You can check the alignment of your anatomical (MPRAGE) and EPI by setting the underlay as the anatomical and the overlay as the EPI and setting the t-stat bar to 0.00. Alternatively, you can use @AddEdge. Alignment images can be saved using either the save button in the viewer or by constructing a script that uses the plugout drive in AFNI. @AddEdge can be very helpful and you can run it automatically in align_epi_anat.py.

Usually to check motion in the EPI, you would use the "dfile" output from 3dvolreg in 1dplot. If you are using afni_proc.py, all of your individual run "dfiles" are concatenated together and you could do this:

1dplot -volreg dfile_rall.1D

There are options in 1dplot to save the image while viewing it or you can add a save image flag (e.g. -jpg / -png) to save the plot to a file. It can be particularly handy to use the -censor option and feed 1dplot the censor file created automatically by afni_proc.py. This will show highlights of all of the TRs that are censored due to motion or outliers. Using the other censor files, you can look at just outliers or just motion.

1dplot -censor censor_Subj001_combined_2.1D -volreg dfile_rall.1D

Edited 3 time(s). Last edit at 04/02/2013 09:40AM by Peter Molfese.