AFNI & FSL Interoperation

AFNI is a set of C programs for processing, analyzing, and displaying FMRI data. It runs on Unix+X11+Motif systems, including SGI, Solaris, Linux, and Mac OS X. It is available free (in C source code format, and some precompiled binaries) for research purposes.

One of AFNI's particular strengths is that it is a powerful display tool. Bob Cox has very kindly made some changes in AFNI which make it very easy to view FSL output, in particular, FEAT output, using AFNI. You can easily:

• View thresholded or unthresholded FEAT stats images, colour-overlaid onto lowres (example_func.hdr), structural (highres.hdr) or standard-space (standard.hdr) images, without having to transform the stats images, because AFNI understands the registration transforms saved in the FEAT directory.
• View thresholded or unthresholded FEAT stats images, colour-overlaid onto the filtered 4D data (filtered_func_data.hdr), and view time series by clicking on the coloured stats overlays.

To get this working, download and install the latest version of AFNI. Then:

• feat2afni <featdirectory.feat> (this is a short script necessary for FEAT5 analyses which makes links to certain files in the FEAT directory for AFNI to use - it will probably not be necessary once we have finished working with Bob Cox on the interoperation of AFNI and FSL).
  
  
• cd <featdirectory.feat>
  afni
  
  
• Load in an Anatomy image (eg example_func.hdr) by pressing Switch Anatomy (don't select by double-clicking; click once then press Set). Press one or more Image buttons.
  
  
• To view voxel intensity at the crosshair, you have to open all Image views and have the Define function view open. Then the value is displayed.
  
  
• Load in a stats image (eg thresh_zstat1.hdr) by pressing Switch Function. Press See Function.
  
  
• To make the colour overlay transparent press the down-arrow next to the 9 on an image viewer.
  
  
• To view stats overlaid on either highres or standard press Switch Anatomy and select the apropriate image.
  
  
• To view time series, load in filtered_func_data.hdr using Switch Anatomy and press one or more Graph buttons.
  
  
• To view a histogram of the current anatomical image, press Define Datamode -> Plugins -> Histogram.
  
  
• If you create a new image in a directory after starting afni, to get afni to realise it's there, you must press Define Datamode -> Rescan -> This.
  
  
• To create an image mask using AFNI: Load in an anatomical image by pressing Switch Anatomy. Press all three Image buttons. Press Define Datamode -> Plugins -> Draw Dataset. Press Choose Dataset and select your anatomical image. Set the Drawing Value to a value greater than the maximum value in your image. Set Drawing Mode to Filled Curve. Draw on any of the three Images using the middle mouse button. To undo the previous drawing click Undo in the AFNI Editor window (you can only undo one previous fill). Save the mask by clicking Save As in the AFNI Editor window (suppose you choose grot; your file will get saved as grot+orig.BRIK). To convert your mask from afni to analyse format run afni2avw grot+orig from the command line. To remove the background brain image and binarise your mask run
  avwmaths grot+orig -thr <val> -bin grot+orig from the command line, where the threshold value used is just below the value you filled the mask with.