When running the following command on my system, volume registered datasets are produced in the current directory, but the final, aligned datasets are ending up in the dset2 directory (whether omitting -output_dir or using “-output_dir .”).
align_epi_anat.py -dset1 dset1+orig -dset2 ../../dset2_dir/dset2+orig \
-child_dset2 ../../dset2_dir/dset2_child+orig -dset2to1 -volreg on \
-volreg_opts '-cubic -zpad 10' -volreg_base 0 -giant_move -master_dset2 MIN_DXYZ \
-save_vr -volreg_method 3dvolreg -suffix '_aligned' -output_dir .
I can just move the aligned files with a separate command, but I thought I would check if this might be unintended behavior and if there is a more direct way to get all of the output in the current directory.
Thanks!
Dillon
Version: Precompiled binary linux_openmp_64: Dec 16 2015 (Version AFNI_2011_12_21_1014)