CNT_scripts/determTract_KD.sh at master · adpines/CNT_scripts · GitHub

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#!/bin/bash
cdir=/data/jux/BBL/applications-from-joy/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

#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

#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

#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

#schaefer to seqspace change to MNI

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

#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

#fitTensorsinCamino
#mkdir $out/tractography
export CAMINO_HEAP_SIZE=10000

$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

$cdir/image2voxel -4dimage $in/prestats/eddy/${bblIDs}_${SubDate_and_ID}_eddied.nii.gz -outputfile $out/tractography/${bblIDs}_${SubDate_and_ID}_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

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

#dilate intersect
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

#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}"

################################################
### 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

# 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

# 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

# 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

done