Thank you Tom! I do get a graphical interface screen and I do enter 250 for the FOV, as 25X25cm is the FOV of my images.

I just found instructions on how to enter FOV into command line (http://afni.nimh.nih.gov/pub/dist/doc/program_help/to3d.html) and this is the command I used:

to3d -time:zt 124 1 1s seq+z -xFOV 250A-P -yFOV 250S-I -zFOV 90L-90R '3D:-1:0:256:256:1:filename'

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THE INSTRUCTIONS FROM THE SITE ABOVE:
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COMMAND LINE GEOMETRY SPECIFICATION [* NEW IN 1996 *]
-xFOV -
or or
-xSLAB -

(Similar -yFOV, -ySLAB, -zFOV and -zSLAB option are also present.)

These options specify the size and orientation of the x-axis extent
of the dataset. means a dimension (in mm); is
an anatomical direction code, chosen from
A (Anterior) P (Posterior) L (Left)
I (Inferior) S (Superior) R (Right)
Thus, 20A-30P means that the x-axis of the input images runs from
20 mm Anterior to 30 mm Posterior. For convenience, 20A-20P can be
abbreviated as 20A-P.

-xFOV is used to mean that the distances are from edge-to-edge of
the outermost voxels in the x-direction.
-xSLAB is used to mean that the distances are from center-to-center
of the outermost voxels in the x-direction.

Under most circumstance, -xFOV , -yFOV , and -zSLAB would be the
correct combination of geometry specifiers to use. For example,
a common type of run at MCW would be entered as
-xFOV 120L-R -yFOV 120A-P -zSLAB 60S-50I

Z-AXIS SLICE OFFSET ONLY
-zorigin distz Puts the center of the 1st slice off at the
given distance ('distz' in mm). This distance
is in the direction given by the corresponding
letter in the -orient code. For example,
-orient RAI -zorigin 30
would set the center of the first slice at
30 mm Inferior.
N.B.: This option has no effect if the FOV or SLAB options
described above are used.

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We have a 25cmX25cm matrix, so 250 means 250mm. We also have 128 slices 1.4mm thick, so from the center point, the distance to the left of the brain (and to the right) would be 90mm.

After entering this command, I get the interface screen and the orientation of the image is automatically set up to x=Anterior-Posterior, y=Superior-Inferior, z=Left-Right (this is correct, since we have a sagittal image set) and the FOV is automatically set at 500. I tried overlaying my functional images over the anatomical dataset created using this new FOV, but the compression persists.

For some reason, AFNI is stretching the functional image activation to the size of the anatomical images and across the slices, instead of converting the activation proportionally. Again, the anatomical images are RESOLUTION = 256X256, FOV = 25X25cm, SLICES = 128, SLICE THICKNESS = 1.4mm. The functional images are RES = 64X64, FOV = ?, SLICES = 16, SLICE THICKNESS = 5mm.

Anything else you could suggest?

Thanks so much for your time! :)
-Dmitry