Hi, Mrinmayi-

Just to add a bit to Hendrik's useful comment:
+ AFNI doesn't actively support any matlab stuff anymore
+ There used to be a brikload() function, that might still work.
+ AFNI reads/writes NIFTI, as well as BRIK/HEAD files. Some programs can output NIFTI directly, depending on your "-prefix .." option or other explicit flags, but others will mainly output BRIK/HEAD, which can be converted.
+ 3dAFNItoNIFTI is one way to convert, but you could also use 3copy, e.g.:

3dcopy DSET_BRIK DSET_NEW.nii.gz

or 3dcalc:

3dcalc -a DSET_BRIK -expr 'a' -prefix DSET_NEW.nii.gz

.... and you could use subbrick selectors in the latter, if that is useful.
+ Note that AFNI programs will often make use of an "AFNI extension" in the header, whether in a BRIK/HEAD or NIFTI file. We use these to store helpful information-- like file history, labels, degree of freedom info, etc. Other software don't propagate these, even if they are in a NIFTI file (which is fine, just their decision). It is possible/likely that the file you output from your Matlab processing will not have any of this useful information in it, just an FYI (that is, the history will not just be not added to, but it will probably not exist at all in that new file). I am not *sure* if this is the case, because I don't use Matlab, but just so you know that is something that might happen.

And I hope things are good in Milwaukee!

--pt