<code bash>
#!/bin/bash

SUBJ=$1
ANATDIR=~/net/selye/data/MIRECC.03/Data/Anat/$SUBJ

FSLDATADIR=/data/mireccAnat/data/$SUBJ/dti

mkdir -p $FSLDATADIR

#### converts dti and orient as LAS ####
bxhreorient --orientation=LAS $ANATDIR/series005/*bxh $ANATDIR/temp.bxh
bxh2analyze -s --niigz $ANATDIR/temp.bxh $ANATDIR/dti
rm $ANATDIR/temp.*


#### skull strip the dti
bet $ANATDIR/dti $FSLDATADIR/dti_brain -F -f .25

rm -r $ANATDIR/dti*

#### eddy current correction
eddy_correct $FSLDATADIR/dti_brain $FSLDATADIR/data 0   
rm $FSLDATADIR/dti_brain.nii.gz
mv $FSLDATADIR/dti_brain_mask.nii.gz $FSLDATADIR/nodif_brain_mask.nii.gz
fslsplit $FSLDATADIR/data $FSLDATADIR/tmp -t
mv $FSLDATADIR/tmp0000.nii.gz $FSLDATADIR/nodif_brain.nii.gz 
rm $FSLDATADIR/tmp*

##copy the bv-files to the directory
cp -r /data/mireccAnat/scripts/dif_files/* $FSLDATADIR/.

##run dtifit
dtifit -k $FSLDATADIR/data -m $FSLDATADIR/nodif_brain_mask -o $FSLDATADIR/dti -r $FSLDATADIR/bvecs -b $FSLDATADIR/bvals

</code>

  * note of caution, if you view the data and there are parts of brain missing, you need to reduce the skull stripping threshold (-f .25) and re-run.
  * lower numbers mean a more lenient threshold