Afni3dmerge

Afni3dmerge is a wrapper for the AFNI (RW Cox, NIH) waver application.
3dmerge -- Program to average or otherwise merge multiple 3D datasets
AFNI 3dmerge was written by R.W. Cox, Medical College of Wisconsin.
For more information about the AFNI package, see the AFNI Homepage

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 Afni3dmerge

Afni3dmerge window

Information to be entered

• Image dataset(s)
  The datasets can be specified by one with the Browse and Brick buttons.
• Image directory
  All of the datasets in the given directory will be used.
• Image filelist
  All of the datasets listed in this text file will be used.
• Brick...
• Prefix
  The general form of the dataset filenames is "prefix+view.NAME" and the text typed in will replace the "prefix" section of the output filename. Note that this program will fail if you specfify a prefix that is already used by another file in the same directory.
• Session
  This the directory where the output dataset will be written.
• Copy threshold data to output dataset
  If there is one functional input dataset, then the theshold data from the dataset will be copied to the output dataset without any alterations.
• Select intensity storage type
  The intensity storage type may be chosen from the following:
  • byte
  • short
  • float
• Select threshold storage type
  The threshold storage type may be chosen from the following:
  • byte
  • short
  • float
• Delete voxels that are zero in N datasets
  Remove voxels that are zero in N or more datasets.
• Perform clustering
  Remove data not inside the clusters.
• Cluster Connection Radius in mm
  The cluster connectivity distance in mm. It is required that this value be positive and should be slightly over one voxel width.
• Minimum Cluster Volume in ml
  It is required that this value not be zero and in micro liters.
• Perform merging
  Specify how input datasets are merged.
• No scaling
  If the output dataset is written as shorts, then the output dataset will not be scaled to the max range.
• Type of merging
  The user may choose the following ways to merge the input datasets:
  • mean - merge by averaging intensities
  • non-zero mean - merge by averaging intensities, not counting zeros
  • max - merge by taking the max intensity
  • abs max - merge by taking the max absolute intensity
  • signed abs max - merge by taking the max signed intensity
  • count - merge counting the number of non-zero voxels
  • order - merge by taking the first non-zero voxel
  • fisher - merge by taking the arctanh of each input dataset, averaging them, and then outputing the tanh of the average. If the input datasets are stored as shorts, the input values are scaled by 0.0001 and the output values are scaled by 10000. This option is for merging bricks of correlation coefficients.
• Editing Options...
• Merge thresholds with fisher method
  This option merges threshold data using the same method as with intensities. This option is applicable if the input datsets are either fico or fith types.
• Apply merging and editing options to all sub bricks uniformly
  This allows 3d + time datasets can be used as input. Please read the documentation from the program since there are some restrictions that come with its use.
• Verbose
  Print out extra information about the operation of 3dmerge.
  

• Menubar
• Toolbar
• Output window