Hi, Shankar-

OK, cool, let's see how long that takes.

The reason that the extents might matter: the warping program at the heart of @SSwarper (the latter is actually a wrapper for a few AFNI programs, with 3dQwarp being the primary workhorse) has to make a grid encompassing both dsets on which to work; so, if the source and base dsets are veery far apart, then it has to make a big grid, using lots of memory, and that might slow things down.

The extents you listed don't look super egregious; they might still be a bit far apart, for example consider the extents of MNI template for @SSwarper:

3dinfo -extent MNI152_2009_template_SSW.nii.gz 
-96.000000	96.000000	-96.000000	132.000000	-78.000000	114.000000

The brains you have might be relatively shifted a fair along in the anterior-posterior axis: MNI FOV extent [-96, 132], and one of your dset's FOV extent [-117, 76]-- could be (much) more than 20mm offset; something similar might be happening in the inf-sup directions.

If your current alignment doesn't go well, I think adding in the "-giant_move" option to @SSwarper might help. That will do a pre-alignment center-of-mass alignment (with a couple other alterations) that might help get the grids closer to start.

--pt