Afni3drefit

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 Afni3drefit

For information on how to invoke the command line program, 3drefit, please go here.

Afni3drefit window

Information to be entered

• Input dataset
  The name of the header file that you wish to edit.
• Create backup
  Write a copy of the header file to this file.
• Enable overwrites
  A backup file will be created even if it already exists.
• Orientation
• Change parent
  Change the anatomical parent of the dataset.
• New parent
  The name of the dataset that will be the new anatomical parent.
• No parent
  Delete the anatomical parent information from the dataset.
• Self parent
  Set the anatomical parent of the dataset to itself.
• x-axis in mm
  Set the voxel size in millimeters along the x-axis.
• y-axis in mm
  Set the voxel size in millimeters along the y-axis.
• z-axis in mm
  Set the voxel size in millimeters along the z-axis.
• TR
  Set the TR if the file is a 3D+time dataset.
• Remove time offsets
  Remove the temporal offsets for the slices in a 3D+time dataset.
• Origin
  Set the origin of the dataset.
• Origin Options...
  These settings change the location of the origin.
• Origin Options... Copy from file
  Copy the origin settings from another AFNI dataset.
• Origin Options... Other options
  Allow the choice of a series of options for each axis.
• Origin Options... no change
  Do not change the position of the origin in this dimension.
• Origin Options... recenter
  Recenter the origin in the dimension.
• Origin Options... place at
  Place the origin in this location in millimeters along this dimension.
• Origin Options... shift by
  Shift the origin in millimeters along this dimension. Note that you cannot change the orientation and shift the origin at the same time.
• Generate new id
  Give a new id code to the dataset.
• View
  Change the view of the .HEAD and the .BRIK file to one of the following: orig (Original view), acpc (AC-PC aligned), or tlrc (Talairach-Tournoux grid).
• Remove warp information
  Remove all warping information from the header.
• Byteorder
  Change the byteorder settings in the header to one of the following: NATIVE_ORDER (native of the machine running 3drefit), LSB_FIRST (least significant bit first), or MSB_FIRST (most significant bit first). Note that the .BRIK file will not be changed. Please use the AFNI programs 2swap or 4swap to change the .BRIK file.
• Volreg Options...
  These settings modify VOLREG fields of the header.
• Volreg Options... Change matrix with index
  Change the matrix-vector of the transformation from 3dvolreg. It is possible that there will be more than one entry for the dataset. You can select which one to change by specifying an index. The index corresponds to a sub-brick of the same index.
• Volreg Options... Change input center (x,y,z)
  Change the xyz coordinates (Dicom order) of the center of the input dataset to 3dvolreg.
• Volreg Options... Change base center (x,y,z)
  Change the xyz coordinates (Dicom order) of the center of the base dataset to 3dvolreg.
• Time origin
  Set the time origin of a 3D+time dataset to this value.
• Add empty marker set
  Create a empty set AC-PC markers, if the file is anatomical, an original view, and not a 3D+time dataset.
• Types...
• Statistical parameters
  Set the staticical parameters for functional datasets.
• Keyword
  Change the keyword list for the dataset.
• Keyword Options...
  These settings change the keyword list attribute for the dataset.
• Keyword Options... Append
  Append the current keyword list with the given text.
• Keyword Options... Replace
  Replace the current keyword list with the given text.
• Keyword Options... Delete
  Delete the keyword list.
• Sub Brick
  Change values for sub bricks in the dataset.
• Sub Brick Options...
  These settings change attributes for sub bricks.
• Sub Brick Options... Set a single sub brick
  Apply changes to the single sub brick given only.
• Brick...
• Sub Brick Options... Set all sub bricks
  Apply changes to all sub bricks in the dataset.
• Sub Brick Options... Add label
  Use the given text as a label for the sub brick.
• Statistical Parameters
• Sub Brick Options... Change keyword list
  Change the keyword list for the chosen sub bricks.
• Sub Brick Options... Append
  Append the current sub brick keyword list with the given text.
• Sub Brick Options... Replace
  Replace the current sub brick keyword list with the given text.
• Sub Brick Options... Delete
  Delete the keyword list of the sub brick.

• Menubar
• Toolbar
• Output window