Afni3dvolreg

To see the AFNI postscript documentation please go here.

To read the help documentation generated from the command line go here.

To learn about afni data types follow this link.

Invocation

java  Afni3dvolreg 

Afni3dvolreg window

Information to be entered

• Input dataset
  This is the file to be registered.
• Output prefix
  This is the prefix the output file will have.
• Verbosity
  This indicates the level of verbosity when running the program
• Final interpolation
  This is the method of interpolation used when performing alignments
• Zero pad edges with N voxels
  Pad the edges by N voxels containing the value zero.
• Time shift to slice
  If the input dataset is 3d + time, the slices will be time shifted to this slice prior to spatial registration.
• Clip output sub brick values
  The values in each ouput sub brick will be clipped so that it will be the same range as the corresponding input volume.
• Output 3drotate commands
  Fragmentary 3drotate commands needed to do the relalignments will be printed.
• Write 9 column file
  The motion parameters will be written to this file as a 9 column ascii file. To understand to the format go here.
• Write 6 column file
  The motion parameters will be written to this file as a 6 column ascii file containing roll, pitch, yaw, dS, dL, and dP. This file can be used with fim as an ort file.
• Enable overwrites
  Allow files to be overwritten with motion parameter data.
• 9 column file
  The parameters from the 9 column ascii file will be displayed.
• 6 column file
  The parameters from the 6 column ascii file will be displayed.
• Rotation parent
  The dataset given will be used in an additional transformation before computing the final output dataset.
• Grid parent
  The input dataset will be shifted to match the grid of this dataset.
• Select base sub brick from input or selected dataset
  This sets the sub brick from the base dataset.
• Select dataset
  The dataset given will be used as the base brick.
• Iteration Options...
  These are options which control the iterated linearized weighted least squares algorithm.
  • Iteration Options... Maximum iterations
    This sets the maximum number of iterations for convergence.
  • Iteration Options... Movement threshold
    Iterations converge when maximum movement is less than this value in voxels.
  • Iteration Options... Distance in voxel size
    This is the distance used to comupte image derivatives using finite differences.
  • Iteration Options... Rotation threshold
    Iterations converge when maximum rotation is less than this degrees.
  • Iteration Options... Autotrim intermediate volumes
    Intermediate volumes will be trimmed to a smaller region (determined by the weight volume). This is a measure to conserve memory.
  • Iteration Options... Use first sub-brick as weight in final pass
    The first sub-brick of the input dataset will be used as the weight volume during the final pass.
  • Iteration Options... Interpolation for estimation parameters
    This method is used to perform the initial interpolation.
  • Iteration Options... Perform edging on base brick
    This region around the edges of the base volume will have the default weight set to zero. This region can be specified in pixels or a percentage of brick size.
  • Iteration Options... Set weighting
    The weighting applied to each voxel is made proprotional to the brick specified.
  • Iteration Options... Select sub brick
    This is the sub brick of the dataset to be used for weighting.
  • Iteration Options... Enable two passes
    Allow two passes of the registration algorithm to be performed on the input dataset.
  • Iteration Options... Copy base brick origin
    Make the output dataset have the same origin as the base dataset.
  • Iteration Options... Blurring factor
    This sets the blurring factor of the first pass of the registration algorithm.
  • Iteration Options... Steps
    This is the number of steps along each direction when performing coarse shifts in the first pass.
  • Iteration Options... Step size
    This is the size of the steps in voxels.

• Menubar
• Toolbar
• Output window