Dear Bob et. al.,

I've been playing around with interoperating AFNI and FSL and have come up with the following feature request.

I'm using to3d to convert in my Siemens Numaris 4.0 data (thanks bob!). So far so good, all the images from the same scanning session are essentially registered no matter what slice prescription/orientation I used.

Next I want to convert some of the data to the analyze flavor used by FSL. I use 3dAFNItoANALYZE and I get .img and .hdr. Now I'm in trouble because an axial scan and a sagittal scan are no longer in register as far as FSL is concerned. It would be really slick to generate the .mat file from the .HEAD info. What's an easy way to turn the rotation and translation attributes into a single affine transformation and then make them consistent with the FSL convention?

Now after doing a bunch of stuff in FSL, I want to go back and look at my data in AFNI and use some AFNI tools on it. I can read everything back in as .hdr, .img pairs, but then I've lost orientation information again. I know that if all I care about is overlaying the stats on a hires in "common" space that's solved, but I really would like to get at all the data. I've poked into the thd functions to see how you read in the feat directory stuff and it seems pretty straightforward. Would it be possible to add reading of the .mat files as a generic feature? I'm imagining something like an environment variable that says if the the .img, .hdr pair has an associated .mat file, use it and assume it's FSL convention. A later extension would allow you to say SPM convention - I'm not asking for that one, I'm just imagining what someone else might want .

Sorry for the overly long message. Does any of this make sense? I'm happy to do this work myself if I'm pointed in the right direction and it can be folded into the distribution in some sensible way.

Thanks,
Souheil