Ubuntu Manpage: CreateDTICohort - part of ANTS registration suite

NAME

       CreateDTICohort - part of ANTS registration suite

DESCRIPTION

COMMAND:
CreateDTICohort

CreateDTICohort implements the work of Van Hecke et al. (On the construction of a ground truth
framework for evaluating voxl-based diffusion tensor MRI analysis methods, Neuroimage 46:692-707,
2009) to create simulated DTI data sets. The only difference is that all registrations (both for
the input population and for the output population) are assumed to take place outside of this
program.

OPTIONS:

-d, --image-dimensionality 2/3

This option forces the image to be treated as a specified-dimensional image. If not specified, the
program tries to infer the dimensionality from the input image.

-a, --dti-atlas inputDTIAtlasFileName

A diffusion tensor atlas image is required input for creating the cohort.

-x, --label-mask-image maskImageFileName
lowerThresholdFunction

A mask image can be specified which determines the region(s). to which the simulated pathology
operations are applied. See also the option '--pathology'. If no mask is specified one is created
by thresholding the atlas FA map at 0.2 unless a lower threshold is specified.

-n, --noise-sigma <noiseSigma=18>

This parameter characterizes the Rician noise in the original DWIimages. Van Hecke uses the
noise-estimation method of Sijbers et al. "Automatic estimation of the noise variance from the
histogram of a magnetic resonance image", Phys. Med. Biol. 52:1335-1348, 2007.

-p, --pathology
label[<percentageChangeEig1=-0.05>,<percentageChangeAvgEig2andEig3=0.05>,<numberOfVoxels=all or
percentageOfvoxels>]

The user can specify the simulated pathology in a given area using a label mask. If no label is
prepended to parameters, the specified parameters are applied to all labels.Pathology is simulated
by changing the eigenvalues. Typically this involves a decrease in the largest eigenvalue and an
increase in the average of the remaining eigenvalues. Change is specified as a percentage of the
current eigenvalues. However, care is taken to ensure that diffusion direction does not change.
Additionally, one can specify the number of voxels affected in each region or one can specify the
percentage of voxels affected. Default is to change all voxels. Note that the percentages must be
specified in the range [0,1]. For dimension=3 where the average transverse diffusion eigenvalues
are altered, this change is propagated to the distinct eigenvalues by forcing the ratio to be the
same before the change.

-w, --dwi-parameters [B0Image,directionFile,bvalue]
[B0Image,schemeFile]

This option specifies the parameters of the output diffusion-weighted images including the
directions and b-values. The directions are specified using a direction file which has as its
first line the number of directions.Each successive three lines contains the x, y, and z
directions, respectively, and a single b-value. Note that several direction files of this format
are distributed with the Camino DTI toolkit
(http://web4.cs.ucl.ac.uk/research/medic/camino/pmwiki/pmwiki.php). Alternatively, one can
specify a scheme file where each direction is specified followed by a b-value for that direction,
i.e. <x1> <y1> <z1> <bvalue1> ... <xN><yN><zN><bvalueN>.

-r, --registered-population textFileWithFileNames.txt

If one wants to introduce inter-subject variabilitya registered DTI population to the DTI atlas is
required. This variability is modeled by a PCA decomposition on a combination of the first
eigenvalue image and the average of the second and third eigenvalues.The registered image file
names are specified using a text file where each line is the name of an individual DTI.

-o, --output [outputDirectory,fileNameSeriesRootName,<numberOfControls=10>,<numberOfExperimentals=10>]

The output consists of a set of diffusion-weighted images for each subject. Each file name is
prepended with the word 'Control' or 'Experimental'. The number of control and experimental
subjects can be also be specified on the command line. Default is 10 for each group.