bionic (1) CreateDTICohort.1.gz

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.

       -h

              Print the help menu (short version).  <VALUES>: 0

       --help

              Print the help menu.  <VALUES>: 1, 0