Brain Imaging & Analysis Center

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<code bash>
#!/bin/bash
 
SUBJ=$1
DATADIR=/home/petty/net/selye/data/MIRECC.03/Analysis/ROI/$SUBJ

##create ROIs
fslmaths ${DATADIR}/amyg_free -mul 4 -add ${DATADIR}/amyg_first $DATADIR/tmp_amyg_union
fslmaths ${DATADIR}/hipp_free -mul 4 -add ${DATADIR}/hipp_first $DATADIR/tmp_hipp_union
fslmaths ${DATADIR}/accu_free -mul 4 -add ${DATADIR}/accu_first $DATADIR/tmp_accu_union
fslmaths ${DATADIR}/caud_free -mul 4 -add ${DATADIR}/caud_first $DATADIR/tmp_caud_union


#touch $DATADIR/FF_voxel_counts.txt
echo "FIRST-FREESURFER OVERLAP VOLUMES" >> $DATADIR/FF_voxel_counts.txt
for input in tmp_amyg_union tmp_hipp_union tmp_accu_union tmp_caud_union; do
echo "$DATADIR/$input L" >> $DATADIR/FF_voxel_counts.txt
fslstats $DATADIR/$input -l 4.9 -u 5.1 -V >> $DATADIR/FF_voxel_counts.txt
echo "$DATADIR/$input R" >> $DATADIR/FF_voxel_counts.txt
fslstats $DATADIR/$input -l 9.9 -u 10.1 -V >> $DATADIR/FF_voxel_counts.txt
done

rm ${DATADIR}/tmp_*
</code>

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