location of FSL installation, which is used to do the registration. Such as
".../common/fsl/fslSolaris". FSL must be installed to run mbalign.
-flirtsearchcost < search cost function used in flirt>
Default cost function is "mutualinfo" (Mutual Information). Other options are "corratio",
"normcorr", "normmi" and "leastsq".
-flirttransform < Transformation used in flirt>
Default transformation is "affine". The other option is "rigid".
-omat < file name>
Output transform matrix in ascii format.
-keepjunk
Tells the program to keep temporary files in the directory specified by "-tmpdir".
Default behaviour is to remove all temporary files before program finish.
-slicecheck < file name>
Specifies the root name of an analyze file that you can check the alignment in. After
registration, the file contains the corresponding slice of each DWI for comparison and to
check that nothing weird happened and that the alignment is good. If you omit
-slicecheck, it won't output this pair of files.
-eddy
Specifies registration for eddy-current induced distortion.
-scanner
Regards input file is in scanner-order. Command line example: -scanner -inputfile <file
name>
-scanout < output scanner-order file>
Adds an extra output file in scanner-order. This won't stop default voxel-order output.
-searchrange < angle>
Default is 90, which means search range is between -90 and 90 in all x, y and z
directions.
EXAMPLES
Do the registration on data set A.Bfloat, and store the output in A_AlignAffine.Bfloat:
