Hi Bob,

I ran FSL on some data and tried to visualize in AFNI. At first glance things seemed to work fine.

I took a directory with feat results and ran the FSL feat2afni script on it. That made links to a couple of files in the reg directory. I ran afni and loaded the data and was able to use the 2D viewers to get nice overlays.

From here things stop working. The rendering stuff doesn't work at all. The anatomicals and the functionals are not registered. Also since the data is still in analyze format, I wasn't able to use the reslicing functions, or any other AFNI function that would have helped me get around this. The 3dANALYZEtoAFNI function doesn't take the mat files into account.

I'd like to propse the following:
1. a script to properly convert fsl style analyze files to afni - including the effect of matfiles etc. All that would be needed is the .HEAD files with affine transformations included.
2. a script to take a feat directory and do this on all the files and end up with a sensible naming scheme including view names etc. to replace the feat2afni script with something better.
3. to properly interoperate and go back and forth between the two programs, a 3dAFNItoFSL function that creates FSL style analyze files with mats, etc.

We're happy to do the work, but would like some input from you and anyone else that wants to give it.

Thanks,
Souheil