Delete cmore_diff.sh

dMRI_pipeline/cmore_diff.sh

-#!/bin/bash
-
-#
-# Script name: cmore_diff.sh
-#
-# Description: Script to preprocess dMRI images and calculate MD
-#  (adapted pipeline from dMRI sequence with 3 diffusion directions)
-#
-# Authors: Fidel Alfaro-Almagro, Stephen M. Smith & Mark Jenkinson
-#
-# Copyright 2020 University of Oxford
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#    http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-
-echo "Start: `date`";
-set -x ;
-
-scriptDir="`dirname $0`" ;
-subject="$1" ;
-
-# Clean previous runnings of this pipeline
-rm   -rf $subject/dMRI/dMRI/ ;
-mkdir -p $subject/dMRI/dMRI/dtifit_output ;
-cd       $subject/dMRI/dMRI/ ;
-
-# Create symbolic links to the important files and copy bvals and bvecs if absent
-ln -s ../raw/AP.nii.gz ./AP.nii.gz ;
-ln -s ../raw/PA.nii.gz ./B0_PA.nii.gz ;
-for ED in "AP" "PA" ; do
-    if [ ! -f ../raw/$ED.bval ] ; then
-        cp $scriptDir/$ED.bval ../raw/$ED.bval
-        cp $scriptDir/$ED.bvec ../raw/$ED.bvec
-    fi
-done
-ln -s ../raw/AP.bval ./AP.bval ;
-ln -s ../raw/AP.bvec ./AP.bvec ;
-ln -s ../raw/PA.bval ./PA.bval ;
-ln -s ../raw/PA.bvec ./PA.bvec ;
-
-# Generate aqparams file for topup
-if [[ -e ../raw/AP.json && -e ../raw/PA.json ]]; then
-    echo "Found .json files for dMRI - using to extract total readout time for topup..."
-    APECHOSPACING=`grep EffectiveEchoSpacing ../raw/AP.json | awk '{ print $2 }' | sed 's/,//'`
-    APROLINES=`fslinfo ../raw/AP.nii.gz | grep dim1 | head -1 | awk '{print $2}'`
-    APTOTROTIME=`echo "$APECHOSPACING * ($APROLINES - 1)" | bc | awk '{printf "%f", $0}'`
-    echo "AP total readout time: $APTOTROTIME s"
-
-    PAECHOSPACING=`grep EffectiveEchoSpacing ../raw/PA.json | awk '{ print $2 }' | sed 's/,//'`
-    PAROLINES=`fslinfo ../raw/PA.nii.gz | grep dim1 | head -1 | awk '{print $2}'`
-    PATOTROTIME=`echo "$PAECHOSPACING * ($PAROLINES - 1)" | bc | awk '{printf "%f", $0}'`
-    echo "PA total readout time: $PATOTROTIME s"
-else
-    echo "Cannot find dMRI .json files"
-    APTOTROTIME=0.0335
-    PATOTROTIME=0.0335
-    echo "Assuming AP and PA total readout times are $APTOTROTIME and $PATOTROTIME s (appropriate for GRAPPA = 2)"fi
-fi
-
-echo "0 -1 0 $APTOTROTIME" > ./acqparams.txt
-echo "0 1 0 $PATOTROTIME" >> ./acqparams.txt
-echo 'Diffusion parameters:'
-cat ./acqparams.txt
-
-
-$FSLDIR/bin/eddy_correct ./AP.nii.gz ./Data.nii.gz 0 spline ;
-$FSLDIR/bin/fslroi       ./AP.nii.gz ./B0_AP.nii.gz 0 1 ;
-$FSLDIR/bin/fslmerge -t  ./B0_4D_AP_PA.nii.gz ./B0_AP.nii.gz ./B0_PA.nii.gz ;
-
-$FSLDIR/bin/topup \
-    --imain=./B0_4D_AP_PA.nii.gz \
-    --datain=./acqparams.txt \
-    --config=$scriptDir/topup_b02b0.cnf \
-    --out=TOPUP \
-    --fout=TOPUP_fout \
-    --jacout=TOPUP_jout \
-    --iout=TOPUP_iout ;
-
-# Average output
-$FSLDIR/bin/fslmaths TOPUP_iout -Tmean TOPUP_iout_Tmean
-
-# Convert fieldmap to rad/s
-$FSLDIR/bin/fslmaths TOPUP_fout -mul 2 -mul 3.1415926536 TOPUP_fout_rad_per_s
-
-# Run bet on the corrected b0 image for passing into oxford_asl
-$FSLDIR/bin/bet TOPUP_iout_Tmean TOPUP_iout_Tmean_bet
-
-# Apply topup to the different B0s to get a combined B0
-$FSLDIR/bin/applytopup \
-    --imain=B0_AP,B0_PA \
-    --topup=TOPUP \
-    --datain=./acqparams.txt \
-    --inindex=1,2 \
-    --out=./hifib0.nii.gz ;
-
-# Run a loose (-f 0.2) brain extraction on the B0
-$FSLDIR/bin/bet ./hifib0.nii.gz ./hifib0_brain.nii.gz -R -m -f 0.2;
-
-# Fill holes, and slightly erode the brain mask
-$FSLDIR/bin/fslmaths \
-    ./hifib0_brain_mask.nii.gz \
-    -fillh \
-    -kernel sphere 2.5 \
-    -ero hifib0_brain_mask_ero.nii.gz
-
-# Run applytopup on the data
-$FSLDIR/bin/applytopup \
-    --imain=./Data.nii.gz \
-    --datain=./acqparams.txt \
-    --inindex=1 \
-    --topup=TOPUP \
-    --out=./Data_corr.nii.gz \
-    --method=jac \
-    --interp=spline ;
-
-# Perform GDC on the data
-$BB_BIN_DIR/bb_pipeline_tools/bb_GDC_half_voxel \
-    --workingdir=./data_GDC \
-    --in=./hifib0.nii.gz \
-    --out=./hifib0_ud.nii.gz \
-    --owarp=./hifib0_ud_warp.nii.gz ;
-
-# Estimate a registration from B0 to T1 space
-$FSLDIR/bin/flirt \
-    -in ./hifib0_ud.nii.gz \
-    -ref ../../T1/T1.nii.gz \
-    -out ./hifib0_ud_to_T1.nii.gz \
-    -omat ./hifib0_ud_to_T1.mat \
-    -cost mutualinfo \
-    -interp spline ;
-
-# Invert the previous transformation
-${FSLDIR}/bin/convert_xfm \
-    -omat ./T1_to_hifib0_ud.mat \
-    -inverse ./hifib0_ud_to_T1.mat ;
-
-# Apply GDC to the data after eddy_correct
-${FSLDIR}/bin/applywarp --rel \
-    -i ./Data_corr.nii.gz \
-    -r ./hifib0_ud.nii.gz \
-    -o ./Data_corr_ud.nii.gz \
-    -w ./hifib0_ud_warp.nii.gz \
-    --interp=spline ;
-
-# Run dtifit on the data
-$FSLDIR/bin/dtifit \
-    -m ./hifib0_brain_mask_ero.nii.gz \
-    -k ./Data_corr_ud.nii.gz \
-    -r ./AP.bvec \
-    -b ./AP.bval \
-    -o ./dtifit_output/dti ;
-
-set +x ;
-echo "End: `date`" ;
-