AirAlignlinear

AirAlignlinear is a Java gui wrapper for the AIR 5.2.1 (Roger Woods, UCLA) alignlinear program.
The utility itself is used to align image files. It is a general linear intramodality registration tool (within or across subjects, 2D or 3D).
For more information about the AIR package see the AIR 5 homepage.
AIR documentation for the alignlinear program

Invocation

java  AirAlignlinear 

java  AirToolChest 

java  GlobalWorkbench 

java  GlobalDesktop 

AirAlignlinear window

Information to be entered

• Input dir/file[list]
  File, directory, or ascii filelist, to be aligned.
• Standard file
  Standard file used to align input file(s).
• Air file output dir
  Directory to output the .air file(s) to.
• Logs dir
  Directory to output logs and air_params file (if created) to.
• Reslice
  Check this box if you wish to reslice the input files after they have been aligned.
• Reslice Settings...
  If reslice option is used this button presents all the options of the AirReslice interface.
• Suppress output messages
  This is not an AIR option, using it allows you to suppress default air output to the output window. However; the first and last files run will have their output displayed as well as a primitive progress update.

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Model, Cost, Preprocessing options..., Optimization options..., Init/Term files..., Standard Threshold, and Verbose mode, are explained in Roger Woods documentation of alignlinear.

• Menubar
• Toolbar
• Output window