As it happens, AFNI programs (besided the interactive AFNI itself, that is) can already read .1D files in and treat them as datasets. The way it works is:
* Each column is one sub-brick.
* The default is that multiple column datasets become bucket datasets.
Today I added the feature that
* If environment variable AFNI_1D_TIME is YES, then multi-column .1D files become 3D+time datasets instead (with TR set to 1 second).

So to do what you want, you can do something like so

setenv AFNI_1D_TIME YES
1dtranspose VP1.1D - > VP1_x.1D
3dFourier -prefix QQ_x -lowpass .1 -retrend VP1_x.1D
1dtranspose QQ_x.1D > QQ.1D
1dplot VP1.1D QQ.1D

1dtranspose is necessary to take a normal .1D file (one column, many rows) and turn it into a 1 row, many column file. Then 3dFourier will produce another such file, and 1dtranspose will turn it back into the 1 column format.

To do this, you'll have to download the latest AFNI. The source code distribution is updated now (9:40 EDT), and I'm compiling some binaries at this time.

bob cox

P.S. The main application of treating 1D files as datasets is actually to be able to use the stats programs (3dANOVA, etc.) on datasets defined over surfaces. In this case, each row contains the values of the dataset at the corresponding surface node. We haven't really documented this yet, since not all the mechanism is in place for reading such datasets into SUMA, etc.