AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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Dillon Plunkett
November 18, 2016 10:56AM
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)
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issue with align_epi_anat.py output_dir?

Dillon Plunkett November 18, 2016 10:56AM