Upload bb_asl.sh

bb_ASL/bb_asl.sh

+#!/bin/sh
+#
+# Script name: bb_asl
+#
+# Description: Script to process ASL data with oxford_asl
+#
+# Authors: Thomas Okell, Flora Kennedy McConnell, Ludovica Griffanti, Fidel Alfaro-Almagro
+#
+# Copyright 2021 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.
+#
+
+#. $BB_BIN_DIR/bb_pipeline_tools/bb_set_header
+
+set -x
+
+dirScript=`dirname $0`
+
+export FSLDIR="/opt/fmrib/fsl/"
+export FSLCONFDIR=${FSLDIR}/config
+export FSLOUTPUTTYPE="NIFTI_GZ"
+export PATH="$FSLDIR/bin:$PATH"
+
+echo ">>>>>> Running $0..."
+
+subject="$1"
+
+# Find the relevant files
+ASL=$subject/ASL/ASL.nii.gz
+DIFFCORR=$subject/dMRI/dMRI/TOPUP_iout.nii.gz
+DIFFFMAP=$subject/dMRI/dMRI/TOPUP_fout.nii.gz
+STRUC=$subject/T1/T1_unbiased.nii.gz
+STRUCBRAIN=$subject/T1/T1_unbiased_brain.nii.gz
+FASTSRC=$subject/T1/T1_fast/T1_brain
+WARP=$subject/T1/transforms/T1_to_MNI_warp_coef.nii.gz
+MNI=$FSLDIR/data/standard/MNI152_T1_1mm.nii.gz
+
+ASL=`remove_ext $ASL`
+DIFFCORR=`remove_ext $DIFFCORR`
+DIFFFMAP=`remove_ext $DIFFFMAP`
+STRUC=`remove_ext $STRUC`
+WARP=`remove_ext $WARP`
+
+echo Found files to use:
+echo "ASL:                 $ASL"
+echo "Diffusion corrected: $DIFFCORR"
+echo "Diffusion fieldmap:  $DIFFFMAP"
+echo "Structural:          $STRUC"
+
+# Split up the ASL data into M0 and main ASL data
+rm -rf $subject/ASL/ASL_data $subject/ASL/Perf*
+mkdir  $subject/ASL/ASL_data
+$FSLDIR/bin/fslroi $ASL $subject/ASL/ASL_data/M0 0 1
+$FSLDIR/bin/fslroi $ASL $subject/ASL/ASL_data/ASL 1 60
+$FSLDIR/bin/bet $subject/ASL/ASL_data/M0.nii.gz $subject/ASL/ASL_data/M0_brain.nii.gz -m
+
+$BB_BIN_DIR/bb_pipeline_tools/bb_GDC_half_voxel \
+    --workingdir=$subject/ASL/ASL_data/ASL_GDC/ \
+    --in=$subject/ASL/ASL_data/M0 \
+    --out=$subject/ASL/ASL_data/M0_ud.nii.gz \
+    --owarp=$subject/ASL/ASL_data/ASL_ud_warp.nii.gz
+
+
+# ------- Run the longer processing with the structural ---- #
+echo ''
+echo '>>>>>>> Running oxasl with structural and distortion correction...'
+$FSLDIR/bin/oxford_asl \
+       -i $subject/ASL/ASL_data/ASL \
+       -c $subject/ASL/ASL_data/M0 \
+       -o $subject/ASL/PerfQuantFull \
+       --iaf=tc --ibf=rpt --tis=1.7,2.0,2.3,2.6,2.9,3.2 \
+       --bolus=1.4 --slicedt=0.0452 --casl \
+       --cmethod=voxel \
+       --mc --fixbolus \
+       --tr=10 \
+       --te=14 \
+       -s $STRUC \
+       --sbrain=${STRUC}_brain \
+       --structout \
+       --fastsrc=$FASTSRC \
+       --warp=$WARP \
+       --fmap=$subject/dMRI/dMRI/TOPUP_fout_rad_per_s.nii.gz \
+       --fmapmag=$subject/dMRI/dMRI/TOPUP_iout_Tmean  \
+       --fmapmagbrain=$subject/dMRI/dMRI/TOPUP_iout_Tmean_bet \
+       --gdcwarp=$subject/ASL/ASL_data/ASL_ud_warp.nii.gz \
+       --echospacing=0.000559996 \
+       --pedir=-y \
+       --pvcorr \
+       --debug 
+
+echo ''
+echo ">>>> $0 done!"
+
+set +x 
+
+#. $BB_BIN_DIR/bb_pipeline_tools/bb_set_footer