diff --git a/Desktop/determTract.sh b/Desktop/determTract.sh
index 80e17cf..c63e27c 100644
--- a/Desktop/determTract.sh
+++ b/Desktop/determTract.sh
@@ -1,97 +1,151 @@
 #!/bin/bash
 
 
-### for grmpy format data
-
-
+IDs=$1
 cdir=/data/joy/BBL/applications/camino/bin
 ddir=/share/apps/dsistudio/2016-01-25/bin
-general=/data/joy/BBL/studies/grmpy/rawData/104235/*/
-for i in $general;do 
-	bblIDs=$(echo ${i}|cut -d'/' -f8 |sed s@'/'@' '@g);
-	SubDate_and_ID=$(echo ${i}|cut -d'/' -f9|sed s@'/'@' '@g|sed s@'x'@'x'@g)
-	Date=$(echo ${SubDate_and_ID}|cut -d',' -f1)
-	ID=$(echo ${SubDate_and_ID}|cut -d',' -f2)
-out=/data/joy/BBL/projects/multishell_diffusion/processedData/multishellPipelineFall2017/${bblIDs}/${SubDate_and_ID}
-in=/data/joy/BBL/projects/multishell_diffusion/processedData/multishellPipelineFall2017/${bblIDs}/${SubDate_and_ID}
-
-mkdir $out/tractography
-
-fslmaths /data/joy/BBL/studies/grmpy/processedData/structural/struct_pipeline_20170716/$bblIDs/$SubDate_and_ID/antsCT/*_BrainSegmentation.nii.gz -thr 1 -uthr 1 $out/coreg/${bblIDs}_${SubDate_and_ID}_CSF.nii.gz
+general=/data/jux/daviska/apines/3T_Subjects_NODDI/*/
+#for i in $general;do 
+	#IDs=$(echo ${i}|cut -d'/' -f8 |sed s@'/'@' '@g);
+	#SubDate_and_ID=$(echo ${i}|cut -d'/' -f9|sed s@'/'@' '@g|sed s@'x'@'x'@g)
+	#Date=$(echo ${SubDate_and_ID}|cut -d',' -f1)
+	#ID=$(echo ${SubDate_and_ID}|cut -d',' -f2)
+###mkdir /data/jux/daviska/apines/3T_Subjects_NODDI/${IDs}/tractography
+out=/data/jux/daviska/apines/3T_Subjects_NODDI/${IDs}
+in=/data/jux/daviska/apines/3T_Subjects_NODDI/${IDs}/AMICO/
+MNI=/data/jux/daviska/apines/atlases/MNI152_T1_1mm_brain.nii.gz
+AAL=/data/jux/daviska/apines/atlases/AAL_MNI.nii
+
+# re-mask DWI_t1Warp_BWarped
+
+fslmaths $out/prestats/${IDs}_eddied_undistort_warped.nii.gz -mas $out/prestats/eddy/${IDs}_seqSpaceT1Mask.nii.gz  $out/prestats/${IDs}_eddied_undistort_warped_t1Masked.nii.gz
+
+# Make CSF and High ISO into an exclusion path for tractography
+fslmaths /data/jux/daviska/apines/3T_Subjects_NODDI/${IDs}/coreg/${IDs}_T1_betted_seg.nii.gz -thr 1 -uthr 1 $out/coreg/${IDs}_CSF.nii.gz
+fslmaths /data/jux/daviska/apines/3T_Subjects_NODDI/${IDs}/AMICO/NODDI/FIT_ISOVF.nii.gz -thr .8 -uthr 1 $out/coreg/${IDs}_8ISO.nii.gz
+csf=${out}/coreg/${IDs}_CSF.nii.gz
 
 #csf to seq space
-antsApplyTransforms -e 3 -d 3 -i $out/coreg/${bblIDs}_${SubDate_and_ID}_CSF.nii.gz -r /data/joy/BBL/projects/multishell_diffusion/processedData/multishellPipelineFall2017/${bblIDs}/${SubDate_and_ID}/prestats/eddy/${bblIDs}_${SubDate_and_ID}_eddied_topupMasked_b0.nii.gz -o $out/coreg/${bblIDs}_${SubDate_and_ID}_seqspaceCSF.nii.gz -t [/data/joy/BBL/projects/multishell_diffusion/processedData/multishellPipelineFall2017/${bblIDs}/${SubDate_and_ID}/coreg/${bblIDs}_${SubDate_and_ID}_MultiShDiff2StructRas.mat,1] -n NearestNeighbor
+antsApplyTransforms -e 0 -d 3 -i ${csf} -r ${out}/coreg/${IDs}_DWISpaceT1.nii.gz -o $out/coreg/DWISpace_csf.nii.gz -t [$out/coreg/${IDs}_MultiShDiff2StructRas.mat,1] -n MultiLabel
+
+#Combine with highest ISO values in NODDI output
+fslmaths $out/coreg/DWISpace_csf.nii.gz -add $out/coreg/${IDs}_8ISO.nii.gz -bin ${out}/coreg/CSFandISO.nii.gz
 
 #wm to seq space
-antsApplyTransforms -e 3 -d 3 -i $out/coreg/${bblIDs}_${SubDate_and_ID}_Struct_WM.nii.gz -r /data/joy/BBL/projects/multishell_diffusion/processedData/multishellPipelineFall2017/${bblIDs}/${SubDate_and_ID}/prestats/eddy/${bblIDs}_${SubDate_and_ID}_eddied_topupMasked_b0.nii.gz -o $out/coreg/${bblIDs}_${SubDate_and_ID}_seqspaceWM.nii.gz -t [/data/joy/BBL/projects/multishell_diffusion/processedData/multishellPipelineFall2017/${bblIDs}/${SubDate_and_ID}/coreg/${bblIDs}_${SubDate_and_ID}_MultiShDiff2StructRas.mat,1] -n NearestNeighbor
+antsApplyTransforms -e 3 -d 3 -i $out/coreg/${IDs}_Struct_WM.nii.gz -r $out/coreg/${IDs}_DWISpaceT1.nii.gz -o $out/coreg/${IDs}_seqspaceWM.nii.gz -t [$out/coreg/${IDs}_MultiShDiff2StructRas.mat,1] -n NearestNeighbor
 
 #dilate seqspace wm
-ImageMath 3 $out/coreg/${bblIDs}_${SubDate_and_ID}_seqspaceWM_dil.nii.gz GD $out/coreg/${bblIDs}_${SubDate_and_ID}_seqspaceWM.nii.gz 1
+ImageMath 3 $out/coreg/${IDs}_seqspaceWM_dil.nii.gz GD $out/coreg/${IDs}_seqspaceWM.nii.gz 1
+
+#dilate hippocamp region
+##ImageMath 3 $out/coreg/BinarizedHippo_dil.nii.gz GD $out/coreg/BinarizedHippo.nii.gz 1
+
+# Convert FSL omat to Ras
+	
+###c3d_affine_tool -src ${MNI} -ref ${out}/coreg/${IDs}_T1_betted.nii.gz $out/coreg/${IDs}_MNI2StructFSL.mat -fsl2ras -oitk $out/coreg/${IDs}_MNIStructRas.mat
+
+# Calculate non-affine
 
-#schaefer to seqspace change to MNI
+#####/data/jux/daviska/apines/ANTs/Scripts/antsRegistrationSyN.sh -d 3 -f $out/coreg/${IDs}_T1_betted.nii.gz -m ${MNI} -o /data/jux/daviska/apines/3T_Subjects_NODDI/${IDs}/coreg/${IDs}_MNI_T1_Warp
 
-antsApplyTransforms -e 0 -d 3 -i /data/joy/BBL/applications/xcpEngine/networks/SchaeferPNC_200.nii.gz -r /data/joy/BBL/projects/multishell_diffusion/processedData/multishellPipelineFall2017/${bblIDs}/${SubDate_and_ID}/prestats/eddy/${bblIDs}_${SubDate_and_ID}_eddied_topupMasked_b0.nii.gz -o $out/coreg/${bblIDs}_${SubDate_and_ID}_seqspaceSchaefPNC_200.nii.gz -n NearestNeighbor -t [$out/coreg/${bblIDs}_${SubDate_and_ID}_MultiShDiff2StructRas.mat, 1] -t /data/joy/BBL/studies/grmpy/processedData/structural/struct_pipeline_20170716/$bblIDs/$SubDate_and_ID/antsCT/${bblIDs}_${SubDate_and_ID}_TemplateToSubject1GenericAffine.mat -t /data/joy/BBL/studies/grmpy/processedData/structural/struct_pipeline_20170716/$bblIDs/$SubDate_and_ID/antsCT/${bblIDs}_${SubDate_and_ID}_TemplateToSubject0Warp.nii.gz
+antsApplyTransforms -d 3 -e 0 -i ${AAL} -r /data/jux/daviska/apines/3T_Subjects_NODDI/${IDs}/coreg/${IDs}_DWISpaceT1.nii.gz -o  $out/coreg/${IDs}_DWISpace_AAL.nii.gz -t /data/jux/daviska/apines/3T_Subjects_NODDI/${IDs}/coreg/${IDs}_MNI_T1_Warp1Warp.nii.gz -t  $out/coreg/${IDs}_MNI_T1_Warp0GenericAffine.mat -n NearestNeighbor
 
-#get convergence of schaefer and dilated wm
-fslmaths $out/coreg/${bblIDs}_${SubDate_and_ID}_seqspaceSchaefPNC_200.nii.gz -mas $out/coreg/${bblIDs}_${SubDate_and_ID}_seqspaceWM_dil.nii.gz $out/coreg/${bblIDs}_${SubDate_and_ID}_SchaefPNC_200_WM_intersect.nii.gz
+### Weird combination of fslmaths to distinguish left and right hippo, remove ashs-generated rois from AAL (or other atlas if subbed in)
+
+#distinguish
+fslmaths ${out}/coreg/RBinarizedHippo.nii.gz -mul 2 ${out}/coreg/RBinarizedHippoPlus1.nii.gz
+fslmaths ${out}/coreg/RBinarizedHippoPlus1.nii.gz -add ${out}/coreg/LBinarizedHippo.nii.gz ${out}/coreg/RLBinHippo.nii.gz
+
+# remove ashs-generated rois from AAL (or other atlas if subbed in)
+fslmaths $out/coreg/BinarizedHippo.nii.gz -sub 1 $out/coreg/sub1.nii.gz
+fslmaths $out/coreg/sub1.nii.gz -mul -1 $out/coreg/0ed.nii.gz
+fslmaths $out/coreg/${IDs}_DWISpace_AAL.nii.gz -mul $out/coreg/0ed.nii.gz $out/coreg/${IDs}_DWISpace_AAL_noH.nii.gz
+fslmaths ${out}/coreg/RLBinHippo.nii.gz -add $out/coreg/${IDs}_DWISpace_AAL_noH.nii.gz $out/coreg/${IDs}_DWISpace_AAL_ASH.nii.gz
+
+subAAL=$out/coreg/${IDs}_DWISpace_AAL_ASH.nii.gz
+
+###fslmaths ${subAAL} -thr 6301 -uthr 6302 $out/tractography/${IDs}_Precun.nii.gz
+
+
+#get convergence of ROIs and dilated wm
+##fslmaths ${subAAL} -mas $out/coreg/${IDs}_seqspaceWM_dil.nii.gz $out/coreg/${IDs}_seqspaceWM_AAL_Intersect.nii.gz
+###fslmaths $out/tractography/${IDs}_Precun.nii.gz -mas $out/coreg/${IDs}_seqspaceWM.nii.gz $out/coreg/${IDs}_seqspaceWM_Precun_Intersect.nii.gz
 
 #fitTensorsinCamino
-#mkdir $out/tractography
-export CAMINO_HEAP_SIZE=10000
+mkdir $out/tractography
 
-$cdir/fsl2scheme -bvecfile $in/prestats/eddy/${bblIDs}_${SubDate_and_ID}_eddied.eddy_rotated_bvecs -bvalfile $in/prestats/qa/${bblIDs}_${SubDate_and_ID}_roundedbval.bval > $out/tractography/${bblIDs}_${SubDate_and_ID}.scheme
+export CAMINO_HEAP_SIZE=10000
 
-$cdir/image2voxel -4dimage $in/prestats/eddy/${bblIDs}_${SubDate_and_ID}_eddied.nii.gz -outputfile $out/tractography/${bblIDs}_${SubDate_and_ID}_i2v.Bfloat
+$cdir/fsl2scheme -bvecfile $in/bvecs -bvalfile $in/bvals > $out/tractography/${IDs}.scheme
+$cdir/image2voxel -4dimage $out/prestats/${IDs}_eddied_undistort_warped_t1Masked.nii.gz -outputfile $out/tractography/${IDs}_i2v.Bfloat
 
 #wdt reconstruction
-$cdir/wdtfit $out/tractography/${bblIDs}_${SubDate_and_ID}_i2v.Bfloat $out/tractography/${bblIDs}_${SubDate_and_ID}.scheme -bgmask $in/prestats/eddy/${bblIDs}_${SubDate_and_ID}_seqSpaceT1Mask.nii.gz -outputfile $out/tractography/${bblIDs}_${SubDate_and_ID}_WdtModelFit.Bdouble
-mv $out/coreg/${bblIDs}_${SubDate_and_ID}_Schaef_WM_intersect.nii.gz  $out/coreg/${bblIDs}_${SubDate_and_ID}_SchaefPNC_200_WM_intersect.nii.gz
+$cdir/wdtfit $out/tractography/${IDs}_i2v.Bfloat $out/tractography/${IDs}.scheme -bgmask $in/brainMask.nii -outputfile $out/tractography/${IDs}_WdtModelFit.Bdouble
+#mv $out/coreg/${bblIDs}_${SubDate_and_ID}_Schaef_WM_intersect.nii.gz  $out/coreg/${bblIDs}_${SubDate_and_ID}_SchaefPNC_200_WM_intersect.nii.gz
 
-seed_path=$out/coreg/${bblIDs}_${SubDate_and_ID}_SchaefPNC_200_WM_intersect.nii.gz
-schaef_path=$out/coreg/${bblIDs}_${SubDate_and_ID}_seqspaceSchaefPNC_200.nii.gz
-model_fit_path=$out/tractography/${bblIDs}_${SubDate_and_ID}_WdtModelFit.Bdouble
-waypoint_path=$out/coreg/${bblIDs}_${SubDate_and_ID}_seqspaceWM.nii.gz
-exclusion_path=$out/coreg/${bblIDs}_${SubDate_and_ID}_seqspaceCSF.nii.gz
-dsource=$out/dsi/${bblIDs}_${SubDate_and_ID}t1_maskedEddied.src.gz.fy.dti.fib.gz
-tractography_output=$out/tractography/${bblIDs}_${SubDate_and_ID}_Tract.Bdouble
+seed_path=${out}/coreg/RLBinHippo.nii.gz
+atlas_path=${subAAL}
+model_fit_path=$out/tractography/${IDs}_WdtModelFit.Bdouble
+waypoint_path=$out/coreg/${IDs}_seqspaceWM_dil.nii.gz
+exclusion_path=${out}/coreg/CSFandISO.nii.gz
+
+dsource=$out/prestats/${IDs}_eddied_undistort_warped_t1Masked.nii.gz
+tractography_output=$out/tractography/${IDs}_HippoTract.Bdouble
 
 #dilate intersect
-ImageMath 3 $out/coreg/${bblIDs}_${SubDate_and_ID}_SchaefPNC_200_WM_intersect_Dil1.nii.gz GD $seed_path 1
+##ImageMath 3 $out/coreg/${bblIDs}_${SubDate_and_ID}_SchaefPNC_200_WM_intersect_Dil1.nii.gz GD $seed_path 1
+
+##dilSeed_path=$out/coreg/${bblIDs}_${SubDate_and_ID}_SchaefPNC_200_WM_intersect_Dil1.nii.gz
+
+## Merge ROIs for endpointfile, to find streamlines between them.
+fslmaths ${out}/coreg/RBinarizedHippo.nii.gz -mul 2 ${out}/coreg/RBinarizedHippoPlus1.nii.gz
+fslmaths ${out}/coreg/RBinarizedHippoPlus1.nii.gz -add ${out}/coreg/LBinarizedHippo.nii.gz ${out}/coreg/RLBinHippo.nii.gz
+##fslmaths ${out}/coreg/RLBinHippo.nii.gz -add $out/tractography/${IDs}_Precun.nii.gz ${out}/tractography/endpoint.nii.gz
 
-dilSeed_path=$out/coreg/${bblIDs}_${SubDate_and_ID}_SchaefPNC_200_WM_intersect_Dil1.nii.gz
+$cdir/analyzeheader -datadims 96 96 50 -voxeldims 2.5 2.5 2.5 -datatype double > $out/tractography/${IDs}_Camino_FA.hdr
+
+# Generate FA from camino
+$cdir/fa < $out/tractography/${IDs}_WdtModelFit.Bdouble > $out/tractography/${IDs}_Camino_FA.img
+
+#hdr/img to nii.gz
+c3d $out/tractography/${IDs}_Camino_FA.img -o $out/tractography/${IDs}_Camino_FA.nii.gz
+rm $out/tractography/${IDs}_Camino_FA.hdr
+rm $out/tractography/${IDs}_Camino_FA.img
+
+#shady step to make FA and Schaef_WM_Interesect equivalent
+fslcpgeom $seed_path $out/tractography/${IDs}_Camino_FA.nii.gz
 
 #Camino tractography
-$cdir/track -inputmodel dt -seedfile "${seed_path}" -inputfile "${model_fit_path}" -tracker euler -interpolator linear -iterations 20 -curvethresh 60 | $cdir/procstreamlines -waypointfile "${waypoint_path}" -exclusionfile "${exclusion_path}" -truncateinexclusion -endpointfile "${seed_path}" -outputfile "${tractography_output}"
+cdir/track -inputmodel dt -seedfile "${seed_path}" -inputfile "${model_fit_path}" -tracker euler -interpolator linear -iterations 10 -curvethresh 60 | $cdir/procstreamlines -exclusionfile "${exclusion_path}" -truncateinexclusion -outputfile "${tractography_output}"
+##$cdir/track -inputmodel dt -seedfile "${seed_path}" -inputfile "${model_fit_path}" -tracker fact -iterations 20 -curvethresh 60 | $cdir/procstreamlines -waypointfile ${waypoint_path} -exclusionfile ${exclusion_path} -endpointfile ${out}/tractography/endpoint.nii.gz -outputfile "${tractography_output}"
+##$cdir/track -inputmodel dt -seedfile "${seed_path}" -inputfile "${model_fit_path}" -tracker fact -iterations 20 -curvethresh 70 | $cdir/procstreamlines -exclusionfile ${exclusion_path} -endpointfile ${out}/tractography/endpoint.nii.gz -outputfile "${tractography_output}"
+
+
+### Convert camino tracts to trackvis format
+/data/jux/daviska/apines/camino-trackvis-0.2.8.1/bin/camino_to_trackvis -i ${tractography_output} -o ${out}/tractography/${IDs}_streamlines.trk -l 15 --nifti $out/prestats/${IDs}_eddied_undistort_warped_t1Masked.nii.gz --phys-coords
 
 ################################################
 ### Generate connectivity matrices in Camino ###
 ################################################
 
-# Generate FA from camino
-#$cdir/fa < $out/tractography/${bblIDs}_${SubDate_and_ID}_WdtModelFit.Bdouble > $out/tractography/${bblIDs}_${SubDate_and_ID}_Camino_FA.img
-
-#$cdir/analyzeheader -datadims 140 140 92 -voxeldims 1.5 1.5 1.5 -datatype double > $out/tractography/${bblIDs}_${SubDate_and_ID}_Camino_FA.hdr
-
-#hdr/img to nii.gz
-#c3d $out/tractography/${bblIDs}_${SubDate_and_ID}_Camino_FA.img -o $out/tractography/${bblIDs}_${SubDate_and_ID}_Camino_FA.nii.gz
 
 #copy scalars to coreg folder so conmat can run
-#cp $out/AMICO/NODDI/${bblIDs}_${SubDate_and_ID}_FIT_ICVF.nii.gz $out/coreg/
-#cp $out/AMICO/NODDI/${bblIDs}_${SubDate_and_ID}_FIT_OD.nii.gz $out/coreg/
-#rm $out/coreg/${bblIDs}_${SubDate_and_ID}_Camino_FA.hdr 
-#rm $out/coreg/${bblIDs}_${SubDate_and_ID}_Camino_FA.img
-#cp $out/tractography/${bblIDs}_${SubDate_and_ID}_Camino_FA.nii.gz $out/coreg
-
-#shady step to make FA and Schaef_WM_Interesect equivalent
-fslcpgeom $seed_path $out/coreg/${bblIDs}_${SubDate_and_ID}_Camino_FA.nii.gz
+cp $out/AMICO/NODDI/FIT_ICVF.nii $out/coreg/
+cp $out/AMICO/NODDI/FIT_OD.nii $out/coreg/
+rm $out/tractography/${IDs}_Camino_FA.hdr
+rm $out/tractography/${IDs}_Camino_FA.img
+cp $out/tractography/${IDs}_Camino_FA.nii.gz $out/coreg
 
 # Mean ICVF matrix
-$cdir/conmat -inputfile "${tractography_output}" -targetfile "${seed_path}" -scalarfile $out/coreg/${bblIDs}_${SubDate_and_ID}_FIT_ICVF.nii.gz -tractstat mean -outputroot $out/tractography/${bblIDs}_${SubDate_and_ID}_ICVF_matrix
+$cdir/conmat -inputfile "${tractography_output}" -targetfile ${subAAL} -scalarfile $out/coreg/FIT_ICVF.nii -tractstat mean -outputroot $out/tractography/${IDs}_ICVF_matrix
 
 # Mean ODI matrix
-$cdir/conmat -inputfile "${tractography_output}" -targetfile "${seed_path}" -scalarfile $out/coreg/${bblIDs}_${SubDate_and_ID}_FIT_OD.nii.gz -tractstat mean -outputroot $out/tractography/${bblIDs}_${SubDate_and_ID}_ODI_matrix
+$cdir/conmat -inputfile "${tractography_output}" -targetfile ${subAAL} -scalarfile $out/coreg/FIT_OD.nii -tractstat mean -outputroot $out/tractography/${IDs}_ODI_matrix
 
 # Mean FA matrix
-$cdir/conmat -inputfile "${tractography_output}" -targetfile "${seed_path}" -scalarfile $out/coreg/${bblIDs}_${SubDate_and_ID}_Camino_FA.nii.gz -tractstat mean -outputroot $out/tractography/${bblIDs}_${SubDate_and_ID}_FA_matrix
+#shady step to make FA and AAL equivalent
+fslcpgeom ${subAAL} $out/tractography/${IDs}_Camino_FA.nii.gz
+
+$cdir/conmat -inputfile "${tractography_output}" -targetfile ${subAAL} -scalarfile $out/tractography/${IDs}_Camino_FA.nii.gz -tractstat mean -outputroot $out/tractography/${IDs}_FA_matrix
 
-done
+#done