The programs in the AIR package can be subdivided according to the types of files that they generate or modify.

Programs are available that will:

• generate new .air files
• modify or combine .air files
• generate new .warp files
• modify or combine .warp files
• generate or modify header files
• generate new image files
• use or generate ucf files
• use or generate binary files
• display information about a file
• create initialization files

• Programs that will generate new .air files
  • alignlinear (all forms of registration)
  • manualreslice (trial and error registration)
  • crop (crops empty planes from images)
  • reorient (rotates file 90 or 180 degrees or creates file's mirror image)
  • resize (clipping, shifting or padding with no rotation)
  • zoomer (interpolates file to cubic voxels)
• Programs that will modify or combine .air files
  • cd_air (change target directory)
  • combine_air (combine multiple .air files)
  • combine_warp (combine .air and .warp files)
  • definecommon_air (average together .air files)
  • invert_air (interconvert reslice file and standard file)
  • mv_air (change reslice file)
  • reconcile_air (resolve inconsistencies between .air files)
• Programs that will generate new .warp files
  • align_warp (nonlinear registration)
• Programs that will modify or combine .warp files
  • cd_warp (change target directory)
  • combine_warp (combine .air and .warp files)
  • mv_warp (change reslice file)
• Programs that will generate or modify header files
  • fixheader (correct header voxel sizes)
  • makeaheader (create new header)
  • setheadermax (change header maximum)
• Programs that will generate image files
  • crop (crops empty planes from images)
  • fuse (joins 3D volumes at their edges)
  • gsmooth (Gaussian smoothing)
  • layout (composite multiple slices onto a single 2D image)
  • magnify (Fourier interpolation to increase number of pixels)
  • manualreslice (arbitrary repositioning)
  • overlay_mask (superimposes a mask file onto a regular image file)
  • reorient (rotate 90 or 180 degrees or mirror image)
  • resize (clip, shift or pad data to change matrix size)
  • reslice (reposition based on .air file)
  • reslice_unwarp (reslices data based on numerical inversion of specified .warp file)
  • reslice_vector (reslices data based on specified vector field file)
  • reslice_warp (reposition based on .warp file)
  • reunite (combine single slices into multivolume data set)
  • separate (split multivolume data into single slices)
  • softmean (average files together)
  • zoomer (interpolate file to cubic voxels)
• Programs that will use or generate ucf files
  • reslice_ucf (reslices point list using a .air file)
  • reslice_unwarp_ucf (reslices point list based on numerical inversion of specified .warp file)
  • reslice_warp_ucf (reslices point list based on specified .warp file)
• Programs that will use or create binary files
  • binarize (use threshold to convert non-binary file to binary file)
  • binarymask (apply binary file to mask non-binary file)
  • binarymath (combine or compare binary files to create new binary file)
  • determinant_mask (creates a mask where the determinant of a .warp file is positive)
  • overlay_mask (superimposes a mask file onto a regular image file)
• Programs that will display information about a file
  • identify (compute hash value, verify header and image compatibility)
  • scanair (display contents of .air file)
  • scanheader (display contents of header file)
  • scan_vector (displays contents of .vector file)
  • scan_warp (display contents of .warp file)
• Programs that will create initialization files
  • manualreslice