Hi Ed,
> In the first step, tbss_1_preproc, the directory called
> origdata is created to which the original FA files are
> moved.
> I'm wondering if this directory is ever used in any
> subsequent processing? In other words, is it
> possible to skip this step in tbbs_1_preproc?
This directory is here to ensure that you will always have available the original images not eroded/preprocessed by tbss1. It is not used by tbss afterwards.
I am not sure why you would want to delete/skip the origdata, but if this is to save some space because you have the original data *somewhere else* (please make sure of this before deleting anything, there is no going back after tbss_1_preproc apart from starting from scratch with dtifit again), then you could always remove:
mkdir -p origdata
from tbss_1_preproc
and replace:
$FSLDIR/bin/immv $f origdata
by:
$FSLDIR/bin/imrm $f
Cheers,
Gwenaelle
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