hi rich,

thanks a lot indeed for your message.

>
> 1. Do you have any reason to believe that your T-image and the
> AFNI SPGR image are in the same coordinate space?

not really. i was using the 'orig' views of both the images. however, using the AC-PC aligned view didn't improve things.
also, i was using the -orient LPI tag with to3d , but that option doesn't exist with 3dcopy.

> 2. SPM may have stored the required information only in the
> .mat file, which AFNI does not process. It is possible that
> reslicing your data in SPM will fix some of these problems
> (That should zero out your .mat file and put as much of
> the relevant data as possible into the ANALYZE header).
>

i did as you suggested, it certainly improved the overlap a lot. however, the overlay still doesn't quite cover the whole brain.

> If you want me to take a look at it, upload your dataset
> using the "upload data" button on the message board.

that's indeed very kind. i am uploading the file named bhisma.tar.gz for your perusal. it has a readme with the problems.

>
> Also, I need to know exactly which AFNI SPGR file you are
> using.
>
i am using the SPGR that came with the latest AFNI distribution (6sep 2005), as part of the AFNI_data1/afni/ folder. the images are called anat* .


many thanks again for your help,

bhisma