Applying 3dAllineate transformation matrix to other sequences

I am trying to register my DTI scalars to FLAIR so the scalars are in FLAIR space (structural to structural).

I used 3dAllineate to register the MD scalar to FLAIR successfully and generated a *.aff12.1D transformation matrix. I would like to apply this transformation matrix to the rest of my scalars. Is there a way to do this on AFNI?

Alternatively, would I be able to convert the *.aff12.1D transformation matrix to a .mat file and use FSL's flirt using -applyxfm and -init?

Thanks in advance.

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You should be able to use 3dAllineate itself to apply a saved .aff12.1D file to other datasets.
The option to use is -1Dmatrix_apply and is described in the program's -help output, which can be found at
or at
The documentation linked above will show you how to use this option.