/usr/local/freesurfer/bin/trac-preproc 
mri_convert /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/diffree/diffdata.mnc /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dwi_orig.nii.gz
cp /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/diffree/bvecs_t /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dwi_orig.mghdti.bvecs
cp /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/diffree/bvals_t /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dwi_orig.mghdti.bvals
flip4fsl /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dwi_orig.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dwi_orig_flip.nii.gz
mv -f /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dwi_orig_flip.mghdti.bvecs /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/bvecs
mv -f /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dwi_orig_flip.mghdti.bvals /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/bvals
eddy_correct /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dwi_orig_flip.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dwi.nii.gz 0
mv -f /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/bvecs /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/bvecs.norot
xfmrot /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dwi.ecclog /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/bvecs.norot /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/bvecs
ln -sf /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dwi.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/data.nii.gz
mri_convert --frame 0 /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dwi.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dwi_frame0.nii.gz
mri_concat --i /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dwi_frame0.nii.gz --mean --o /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb.nii.gz
bet /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb_brain.nii.gz -m -f 0.3
mv -f /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb_brain_mask.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff
mri_convert /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/mri/brain.mgz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/brain_anat_orig.nii.gz
flip4fsl /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/brain_anat_orig.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/brain_anat.nii.gz
tkregister2 --mov /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/brain_anat_orig.nii.gz --targ /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anatorig2anat.mat --reg /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2anatorig.dat
convert_xfm -omat /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2anatorig.mat -inverse /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anatorig2anat.mat
convert_xfm -omat /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anatorig2diff.bbr.mat -inverse /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/diff2anatorig.bbr.mat
convert_xfm -omat /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2diff.bbr.mat -concat /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anatorig2diff.bbr.mat /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2anatorig.mat
convert_xfm -omat /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/diff2anat.bbr.mat -inverse /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2diff.bbr.mat
flirt -in /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/brain_anat.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain -out /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/brain_anat_mni.nii.gz -omat /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2mni.mat -cost mutualinfo
convert_xfm -omat /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/mni2anat.mat -inverse /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2mni.mat
convert_xfm -omat /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/diff2mni.bbr.mat -concat /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2mni.mat /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/diff2anat.bbr.mat
convert_xfm -omat /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/mni2diff.bbr.mat -inverse /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/diff2mni.bbr.mat
convert_xfm -omat /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anatorig2mni.mat -concat /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2mni.mat /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anatorig2anat.mat
convert_xfm -omat /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/mni2anatorig.mat -inverse /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anatorig2mni.mat
mri_binarize --i /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --o /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anatorig/White-Matter.nii.gz
mri_binarize --i /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/mri/aparc+aseg.mgz --match 2 --match 7 --match 41 --match 46 --match 77 --match 28 --match 60 --match 16 --o /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anatorig/White-Matter++.nii.gz
mri_binarize --i /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/mri/aparc+aseg.mgz --match 4 --match 43 --binval 0 --binvalnot 1 --o /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anatorig/notventricles.nii.gz
mri_aparc2aseg --s 02ST --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anatorig/aparc+aseg+2mm.nii.gz
mri_binarize --i /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 2999 --o /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anatorig/cortex.nii.gz
mri_binarize --i /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anatorig/aparc+aseg+2mm.nii.gz --min 1000 --max 4999 --o /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anatorig/cortex+2mm.nii.gz
mri_binarize --i /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/mri/aparc+aseg.mgz --match 16 --o /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anatorig/Brain-Stem.nii.gz
fslmaths /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anatorig/cortex+2mm.nii.gz -add /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anatorig/Brain-Stem.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anatorig/cortex+2mm+bs.nii.gz
mri_convert /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/mri/brainmask.mgz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anatorig/anat_brain_mask.nii.gz
fslmaths /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anatorig/anat_brain_mask.nii.gz -mul /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anatorig/notventricles.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anatorig/anat_brain_mask-vent.nii.gz
mri_convert /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/mri/aparc+aseg.mgz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anatorig/aparc+aseg.nii.gz
fslmaths /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anatorig/aparc+aseg.nii.gz -dilM -bin /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anatorig/aparc+aseg_mask.nii.gz
flip4fsl /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anatorig/White-Matter.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anat/White-Matter.nii.gz
flirt -in /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anat/White-Matter.nii.gz -ref /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb.nii.gz -out /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/White-Matter.bbr.nii.gz -applyxfm -init /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anat/White-Matter.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain -out /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/White-Matter.nii.gz -applyxfm -init /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anatorig/White-Matter++.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anat/White-Matter++.nii.gz
flirt -in /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anat/White-Matter++.nii.gz -ref /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb.nii.gz -out /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/White-Matter++.bbr.nii.gz -applyxfm -init /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anat/White-Matter++.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain -out /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/White-Matter++.nii.gz -applyxfm -init /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anatorig/notventricles.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anat/notventricles.nii.gz
flirt -in /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anat/notventricles.nii.gz -ref /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb.nii.gz -out /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/notventricles.bbr.nii.gz -applyxfm -init /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anat/notventricles.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain -out /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/notventricles.nii.gz -applyxfm -init /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anatorig/cortex.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anat/cortex.nii.gz
flirt -in /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anat/cortex.nii.gz -ref /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb.nii.gz -out /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/cortex.bbr.nii.gz -applyxfm -init /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anat/cortex.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain -out /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/cortex.nii.gz -applyxfm -init /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anatorig/cortex+2mm.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anat/cortex+2mm.nii.gz
flirt -in /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anat/cortex+2mm.nii.gz -ref /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb.nii.gz -out /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/cortex+2mm.bbr.nii.gz -applyxfm -init /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anat/cortex+2mm.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain -out /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/cortex+2mm.nii.gz -applyxfm -init /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anatorig/cortex+2mm+bs.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anat/cortex+2mm+bs.nii.gz
flirt -in /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anat/cortex+2mm+bs.nii.gz -ref /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb.nii.gz -out /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/cortex+2mm+bs.bbr.nii.gz -applyxfm -init /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anat/cortex+2mm+bs.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain -out /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/cortex+2mm+bs.nii.gz -applyxfm -init /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anatorig/aparc+aseg.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anat/aparc+aseg.nii.gz
flirt -in /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anat/aparc+aseg.nii.gz -ref /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb.nii.gz -out /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/aparc+aseg.bbr.nii.gz -applyxfm -init /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anat/aparc+aseg.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain -out /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/aparc+aseg.nii.gz -applyxfm -init /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anatorig/aparc+aseg+2mm.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anat/aparc+aseg+2mm.nii.gz
flirt -in /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb.nii.gz -out /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/aparc+aseg+2mm.bbr.nii.gz -applyxfm -init /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anat/aparc+aseg+2mm.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain -out /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/aparc+aseg+2mm.nii.gz -applyxfm -init /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anatorig/aparc+aseg_mask.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anat/aparc+aseg_mask.nii.gz
flirt -in /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anat/aparc+aseg_mask.nii.gz -ref /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb.nii.gz -out /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anat/aparc+aseg_mask.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain -out /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/aparc+aseg_mask.nii.gz -applyxfm -init /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anatorig/anat_brain_mask.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anat/anat_brain_mask.nii.gz
flirt -in /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anat/anat_brain_mask.nii.gz -ref /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb.nii.gz -out /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/anat_brain_mask.bbr.nii.gz -applyxfm -init /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anat/anat_brain_mask.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain -out /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/anat_brain_mask.nii.gz -applyxfm -init /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2mni.mat -interp nearestneighbour
flip4fsl /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anatorig/anat_brain_mask-vent.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anat/anat_brain_mask-vent.nii.gz
flirt -in /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb.nii.gz -out /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/anat_brain_mask-vent.bbr.nii.gz -applyxfm -init /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour
flirt -in /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anat/anat_brain_mask-vent.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain -out /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/anat_brain_mask-vent.nii.gz -applyxfm -init /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2mni.mat -interp nearestneighbour
fslstats -t /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dwi.nii.gz -k /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/White-Matter++.bbr.nii.gz -m -s | awk '{print $1/$2}' > /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dwi_snr.txt
flirt -in /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/lowb_brain_mask.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain -out /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lowb_brain_mask.bbr.nii.gz -applyxfm -init /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/diff2mni.bbr.mat -interp nearestneighbour
flirt -in /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/lowb_brain_mask.nii.gz -ref /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/brain_anat_orig.nii.gz -out /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/anatorig/lowb_brain_mask.bbr.nii.gz -applyxfm -init /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/diff2anatorig.bbr.mat -interp nearestneighbour
ln -sf /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/aparc+aseg_mask.bbr.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/nodif_brain_mask.nii.gz
dtifit -k /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dwi.nii.gz -m /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/bvecs -b /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/bvals -o /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dtifit
flirt -in /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dtifit_FA.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain -out /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/mni/dtifit_FA.bbr.nii.gz -applyxfm -init /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/diff2mni.bbr.mat
flirt -in /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dtifit_L1.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain -out /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/mni/dtifit_L1.bbr.nii.gz -applyxfm -init /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/diff2mni.bbr.mat
flirt -in /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dtifit_L2.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain -out /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/mni/dtifit_L2.bbr.nii.gz -applyxfm -init /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/diff2mni.bbr.mat
flirt -in /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dtifit_L3.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain -out /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/mni/dtifit_L3.bbr.nii.gz -applyxfm -init /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/diff2mni.bbr.mat
flirt -in /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dtifit_MD.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain -out /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/mni/dtifit_MD.bbr.nii.gz -applyxfm -init /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/diff2mni.bbr.mat
flirt -in /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dtifit_MO.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain -out /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/mni/dtifit_MO.bbr.nii.gz -applyxfm -init /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/diff2mni.bbr.mat
flirt -in /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dtifit_S0.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain -out /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/mni/dtifit_S0.bbr.nii.gz -applyxfm -init /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/diff2mni.bbr.mat
/usr/local/freesurfer/bin/dmri_train --outdir /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.02ST.6053.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/aparc+aseg_mask.nii.gz --fa /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dtifit_FA.nii.gz --cptdir /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff --reg /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/mni2diff.bbr.mat --ncpts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc