/usr/local/freesurfer/bin/trac-preproc 
mri_convert /media/Data/Temple/Temple_Tracula/31313422_10128/dti_dicom/31313422_10128.MR.Temple.9.1.20140806.182244.xfrp16.dcm /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_orig.nii.gz
mri_probedicom --i /media/Data/Temple/Temple_Tracula/31313422_10128/dti_dicom/31313422_10128.MR.Temple.9.1.20140806.182244.xfrp16.dcm > /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dcminfo.dat
cp /media/Data/Temple/Temple_Tracula/31313422_10128/dti/31313422_10128_MR1_seq9_bvecs /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_orig.mghdti.bvecs
cp 31313422_180455/dti/31313422_180455_MR1_seq9_bvals /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_orig.mghdti.bvals
mv -f /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.tmp /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_orig.mghdti.bvecs
mv -f /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvals.tmp /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_orig.mghdti.bvals
flip4fsl /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_orig.nii.gz /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_orig_flip.nii.gz
mv -f /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_orig_flip.mghdti.bvecs /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs
mv -f /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_orig_flip.mghdti.bvals /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvals
eddy_correct /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_orig_flip.nii.gz /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.nii.gz 0
mv -f /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot
xfmrot /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.ecclog /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs
mv -f /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.nii.gz /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz
mri_convert //media/Data/Temple/Temple_Tracula/31313422_10128/dti_dicom/31313422_10128.MR.Temple.9.1.20140806.182244.xfrp16.dcm /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0mag.nii.gz
flip4fsl /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0mag.nii.gz /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0mag.nii.gz
mri_convert //media/Data/Temple/Temple_Tracula/31313422_10128/dti_dicom/31313422_10128.MR.Temple.9.1.20140806.182244.xfrp16.dcm /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0pha.nii.gz
flip4fsl /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0pha.nii.gz /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0pha.nii.gz
mri_probedicom --i //media/Data/Temple/Temple_Tracula/31313422_10128/dti_dicom/31313422_10128.MR.Temple.9.1.20140806.182244.xfrp16.dcm > /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0info.dat
fslroi /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/lowb.nii.gz 0 1