AirAlign

AirAlign is a wrapper to run the Automated Image Registration (AIR) alignlinear and reslice programs over a directory of images in ANALYZE format. For more information about the AIR package, by Roger Woods, UCLA, see the AIR homepage

Invocation

java  AirAlign 

AirAlign window

AirAlign takes ANALYZE format images as input. To convert image to data to ANALYZE format, see the FormatConvert program. This GUI only permits the user to set a subset of the alignlinear flags, those that are commonly changed in registering functional MRI images. Default values are used for the remaining paraemters. See the AIR homepage for details.

Information to be entered

• Input directory
  Enter the directory containing the images, in analyze format, to be aligned. All images in the directory will be aligned.
• Air files directory
  Enter the name of an output directory, where the AIR matrix files will be written. This directory will be created if it does not exist. If it already exists, it must be empty.
• Reslice directory
  Enter the name of the direcctory where the resliced (aligned) images will be written. This directory will be created if it does not exist. If it does exist, it must be empty. If you do not choose to reslice your images, this field will be ignored.
• Logs directory
  Enter a directory to hold the various log files generated by this program: output logs from alignlinear and reslice, and the files containing the list of images that were aligned. If this directory does not exist, it will be created.
• Temp directory
  Enter the name of the temp directory that will be used if files need to be uncompressed, or split out into individual slice files. A uniquely named directory will be created in this temp directory, and then deleted. The temp directory you enter here must already exist.
• Parallelism
  If AirAlign has been installed for parallel usage, you may select the number of processors to use and the align operation will run in parallel. Note that of the number of processors you select, one will be a "master" processor, so, choose one more than the number of processors that you really want busy.
• Verbose output
  Check this box to get additional output information.
• View results
  
  • on -- show graphs of estimated pitch/roll/yaw x/y/z motion
  • off -- no graph display
  • view ONLY -- only show graphs from a previous run, do not run an alignjob. In this case the air files in the Air Files Directory are displayed, all other input fields are ignored.
• Align options...
  The align options pertain to flags that will be passed to the AIR alignlinear program. Defaults will be used for the parameters not set here, see the AIR web page for details.
  • Align options... Standard file
    Enter the name of the standard file, ie the file to which all the other files will be registered (the standard file will also be registered to itself). This file must exist in the input directory.
  • Align options... Threshold
    Enter the intensity threshold, such that all voxels with intensities above this threshold are brain voxels, and all voxels with intensities below this threshold are background voxels. This value will be passed to the alignlinear t1 and t2 flags.
  • Align options... Smoothing fwhm xy
    Set the full width half max (FWHM) value, in mm, for the smoothing applied along the x and y dimensions of the standard and target images. This smoothing is only used internally during the parameter search and is not reflected in the final resliced images. This value will be passed as the first 2 parameters to the alignlinear b1 and b2 flags.
  • Align options... Smoothing fwhm z
    Set the full width half max (FWHM) value, in mm, for the smoothing applied along the z dimension of the standard and target images. This smoothing is only used internally during the parameter search and is not reflected in the final resliced images. This value will be passed as the 3rd parameter to the alignlinear b1 and b2 flags.
  • Align options... Convergence
    Set the convergence threshold for determining when the cost function's difference estimation is small enough to halt the iterative parameter search. This value will be passed to the alignlinear -c flag.
  • Align options... Model (dof)
    Choose the model used for the registration parameters:
    • 2D-3dof: 2D, slicewise registration, 3 degrees of freedom, yaw, xshift yshift. AIR model -m 23
    • 2D-6dof: 2D, slicewise registration, 6 degrees of freedom, yaw, xshift, yshift, plus affine parameters. AIR model -m 26
    • 3D-6dof: 3D registration, 6 degrees of freedom, roll, pitch yaw, xshift, yshift, zshift. AIR model -m 6
    • 3D-12dof: 3D registration, 12 degrees of freedom, roll, pitch yaw, xshift, plus affine parameters. AIR model -m 12
  • Align options... Cost function
    Choose the cost function used to estimate the similarity between the standard and target images, and minimized during the parameter search.
    • std. dev. of ratio: standard deviation of image ratio, AIR function -x 1
    • least sq.: least squares, AIR function -x 2
    • scaled least sq.: scaled least squares, AIR function -x 3
  • Align options... Initial sampling
    Choose the initial sampling factor to select a subset of voxels for the first pass in the hierarchical registration algorithm. This factor will be passed to the alignlinear -s flag, with default decrement ratio of 3 and final sampling of 1.
  • Align options... Save params in text file
    Check this box to have AirAlign write an ascii tab delimited file to the logs directory containing the pitch/roll/yaw x/y/z parameter data. Enter the filename in the textbox. The file will have 6 columns: pitch roll yaw xshift yshift zshift, and, 1 row for each image/slice aligned.


• Reslice options...
  The reslice options pertain to flags that will be passed to the AIR reslice program.
  • Reslice options... Produce resliced images
    Check this box to call the AIR reslice program and transform the input images based on the air matrix files calculated by alignlinear.
  • Reslice options... Interpolate to cubic voxels
    Check this box to enable interpolation to cubic output image voxels. The default, off, leaves voxel sizes in the output images the same as in the input images.

• Menubar
• Toolbar
• Output window