
Processing auto block: tcat

This is the last step to copy input data into the results directory.  The
3dTcat program is used to copy the EPI data into the results directory, while
removing the first TRs from every run (according to the afni_proc.py option,
-tcat_remove_first_trs).  This is done even if no TRs are being removed.

In this example, the first 2 TRs are removed (TR indices 0 and 1).

      3dTcat -prefix $output_dir/pb00.$subj.r01.tcat FT/FT_epi_r1+orig'[2..$]'
      3dTcat -prefix $output_dir/pb00.$subj.r02.tcat FT/FT_epi_r2+orig'[2..$]'
      3dTcat -prefix $output_dir/pb00.$subj.r03.tcat FT/FT_epi_r3+orig'[2..$]'

So data is copied from TR #2 until the last TR.  Consider the first input
"FT/FT_epi_r1+orig'[2..$]'".  The dataset is found under the FT directory as
FT/FT_epi_r1+orig.  It has 152 sub-bricks (indices 0..151).  Skipping the first
two could be done with '[2..151]', but '$' is used for convenience to mean the
last sub-brick.

The output dataset is put in the results directory ($output_dir) as dataset
pb00.$subj.r01.tcat.  The EPI datasets are copied as names r01, r02 and r03,
regardless of the input names.

----------------------------------------

Now that all data has been copied into the results directory, it is time to
enter that directory and process the data.  The final line of the 'tcat'
processing block is to enter the results directory.

      cd $output_dir

