From 24f265cdb5e5571138c36a87609a67da4aacee75 Mon Sep 17 00:00:00 2001
From: rhancockn <rhancock@gmail.com>
Date: Tue, 5 Dec 2017 11:07:07 -0500
Subject: [PATCH 1/7] One solution to HW4

---
 example_solution/scripts/README.md            |  9 +++
 example_solution/scripts/inputs.txt           |  2 +
 example_solution/scripts/run_all.sh           | 14 ++++
 example_solution/scripts/run_bedpost.sh       |  4 +
 example_solution/scripts/run_bedpost_post.sh  |  3 +
 example_solution/scripts/run_bedpost_pre.sh   | 10 +++
 example_solution/scripts/run_dtifit.sh        | 10 +++
 example_solution/scripts/run_eddy.sh          | 20 +++++
 example_solution/scripts/run_topup.sh         | 80 +++++++++++++++++++
 example_solution/scripts/sbatch_bedpost.sh    | 43 ++++++++++
 .../scripts/sbatch_bedpost_post.sh            | 43 ++++++++++
 .../scripts/sbatch_bedpost_pre.sh             | 43 ++++++++++
 example_solution/scripts/sbatch_dtifit.sh     | 44 ++++++++++
 example_solution/scripts/sbatch_eddy.sh       | 44 ++++++++++
 example_solution/scripts/sbatch_topup.sh      | 44 ++++++++++
 15 files changed, 413 insertions(+)
 create mode 100644 example_solution/scripts/README.md
 create mode 100644 example_solution/scripts/inputs.txt
 create mode 100755 example_solution/scripts/run_all.sh
 create mode 100755 example_solution/scripts/run_bedpost.sh
 create mode 100755 example_solution/scripts/run_bedpost_post.sh
 create mode 100755 example_solution/scripts/run_bedpost_pre.sh
 create mode 100755 example_solution/scripts/run_dtifit.sh
 create mode 100755 example_solution/scripts/run_eddy.sh
 create mode 100755 example_solution/scripts/run_topup.sh
 create mode 100755 example_solution/scripts/sbatch_bedpost.sh
 create mode 100755 example_solution/scripts/sbatch_bedpost_post.sh
 create mode 100755 example_solution/scripts/sbatch_bedpost_pre.sh
 create mode 100755 example_solution/scripts/sbatch_dtifit.sh
 create mode 100755 example_solution/scripts/sbatch_eddy.sh
 create mode 100755 example_solution/scripts/sbatch_topup.sh

diff --git a/example_solution/scripts/README.md b/example_solution/scripts/README.md
new file mode 100644
index 0000000..9af98d4
--- /dev/null
+++ b/example_solution/scripts/README.md
@@ -0,0 +1,9 @@
+# Example HW4 solution
+
+On HPC:
+
+1. Run the `mk_skel.sh hw4` script
+2. Copy the contents of the `scripts` directory here to `/scratch/$USER/hw4/scripts`
+3. `cd /scratch/$USER/hw4/scripts`
+4. `./run_all.sh`
+
diff --git a/example_solution/scripts/inputs.txt b/example_solution/scripts/inputs.txt
new file mode 100644
index 0000000..9a4d210
--- /dev/null
+++ b/example_solution/scripts/inputs.txt
@@ -0,0 +1,2 @@
+100206_3T_DWI_dir95_LR 100206_3T_DWI_dir95_LR.bval 100206_3T_DWI_dir95_LR.bvec -1 0 0 .1115
+100206_3T_DWI_dir95_RL 100206_3T_DWI_dir95_RL.bval 100206_3T_DWI_dir95_RL.bvec 1 0 0 .1115
diff --git a/example_solution/scripts/run_all.sh b/example_solution/scripts/run_all.sh
new file mode 100755
index 0000000..b884a24
--- /dev/null
+++ b/example_solution/scripts/run_all.sh
@@ -0,0 +1,14 @@
+#!/bin/bash
+#Run everything
+#This script calls the required SLURM submission scripts
+#and illustrates the use of job dependencies
+#there is a possibility this won't work with afterok. 
+#You can try afterany to ignore the job exit status
+
+j_topup=$( sbatch sbatch_topup.sh )
+j_eddy=$( sbatch --dependency=afterok:$j_topup sbatch_eddy.sh )
+j_dtifit=$( sbatch --dependency=afterok:$j_eddy sbatch_dtifit.sh )
+j_bedpostprep=$( sbatch --dependency=afterok:$j_eddy sbatch_bedpost_pre.sh )
+j_bedpost=$( sbatch --dependency=afterok:$j_bedpostprep sbatch_bedpost.sh )
+sbatch --dependency=afterok:$j_bedpost sbatch_bedpost_post.sh
+
diff --git a/example_solution/scripts/run_bedpost.sh b/example_solution/scripts/run_bedpost.sh
new file mode 100755
index 0000000..292bd17
--- /dev/null
+++ b/example_solution/scripts/run_bedpost.sh
@@ -0,0 +1,4 @@
+#!/bin/bash
+cd /bin/data_out/bedpostX
+bedpostx_single_slice.sh $1 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=2 --cnonlinear  --rician
+
diff --git a/example_solution/scripts/run_bedpost_post.sh b/example_solution/scripts/run_bedpost_post.sh
new file mode 100755
index 0000000..185ec7b
--- /dev/null
+++ b/example_solution/scripts/run_bedpost_post.sh
@@ -0,0 +1,3 @@
+#!/bin/bash
+cd /bind/data_out
+bedpostx_postproc.sh bedpostX
diff --git a/example_solution/scripts/run_bedpost_pre.sh b/example_solution/scripts/run_bedpost_pre.sh
new file mode 100755
index 0000000..d30b7d0
--- /dev/null
+++ b/example_solution/scripts/run_bedpost_pre.sh
@@ -0,0 +1,10 @@
+#!/bin/bash
+#prepare for bedpost
+cd /bind/data_out
+mkdir bedpostX
+imcp corrected bedpostX/data
+imcp brain_mask bedpostX/nodif_brain_mask
+cp bvals bedpostX/bvals
+cp corrected.eddy_rotated_bvecs bedpostX/bvecs
+bedposx_preproc.sh bedpostX
+
diff --git a/example_solution/scripts/run_dtifit.sh b/example_solution/scripts/run_dtifit.sh
new file mode 100755
index 0000000..49d79fa
--- /dev/null
+++ b/example_solution/scripts/run_dtifit.sh
@@ -0,0 +1,10 @@
+#!/bin/bash
+
+#Fit a tensor model
+#Assume the preprocessed inputs are in /bind/data_out
+
+cd /bind/data_out
+dtifit -k corrected -m brain_mask -r corrected.eddy_rotated_bvecs -b bvals -o dti
+
+
+
diff --git a/example_solution/scripts/run_eddy.sh b/example_solution/scripts/run_eddy.sh
new file mode 100755
index 0000000..57bd3f2
--- /dev/null
+++ b/example_solution/scripts/run_eddy.sh
@@ -0,0 +1,20 @@
+#!/bin/bash
+#Run eddy
+#Assume the preprocessed inputs are in /bind/data_out
+#and original source files are in /bind/data_in
+#Multiband factor=3, top slice removed
+
+cd /bind/data_out
+eddy_cuda --mask=brain_mask \
+--acqp=acqparams.txt \
+--index=index.txt \
+--imain=merged_dwi \
+--bvecs=bvecs \
+--bvals=bvals \
+--out=corrected \
+--mb=3 \
+--mb_offs=1 \
+--ol_type=gw \
+--cnr_maps \
+--repol \
+--topup=topup
diff --git a/example_solution/scripts/run_topup.sh b/example_solution/scripts/run_topup.sh
new file mode 100755
index 0000000..1d2dca0
--- /dev/null
+++ b/example_solution/scripts/run_topup.sh
@@ -0,0 +1,80 @@
+#!/bin/bash
+#prep the data and run topup
+#Usage:
+#run_topup.sh inputs.txt
+#Where inputs.txt contains lines of the following form, one per blip
+#dwi_file bval_file bvec_file x y z t
+#x y z t are lines as in the topup acquisition parameter file
+
+inputs=$1
+
+#INDIR=/bind/data_in
+#OUTDIR=/bind/data_out
+
+INDIR=/Users/roh17004/scratch/ibrain_dwi/100206 
+OUTDIR=/Users/roh17004/Dropbox/hw4_solution/out
+
+extract_b0 ()
+{
+	#extract low b0 values as separate volumes
+	#extract_b0 file.bvals dwi.nii.gz prefix offset
+	#assumes series starts with b0
+	local bvals=( $( cat $1 ))
+	local b0in=$2
+	local prefix=$3
+	local rr=$$
+	local i=0
+	local index_i=$4
+	while [ $i -lt ${#bvals[@]} ]; do
+		if [  ${bvals[$i]} -lt 51 ]; then
+			fslroi $b0in `printf "${prefix}.${rr}.%03d $i 1" $i`
+			let index_i=index_i+1 
+		fi
+		let i=i+1
+		echo $(( index_i )) >> ${OUTDIR}/index.txt
+
+	done
+
+	fslmerge -t ${prefix} ${prefix}.${rr}.*
+	rm ${prefix}.${rr}.*
+}
+
+#commands to merge everything
+cmd_merge_dwi="fslmerge -t ${OUTDIR}/merged_dwi "
+cmd_merge_bval="join "
+cmd_merge_bvec="join "
+
+
+offset=0
+while read line; do
+	a=( $( echo $line ) )
+	echo ${INDIR}/${a[0]}
+	cmd_merge_dwi="$cmd_merge_dwi ${INDIR}/${a[0]}"
+	cmd_merge_bval="$cmd_merge_bval ${INDIR}/${a[1]}"
+	cmd_merge_bvec="$cmd_merge_bvec ${INDIR}/${a[2]}"
+	echo "${a[3]} ${a[4]} ${a[5]} ${a[6]}" >> ${OUTDIR}/acqparams.txt
+	prefix=`printf "${OUTDIR}/blip_%03d" $offset`
+	extract_b0 ${INDIR}/${a[1]} ${INDIR}/${a[0]} $prefix $offset
+	let offset=offset+`fslnvols $prefix`
+done <<< "$(cat $inputs)"
+
+`$cmd_merge_dwi`
+echo "$($cmd_merge_bvec)" > ${OUTDIR}/bvecs
+echo "$($cmd_merge_bval)" > ${OUTDIR}/bvals
+
+#merge b0
+fslmerge -t ${OUTDIR}/b0_all ${OUTDIR}/blip_*
+
+#remove top slice from HCP
+fslroi ${OUTDIR}/b0_all ${OUTDIR}/b0_all_cropped 0 -1 0 -1 0 110 0 -1
+fslroi ${OUTDIR}/merged_dwi ${OUTDIR}/merged_dwi_cropped 0 -1 0 -1 0 110 0 -1
+
+#topup
+cd $OUTDIR
+topup --imain=b0_all_cropped --datain=acqparams.txt --config=b02b0.cnf --out=topup —iout=corrected_b0
+
+#create brain mask
+bet corrected_b0 brain -m
+
+
+
diff --git a/example_solution/scripts/sbatch_bedpost.sh b/example_solution/scripts/sbatch_bedpost.sh
new file mode 100755
index 0000000..284d95a
--- /dev/null
+++ b/example_solution/scripts/sbatch_bedpost.sh
@@ -0,0 +1,43 @@
+#!/bin/bash
+#SBATCH --mail-type=ALL 			# Mail events (NONE, BEGIN, END, FAIL, ALL)
+#SBATCH --mail-user=First.Last@uconn.edu	# Your email address
+#SBATCH --nodes=1					# OpenMP requires a single node
+#SBATCH --mem=2048mb				# Memory limit
+#SBATCH --time=04:00:00				# Time limit hh:mm:ss
+#SBATCH -e error_%A_%a.log				# Standard error
+#SBATCH -o output_%A_%a.log				# Standard output
+#SBATCH --job-name=bedpostx			# Descriptive job name
+#SBATCH --partition=serial			# Use a serial partition 24 cores/7days
+#SBATCH --array=0-109
+
+export OMP_NUM_THREADS=1			#<= cpus-per-task
+export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1	#<= cpus-per-task
+##### END OF JOB DEFINITION  #####
+
+#Define user paths
+NETID=$USER
+PROJECT=hw4
+
+export DIR_BASE=/scratch/${NETID}/${PROJECT}
+export DIR_RESOURCES=${DIR_BASE}/resources 	#ro
+export DIR_DATA=${DIR_BASE}/data 				#rw data
+export DIR_DATAIN=${DIR_BASE}/data_in			#ro data
+export DIR_DATAOUT=${DIR_BASE}/data_out		#rw data
+export SUBJECTS_DIR=${DIR_BASE}/freesurfer		#rw for Freesurfer
+export DIR_WORK=/work							#rw /work on HPC is 40Gb local storage
+export DIR_SCRATCH=${DIR_BASE}/scratch 		#rw shared storage
+export DIR_SCRIPTS=${DIR_BASE}/scripts 		#ro, prepended to PATH
+
+
+# Load modules
+module load matlab/2017a				#matlab binaries are bound
+module load singularity/2.3.1-gcc		#required to run the container
+
+#set the matlab license path to the path inside the container
+export LM_LICENSE_FILE=/bind/matlablicense/uits.lic
+
+#finally call the container with any arguments for the job
+#wrapper will bind the appropriate paths
+#environment variables are passed to the container
+
+./burc_wrapper.sh run_bedpost.sh $SLURM_ARRAY_TASK_ID
diff --git a/example_solution/scripts/sbatch_bedpost_post.sh b/example_solution/scripts/sbatch_bedpost_post.sh
new file mode 100755
index 0000000..4ae91d9
--- /dev/null
+++ b/example_solution/scripts/sbatch_bedpost_post.sh
@@ -0,0 +1,43 @@
+#!/bin/bash
+#SBATCH --mail-type=ALL 			# Mail events (NONE, BEGIN, END, FAIL, ALL)
+#SBATCH --mail-user=First.Last@uconn.edu	# Your email address
+#SBATCH --nodes=1					# OpenMP requires a single node
+#SBATCH --ntasks=1					# Run a single serial task
+#SBATCH --cpus-per-task=1           # Number of cores to use
+#SBATCH --time=00:20:00				# Time limit hh:mm:ss
+#SBATCH -e error_%A_%a.log				# Standard error
+#SBATCH -o output_%A_%a.log				# Standard output
+#SBATCH --job-name=bedpostpre			# Descriptive job name
+#SBATCH --partition=serial			# Use a serial partition 24 cores/7days
+
+export OMP_NUM_THREADS=1			#<= cpus-per-task
+export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1	#<= cpus-per-task
+##### END OF JOB DEFINITION  #####
+
+#Define user paths
+NETID=$USER
+PROJECT=hw4
+
+export DIR_BASE=/scratch/${NETID}/${PROJECT}
+export DIR_RESOURCES=${DIR_BASE}/resources 	#ro
+export DIR_DATA=${DIR_BASE}/data 				#rw data
+export DIR_DATAIN=/scratch/birc_ro/ibrain_dwi/100206			#ro data
+export DIR_DATAOUT=${DIR_BASE}/data_out		#rw data
+export SUBJECTS_DIR=${DIR_BASE}/freesurfer		#rw for Freesurfer
+export DIR_WORK=/work							#rw /work on HPC is 40Gb local storage
+export DIR_SCRATCH=${DIR_BASE}/scratch 		#rw shared storage
+export DIR_SCRIPTS=${DIR_BASE}/scripts 		#ro, prepended to PATH
+
+
+# Load modules
+module load matlab/2017a				#matlab binaries are bound
+module load singularity/2.3.1-gcc		#required to run the container
+
+#set the matlab license path to the path inside the container
+export LM_LICENSE_FILE=/bind/matlablicense/uits.lic
+
+#finally call the container with any arguments for the job
+#wrapper will bind the appropriate paths
+#environment variables are passed to the container
+
+./burc_wrapper.sh run_bedpost_post.sh
diff --git a/example_solution/scripts/sbatch_bedpost_pre.sh b/example_solution/scripts/sbatch_bedpost_pre.sh
new file mode 100755
index 0000000..d3891f4
--- /dev/null
+++ b/example_solution/scripts/sbatch_bedpost_pre.sh
@@ -0,0 +1,43 @@
+#!/bin/bash
+#SBATCH --mail-type=ALL 			# Mail events (NONE, BEGIN, END, FAIL, ALL)
+#SBATCH --mail-user=First.Last@uconn.edu	# Your email address
+#SBATCH --nodes=1					# OpenMP requires a single node
+#SBATCH --ntasks=1					# Run a single serial task
+#SBATCH --cpus-per-task=1           # Number of cores to use
+#SBATCH --time=00:20:00				# Time limit hh:mm:ss
+#SBATCH -e error_%A_%a.log				# Standard error
+#SBATCH -o output_%A_%a.log				# Standard output
+#SBATCH --job-name=bedpostpre			# Descriptive job name
+#SBATCH --partition=serial			# Use a serial partition 24 cores/7days
+
+export OMP_NUM_THREADS=1			#<= cpus-per-task
+export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1	#<= cpus-per-task
+##### END OF JOB DEFINITION  #####
+
+#Define user paths
+NETID=$USER
+PROJECT=hw4
+
+export DIR_BASE=/scratch/${NETID}/${PROJECT}
+export DIR_RESOURCES=${DIR_BASE}/resources 	#ro
+export DIR_DATA=${DIR_BASE}/data 				#rw data
+export DIR_DATAIN=/scratch/birc_ro/ibrain_dwi/100206			#ro data
+export DIR_DATAOUT=${DIR_BASE}/data_out		#rw data
+export SUBJECTS_DIR=${DIR_BASE}/freesurfer		#rw for Freesurfer
+export DIR_WORK=/work							#rw /work on HPC is 40Gb local storage
+export DIR_SCRATCH=${DIR_BASE}/scratch 		#rw shared storage
+export DIR_SCRIPTS=${DIR_BASE}/scripts 		#ro, prepended to PATH
+
+
+# Load modules
+module load matlab/2017a				#matlab binaries are bound
+module load singularity/2.3.1-gcc		#required to run the container
+
+#set the matlab license path to the path inside the container
+export LM_LICENSE_FILE=/bind/matlablicense/uits.lic
+
+#finally call the container with any arguments for the job
+#wrapper will bind the appropriate paths
+#environment variables are passed to the container
+
+./burc_wrapper.sh run_bedpost_pre.sh
diff --git a/example_solution/scripts/sbatch_dtifit.sh b/example_solution/scripts/sbatch_dtifit.sh
new file mode 100755
index 0000000..6cf75ce
--- /dev/null
+++ b/example_solution/scripts/sbatch_dtifit.sh
@@ -0,0 +1,44 @@
+#!/bin/bash
+#SBATCH --mail-type=ALL 			# Mail events (NONE, BEGIN, END, FAIL, ALL)
+#SBATCH --mail-user=First.Last@uconn.edu	# Your email address
+#SBATCH --nodes=1					# OpenMP requires a single node
+#SBATCH --ntasks=1					# Run a single serial task
+#SBATCH --cpus-per-task=1           # Number of cores to use
+#SBATCH --mem=2048mb				# Memory limit
+#SBATCH --time=00:20:00				# Time limit hh:mm:ss
+#SBATCH -e error_%A_%a.log				# Standard error
+#SBATCH -o output_%A_%a.log				# Standard output
+#SBATCH --job-name=dtifit			# Descriptive job name
+#SBATCH --partition=serial			# Use a serial partition 24 cores/7days
+
+export OMP_NUM_THREADS=2			#<= cpus-per-task
+export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=2	#<= cpus-per-task
+##### END OF JOB DEFINITION  #####
+
+#Define user paths
+NETID=$USER
+PROJECT=hw4
+
+export DIR_BASE=/scratch/${NETID}/${PROJECT}
+export DIR_RESOURCES=${DIR_BASE}/resources 	#ro
+export DIR_DATA=${DIR_BASE}/data 				#rw data
+export DIR_DATAIN=/scratch/birc_ro/ibrain_dwi/100206			#ro data
+export DIR_DATAOUT=${DIR_BASE}/data_out		#rw data
+export SUBJECTS_DIR=${DIR_BASE}/freesurfer		#rw for Freesurfer
+export DIR_WORK=/work							#rw /work on HPC is 40Gb local storage
+export DIR_SCRATCH=${DIR_BASE}/scratch 		#rw shared storage
+export DIR_SCRIPTS=${DIR_BASE}/scripts 		#ro, prepended to PATH
+
+
+# Load modules
+module load matlab/2017a				#matlab binaries are bound
+module load singularity/2.3.1-gcc		#required to run the container
+
+#set the matlab license path to the path inside the container
+export LM_LICENSE_FILE=/bind/matlablicense/uits.lic
+
+#finally call the container with any arguments for the job
+#wrapper will bind the appropriate paths
+#environment variables are passed to the container
+
+./burc_wrapper.sh run_dtifit.sh
diff --git a/example_solution/scripts/sbatch_eddy.sh b/example_solution/scripts/sbatch_eddy.sh
new file mode 100755
index 0000000..f21c8e3
--- /dev/null
+++ b/example_solution/scripts/sbatch_eddy.sh
@@ -0,0 +1,44 @@
+#!/bin/bash
+#SBATCH --mail-type=ALL 			# Mail events (NONE, BEGIN, END, FAIL, ALL)
+#SBATCH --mail-user=First.Last@uconn.edu	# Your email address
+#SBATCH --nodes=1					# OpenMP requires a single node
+#SBATCH --ntasks=1					# Run a single serial task
+#SBATCH --time=04:00:00				# Time limit hh:mm:ss
+#SBATCH -e error_%A_%a.log			# Standard error
+#SBATCH -o output_%A_%a.log			# Standard output
+#SBATCH --job-name=eddy			# Descriptive job name
+#SBATCH --partition=gpu
+#SBATCH --gres=gpu:1				# Request a GPU
+
+export OMP_NUM_THREADS=1			#<= cpus-per-task
+export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1	#<= cpus-per-task
+##### END OF JOB DEFINITION  #####
+
+#Define user paths
+NETID=$USER
+PROJECT=hw4
+
+export DIR_BASE=/scratch/${NETID}/${PROJECT}
+export DIR_RESOURCES=${DIR_BASE}/resources 	#ro
+export DIR_DATA=${DIR_BASE}/data 				#rw data
+export DIR_DATAIN=/scratch/birc_ro/ibrain_dwi/100206			#ro data
+export DIR_DATAOUT=${DIR_BASE}/data_out		#rw data
+export SUBJECTS_DIR=${DIR_BASE}/freesurfer		#rw for Freesurfer
+export DIR_WORK=/work							#rw /work on HPC is 40Gb local storage
+export DIR_SCRATCH=${DIR_BASE}/scratch 		#rw shared storage
+export DIR_SCRIPTS=${DIR_BASE}/scripts 		#ro, prepended to PATH
+
+
+# Load modules
+module load cuda/8.0.61 					#for GPU/CUDA
+module load matlab/2017a				#matlab binaries are bound
+module load singularity/2.3.1-gcc		#required to run the container
+
+#set the matlab license path to the path inside the container
+export LM_LICENSE_FILE=/bind/matlablicense/uits.lic
+
+#finally call the container with any arguments for the job
+#wrapper will bind the appropriate paths
+#environment variables are passed to the container
+
+./burc_wrapper.sh run_eddy.sh
\ No newline at end of file
diff --git a/example_solution/scripts/sbatch_topup.sh b/example_solution/scripts/sbatch_topup.sh
new file mode 100755
index 0000000..68d3a08
--- /dev/null
+++ b/example_solution/scripts/sbatch_topup.sh
@@ -0,0 +1,44 @@
+#!/bin/bash
+#SBATCH --mail-type=ALL 			# Mail events (NONE, BEGIN, END, FAIL, ALL)
+#SBATCH --mail-user=First.Last@uconn.edu	# Your email address
+#SBATCH --nodes=1					# OpenMP requires a single node
+#SBATCH --ntasks=1					# Run a single serial task
+#SBATCH --cpus-per-task=2           # Number of cores to use
+#SBATCH --mem=4096mb				# Memory limit
+#SBATCH --time=04:00:00				# Time limit hh:mm:ss
+#SBATCH -e error_%A_%a.log				# Standard error
+#SBATCH -o output_%A_%a.log				# Standard output
+#SBATCH --job-name=topup			# Descriptive job name
+#SBATCH --partition=serial			# Use a serial partition 24 cores/7days
+
+export OMP_NUM_THREADS=2			#<= cpus-per-task
+export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=2	#<= cpus-per-task
+##### END OF JOB DEFINITION  #####
+
+#Define user paths
+NETID=$USER
+PROJECT=hw4
+
+export DIR_BASE=/scratch/${NETID}/${PROJECT}
+export DIR_RESOURCES=${DIR_BASE}/resources 	#ro
+export DIR_DATA=${DIR_BASE}/data 				#rw data
+export DIR_DATAIN=/scratch/birc_ro/ibrain_dwi/100206			#ro data
+export DIR_DATAOUT=${DIR_BASE}/data_out		#rw data
+export SUBJECTS_DIR=${DIR_BASE}/freesurfer		#rw for Freesurfer
+export DIR_WORK=/work							#rw /work on HPC is 40Gb local storage
+export DIR_SCRATCH=${DIR_BASE}/scratch 		#rw shared storage
+export DIR_SCRIPTS=${DIR_BASE}/scripts 		#ro, prepended to PATH
+
+
+# Load modules
+module load matlab/2017a				#matlab binaries are bound
+module load singularity/2.3.1-gcc		#required to run the container
+
+#set the matlab license path to the path inside the container
+export LM_LICENSE_FILE=/bind/matlablicense/uits.lic
+
+#finally call the container with any arguments for the job
+#wrapper will bind the appropriate paths
+#environment variables are passed to the container
+
+./burc_wrapper.sh run_topup.sh

From 9fb3b8f9604b46c105f4e66526af425dec01fd5f Mon Sep 17 00:00:00 2001
From: Roeland Hancock <rhancock@gmail.com>
Date: Fri, 26 Jan 2018 15:13:02 -0500
Subject: [PATCH 2/7] Fixing directories in run-topup.sh

---
 example_solution/scripts/run_topup.sh | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/example_solution/scripts/run_topup.sh b/example_solution/scripts/run_topup.sh
index 1d2dca0..70d36f7 100755
--- a/example_solution/scripts/run_topup.sh
+++ b/example_solution/scripts/run_topup.sh
@@ -8,11 +8,9 @@
 
 inputs=$1
 
-#INDIR=/bind/data_in
-#OUTDIR=/bind/data_out
+INDIR=/bind/data_in
+OUTDIR=/bind/data_out
 
-INDIR=/Users/roh17004/scratch/ibrain_dwi/100206 
-OUTDIR=/Users/roh17004/Dropbox/hw4_solution/out
 
 extract_b0 ()
 {

From 3639b60cb414ef4645b707f44cba8bd344ce8779 Mon Sep 17 00:00:00 2001
From: rhancockn <rhancock@gmail.com>
Date: Tue, 30 Jan 2018 17:13:07 -0500
Subject: [PATCH 3/7] Working version

---
 example_solution/scripts/README.md            |  7 +--
 example_solution/scripts/run_all.sh           |  2 +-
 example_solution/scripts/run_bedpost.sh       |  4 +-
 example_solution/scripts/run_bedpost_post.sh  |  3 +-
 example_solution/scripts/run_bedpost_pre.sh   |  5 ++-
 example_solution/scripts/run_dtifit.sh        |  0
 example_solution/scripts/run_eddy.sh          |  2 +-
 example_solution/scripts/run_eddy_mp.sh       | 20 +++++++++
 example_solution/scripts/run_topup.sh         | 18 +++++---
 example_solution/scripts/sbatch_bedpost.sh    |  2 +-
 .../scripts/sbatch_bedpost_post.sh            |  4 +-
 .../scripts/sbatch_bedpost_pre.sh             |  4 +-
 example_solution/scripts/sbatch_dtifit.sh     | 11 +++--
 example_solution/scripts/sbatch_eddy.sh       |  8 ++--
 example_solution/scripts/sbatch_eddy_mp.sh    | 45 +++++++++++++++++++
 example_solution/scripts/sbatch_topup.sh      |  6 +--
 16 files changed, 109 insertions(+), 32 deletions(-)
 mode change 100755 => 100644 example_solution/scripts/run_all.sh
 mode change 100755 => 100644 example_solution/scripts/run_bedpost.sh
 mode change 100755 => 100644 example_solution/scripts/run_bedpost_post.sh
 mode change 100755 => 100644 example_solution/scripts/run_bedpost_pre.sh
 mode change 100755 => 100644 example_solution/scripts/run_dtifit.sh
 mode change 100755 => 100644 example_solution/scripts/run_eddy.sh
 create mode 100644 example_solution/scripts/run_eddy_mp.sh
 mode change 100755 => 100644 example_solution/scripts/run_topup.sh
 mode change 100755 => 100644 example_solution/scripts/sbatch_bedpost.sh
 mode change 100755 => 100644 example_solution/scripts/sbatch_bedpost_post.sh
 mode change 100755 => 100644 example_solution/scripts/sbatch_bedpost_pre.sh
 mode change 100755 => 100644 example_solution/scripts/sbatch_dtifit.sh
 mode change 100755 => 100644 example_solution/scripts/sbatch_eddy.sh
 create mode 100644 example_solution/scripts/sbatch_eddy_mp.sh
 mode change 100755 => 100644 example_solution/scripts/sbatch_topup.sh

diff --git a/example_solution/scripts/README.md b/example_solution/scripts/README.md
index 9af98d4..583bc62 100644
--- a/example_solution/scripts/README.md
+++ b/example_solution/scripts/README.md
@@ -2,8 +2,9 @@
 
 On HPC:
 
-1. Run the `mk_skel.sh hw4` script
-2. Copy the contents of the `scripts` directory here to `/scratch/$USER/hw4/scripts`
-3. `cd /scratch/$USER/hw4/scripts`
+1. Run the `mk_skel.sh martin` script
+2. Copy the input data to `/scratch/$USER/martin/data_in`
+2. Copy the contents of the `scripts` directory here to `/scratch/$USER/martin/scripts`
+3. `cd /scratch/$USER/martin/scripts`
 4. `./run_all.sh`
 
diff --git a/example_solution/scripts/run_all.sh b/example_solution/scripts/run_all.sh
old mode 100755
new mode 100644
index b884a24..bbdee69
--- a/example_solution/scripts/run_all.sh
+++ b/example_solution/scripts/run_all.sh
@@ -6,7 +6,7 @@
 #You can try afterany to ignore the job exit status
 
 j_topup=$( sbatch sbatch_topup.sh )
-j_eddy=$( sbatch --dependency=afterok:$j_topup sbatch_eddy.sh )
+j_eddy=$( sbatch --dependency=afterok:$j_topup sbatch_eddy_mp.sh )
 j_dtifit=$( sbatch --dependency=afterok:$j_eddy sbatch_dtifit.sh )
 j_bedpostprep=$( sbatch --dependency=afterok:$j_eddy sbatch_bedpost_pre.sh )
 j_bedpost=$( sbatch --dependency=afterok:$j_bedpostprep sbatch_bedpost.sh )
diff --git a/example_solution/scripts/run_bedpost.sh b/example_solution/scripts/run_bedpost.sh
old mode 100755
new mode 100644
index 292bd17..155270b
--- a/example_solution/scripts/run_bedpost.sh
+++ b/example_solution/scripts/run_bedpost.sh
@@ -1,4 +1,4 @@
 #!/bin/bash
-cd /bin/data_out/bedpostX
-bedpostx_single_slice.sh $1 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=2 --cnonlinear  --rician
+cd /bind/data_out
+bedpostx_single_slice.sh bedpostX $1 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=2 --cnonlinear  --rician
 
diff --git a/example_solution/scripts/run_bedpost_post.sh b/example_solution/scripts/run_bedpost_post.sh
old mode 100755
new mode 100644
index 185ec7b..4519115
--- a/example_solution/scripts/run_bedpost_post.sh
+++ b/example_solution/scripts/run_bedpost_post.sh
@@ -1,3 +1,4 @@
 #!/bin/bash
 cd /bind/data_out
-bedpostx_postproc.sh bedpostX
+bedpostx_postproc.sh bedpostX.bedpostX
+
diff --git a/example_solution/scripts/run_bedpost_pre.sh b/example_solution/scripts/run_bedpost_pre.sh
old mode 100755
new mode 100644
index d30b7d0..23a8808
--- a/example_solution/scripts/run_bedpost_pre.sh
+++ b/example_solution/scripts/run_bedpost_pre.sh
@@ -6,5 +6,6 @@ imcp corrected bedpostX/data
 imcp brain_mask bedpostX/nodif_brain_mask
 cp bvals bedpostX/bvals
 cp corrected.eddy_rotated_bvecs bedpostX/bvecs
-bedposx_preproc.sh bedpostX
-
+bedpostx_preproc.sh bedpostX
+#make the required directories
+mkdir -p bedpostX.bedpostX/logs/monitor
diff --git a/example_solution/scripts/run_dtifit.sh b/example_solution/scripts/run_dtifit.sh
old mode 100755
new mode 100644
diff --git a/example_solution/scripts/run_eddy.sh b/example_solution/scripts/run_eddy.sh
old mode 100755
new mode 100644
index 57bd3f2..896c9e9
--- a/example_solution/scripts/run_eddy.sh
+++ b/example_solution/scripts/run_eddy.sh
@@ -8,7 +8,7 @@ cd /bind/data_out
 eddy_cuda --mask=brain_mask \
 --acqp=acqparams.txt \
 --index=index.txt \
---imain=merged_dwi \
+--imain=merged_dwi_cropped \
 --bvecs=bvecs \
 --bvals=bvals \
 --out=corrected \
diff --git a/example_solution/scripts/run_eddy_mp.sh b/example_solution/scripts/run_eddy_mp.sh
new file mode 100644
index 0000000..1c58f83
--- /dev/null
+++ b/example_solution/scripts/run_eddy_mp.sh
@@ -0,0 +1,20 @@
+#!/bin/bash
+#Run eddy
+#Assume the preprocessed inputs are in /bind/data_out
+#and original source files are in /bind/data_in
+#Multiband factor=3, top slice removed
+
+cd /bind/data_out
+eddy_openmp --mask=brain_mask \
+--acqp=acqparams.txt \
+--index=index.txt \
+--imain=merged_dwi_cropped \
+--bvecs=bvecs \
+--bvals=bvals \
+--out=corrected \
+--mb=3 \
+--mb_offs=1 \
+--ol_type=gw \
+--cnr_maps \
+--repol \
+--topup=topup
diff --git a/example_solution/scripts/run_topup.sh b/example_solution/scripts/run_topup.sh
old mode 100755
new mode 100644
index 70d36f7..a04f6a2
--- a/example_solution/scripts/run_topup.sh
+++ b/example_solution/scripts/run_topup.sh
@@ -11,6 +11,9 @@ inputs=$1
 INDIR=/bind/data_in
 OUTDIR=/bind/data_out
 
+#clean up
+rm ${OUTDIR}/index.txt
+rm ${OUTDIR}/acqparams.txt
 
 extract_b0 ()
 {
@@ -23,9 +26,13 @@ extract_b0 ()
 	local rr=$$
 	local i=0
 	local index_i=$4
+	eval local acq="$5"
 	while [ $i -lt ${#bvals[@]} ]; do
 		if [  ${bvals[$i]} -lt 51 ]; then
+			#extract this b0
 			fslroi $b0in `printf "${prefix}.${rr}.%03d $i 1" $i`
+			#write the corresponding acquistion parameter line
+			echo "$acq" >> ${OUTDIR}/acqparams.txt
 			let index_i=index_i+1 
 		fi
 		let i=i+1
@@ -39,8 +46,8 @@ extract_b0 ()
 
 #commands to merge everything
 cmd_merge_dwi="fslmerge -t ${OUTDIR}/merged_dwi "
-cmd_merge_bval="join "
-cmd_merge_bvec="join "
+cmd_merge_bval="paste -d ' ' "
+cmd_merge_bvec="paste -d ' ' "
 
 
 offset=0
@@ -50,9 +57,10 @@ while read line; do
 	cmd_merge_dwi="$cmd_merge_dwi ${INDIR}/${a[0]}"
 	cmd_merge_bval="$cmd_merge_bval ${INDIR}/${a[1]}"
 	cmd_merge_bvec="$cmd_merge_bvec ${INDIR}/${a[2]}"
-	echo "${a[3]} ${a[4]} ${a[5]} ${a[6]}" >> ${OUTDIR}/acqparams.txt
+	acq="${a[3]} ${a[4]} ${a[5]} ${a[6]}"
+	#echo "$acq" >> ${OUTDIR}/acqparams.txt
 	prefix=`printf "${OUTDIR}/blip_%03d" $offset`
-	extract_b0 ${INDIR}/${a[1]} ${INDIR}/${a[0]} $prefix $offset
+	extract_b0 ${INDIR}/${a[1]} ${INDIR}/${a[0]} $prefix $offset "\${acq}"
 	let offset=offset+`fslnvols $prefix`
 done <<< "$(cat $inputs)"
 
@@ -69,7 +77,7 @@ fslroi ${OUTDIR}/merged_dwi ${OUTDIR}/merged_dwi_cropped 0 -1 0 -1 0 110 0 -1
 
 #topup
 cd $OUTDIR
-topup --imain=b0_all_cropped --datain=acqparams.txt --config=b02b0.cnf --out=topup —iout=corrected_b0
+topup --imain=b0_all_cropped --datain=acqparams.txt --config=b02b0.cnf --out=topup --iout=corrected_b0
 
 #create brain mask
 bet corrected_b0 brain -m
diff --git a/example_solution/scripts/sbatch_bedpost.sh b/example_solution/scripts/sbatch_bedpost.sh
old mode 100755
new mode 100644
index 284d95a..ea6ccee
--- a/example_solution/scripts/sbatch_bedpost.sh
+++ b/example_solution/scripts/sbatch_bedpost.sh
@@ -16,7 +16,7 @@ export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1	#<= cpus-per-task
 
 #Define user paths
 NETID=$USER
-PROJECT=hw4
+PROJECT=martin
 
 export DIR_BASE=/scratch/${NETID}/${PROJECT}
 export DIR_RESOURCES=${DIR_BASE}/resources 	#ro
diff --git a/example_solution/scripts/sbatch_bedpost_post.sh b/example_solution/scripts/sbatch_bedpost_post.sh
old mode 100755
new mode 100644
index 4ae91d9..e88a1da
--- a/example_solution/scripts/sbatch_bedpost_post.sh
+++ b/example_solution/scripts/sbatch_bedpost_post.sh
@@ -16,12 +16,12 @@ export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1	#<= cpus-per-task
 
 #Define user paths
 NETID=$USER
-PROJECT=hw4
+PROJECT=martin
 
 export DIR_BASE=/scratch/${NETID}/${PROJECT}
 export DIR_RESOURCES=${DIR_BASE}/resources 	#ro
 export DIR_DATA=${DIR_BASE}/data 				#rw data
-export DIR_DATAIN=/scratch/birc_ro/ibrain_dwi/100206			#ro data
+export DIR_DATAIN=${DIR_BASE}/data_in			#ro data
 export DIR_DATAOUT=${DIR_BASE}/data_out		#rw data
 export SUBJECTS_DIR=${DIR_BASE}/freesurfer		#rw for Freesurfer
 export DIR_WORK=/work							#rw /work on HPC is 40Gb local storage
diff --git a/example_solution/scripts/sbatch_bedpost_pre.sh b/example_solution/scripts/sbatch_bedpost_pre.sh
old mode 100755
new mode 100644
index d3891f4..c883a1c
--- a/example_solution/scripts/sbatch_bedpost_pre.sh
+++ b/example_solution/scripts/sbatch_bedpost_pre.sh
@@ -16,12 +16,12 @@ export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1	#<= cpus-per-task
 
 #Define user paths
 NETID=$USER
-PROJECT=hw4
+PROJECT=martin
 
 export DIR_BASE=/scratch/${NETID}/${PROJECT}
 export DIR_RESOURCES=${DIR_BASE}/resources 	#ro
 export DIR_DATA=${DIR_BASE}/data 				#rw data
-export DIR_DATAIN=/scratch/birc_ro/ibrain_dwi/100206			#ro data
+export DIR_DATAIN=${DIR_BASE}/data_in			#ro data
 export DIR_DATAOUT=${DIR_BASE}/data_out		#rw data
 export SUBJECTS_DIR=${DIR_BASE}/freesurfer		#rw for Freesurfer
 export DIR_WORK=/work							#rw /work on HPC is 40Gb local storage
diff --git a/example_solution/scripts/sbatch_dtifit.sh b/example_solution/scripts/sbatch_dtifit.sh
old mode 100755
new mode 100644
index 6cf75ce..216c0c2
--- a/example_solution/scripts/sbatch_dtifit.sh
+++ b/example_solution/scripts/sbatch_dtifit.sh
@@ -5,24 +5,23 @@
 #SBATCH --ntasks=1					# Run a single serial task
 #SBATCH --cpus-per-task=1           # Number of cores to use
 #SBATCH --mem=2048mb				# Memory limit
-#SBATCH --time=00:20:00				# Time limit hh:mm:ss
+#SBATCH --time=00:10:00				# Time limit hh:mm:ss
 #SBATCH -e error_%A_%a.log				# Standard error
 #SBATCH -o output_%A_%a.log				# Standard output
 #SBATCH --job-name=dtifit			# Descriptive job name
 #SBATCH --partition=serial			# Use a serial partition 24 cores/7days
-
-export OMP_NUM_THREADS=2			#<= cpus-per-task
-export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=2	#<= cpus-per-task
+export OMP_NUM_THREADS=1			#<= cpus-per-task
+export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1	#<= cpus-per-task
 ##### END OF JOB DEFINITION  #####
 
 #Define user paths
 NETID=$USER
-PROJECT=hw4
+PROJECT=martin
 
 export DIR_BASE=/scratch/${NETID}/${PROJECT}
 export DIR_RESOURCES=${DIR_BASE}/resources 	#ro
 export DIR_DATA=${DIR_BASE}/data 				#rw data
-export DIR_DATAIN=/scratch/birc_ro/ibrain_dwi/100206			#ro data
+export DIR_DATAIN=${DIR_BASE}/data_in			#ro data
 export DIR_DATAOUT=${DIR_BASE}/data_out		#rw data
 export SUBJECTS_DIR=${DIR_BASE}/freesurfer		#rw for Freesurfer
 export DIR_WORK=/work							#rw /work on HPC is 40Gb local storage
diff --git a/example_solution/scripts/sbatch_eddy.sh b/example_solution/scripts/sbatch_eddy.sh
old mode 100755
new mode 100644
index f21c8e3..41f50e7
--- a/example_solution/scripts/sbatch_eddy.sh
+++ b/example_solution/scripts/sbatch_eddy.sh
@@ -3,6 +3,8 @@
 #SBATCH --mail-user=First.Last@uconn.edu	# Your email address
 #SBATCH --nodes=1					# OpenMP requires a single node
 #SBATCH --ntasks=1					# Run a single serial task
+#SBATCH --cpus-per-task=1           # Number of cores to use
+#SBATCH --mem=4096mb				# Memory limit
 #SBATCH --time=04:00:00				# Time limit hh:mm:ss
 #SBATCH -e error_%A_%a.log			# Standard error
 #SBATCH -o output_%A_%a.log			# Standard output
@@ -16,12 +18,12 @@ export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1	#<= cpus-per-task
 
 #Define user paths
 NETID=$USER
-PROJECT=hw4
+PROJECT=martin
 
 export DIR_BASE=/scratch/${NETID}/${PROJECT}
 export DIR_RESOURCES=${DIR_BASE}/resources 	#ro
 export DIR_DATA=${DIR_BASE}/data 				#rw data
-export DIR_DATAIN=/scratch/birc_ro/ibrain_dwi/100206			#ro data
+export DIR_DATAIN=${DIR_BASE}/data_in			#ro data
 export DIR_DATAOUT=${DIR_BASE}/data_out		#rw data
 export SUBJECTS_DIR=${DIR_BASE}/freesurfer		#rw for Freesurfer
 export DIR_WORK=/work							#rw /work on HPC is 40Gb local storage
@@ -41,4 +43,4 @@ export LM_LICENSE_FILE=/bind/matlablicense/uits.lic
 #wrapper will bind the appropriate paths
 #environment variables are passed to the container
 
-./burc_wrapper.sh run_eddy.sh
\ No newline at end of file
+./burc_wrapper.sh run_eddy.sh
diff --git a/example_solution/scripts/sbatch_eddy_mp.sh b/example_solution/scripts/sbatch_eddy_mp.sh
new file mode 100644
index 0000000..5dfdbf8
--- /dev/null
+++ b/example_solution/scripts/sbatch_eddy_mp.sh
@@ -0,0 +1,45 @@
+#!/bin/bash
+#SBATCH --mail-type=ALL 			# Mail events (NONE, BEGIN, END, FAIL, ALL)
+#SBATCH --mail-user=First.Last@uconn.edu	# Your email address
+#SBATCH --nodes=1					# OpenMP requires a single node
+#SBATCH --ntasks=1					# Run a single serial task
+#SBATCH --cpus-per-task=8           # Number of cores to use
+#SBATCH --mem=8192mb				# Memory limit
+#SBATCH --time=08:00:00				# Time limit hh:mm:ss
+#SBATCH -e error_%A_%a.log			# Standard error
+#SBATCH -o output_%A_%a.log			# Standard output
+#SBATCH --job-name=eddy			# Descriptive job name
+#SBATCH --partition=serial
+
+export OMP_NUM_THREADS=8			#<= cpus-per-task
+export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=18	#<= cpus-per-task
+##### END OF JOB DEFINITION  #####
+
+#Define user paths
+NETID=$USER
+PROJECT=martin
+
+export DIR_BASE=/scratch/${NETID}/${PROJECT}
+export DIR_RESOURCES=${DIR_BASE}/resources 	#ro
+export DIR_DATA=${DIR_BASE}/data 				#rw data
+export DIR_DATAIN=${DIR_BASE}/data_in			#ro data
+export DIR_DATAOUT=${DIR_BASE}/data_out		#rw data
+export SUBJECTS_DIR=${DIR_BASE}/freesurfer		#rw for Freesurfer
+export DIR_WORK=/work							#rw /work on HPC is 40Gb local storage
+export DIR_SCRATCH=${DIR_BASE}/scratch 		#rw shared storage
+export DIR_SCRIPTS=${DIR_BASE}/scripts 		#ro, prepended to PATH
+
+
+# Load modules
+module load cuda/8.0.61 					#for GPU/CUDA
+module load matlab/2017a				#matlab binaries are bound
+module load singularity/2.3.1-gcc		#required to run the container
+
+#set the matlab license path to the path inside the container
+export LM_LICENSE_FILE=/bind/matlablicense/uits.lic
+
+#finally call the container with any arguments for the job
+#wrapper will bind the appropriate paths
+#environment variables are passed to the container
+
+./burc_wrapper.sh run_eddy_mp.sh
diff --git a/example_solution/scripts/sbatch_topup.sh b/example_solution/scripts/sbatch_topup.sh
old mode 100755
new mode 100644
index 68d3a08..ed406c0
--- a/example_solution/scripts/sbatch_topup.sh
+++ b/example_solution/scripts/sbatch_topup.sh
@@ -17,12 +17,12 @@ export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=2	#<= cpus-per-task
 
 #Define user paths
 NETID=$USER
-PROJECT=hw4
+PROJECT=martin
 
 export DIR_BASE=/scratch/${NETID}/${PROJECT}
 export DIR_RESOURCES=${DIR_BASE}/resources 	#ro
 export DIR_DATA=${DIR_BASE}/data 				#rw data
-export DIR_DATAIN=/scratch/birc_ro/ibrain_dwi/100206			#ro data
+export DIR_DATAIN=${DIR_BASE}/data_in			#ro data
 export DIR_DATAOUT=${DIR_BASE}/data_out		#rw data
 export SUBJECTS_DIR=${DIR_BASE}/freesurfer		#rw for Freesurfer
 export DIR_WORK=/work							#rw /work on HPC is 40Gb local storage
@@ -41,4 +41,4 @@ export LM_LICENSE_FILE=/bind/matlablicense/uits.lic
 #wrapper will bind the appropriate paths
 #environment variables are passed to the container
 
-./burc_wrapper.sh run_topup.sh
+./burc_wrapper.sh /bind/scripts/run_topup.sh /bind/scripts/inputs.txt

From 5e0af996ec62419c259bb416ec296eea48d979fa Mon Sep 17 00:00:00 2001
From: rhancockn <rhancock@gmail.com>
Date: Tue, 30 Jan 2018 17:13:28 -0500
Subject: [PATCH 4/7] Permissions

---
 example_solution/scripts/run_all.sh             | 0
 example_solution/scripts/run_bedpost.sh         | 0
 example_solution/scripts/run_bedpost_post.sh    | 0
 example_solution/scripts/run_bedpost_pre.sh     | 0
 example_solution/scripts/run_dtifit.sh          | 0
 example_solution/scripts/run_eddy.sh            | 0
 example_solution/scripts/run_eddy_mp.sh         | 0
 example_solution/scripts/run_topup.sh           | 0
 example_solution/scripts/sbatch_bedpost.sh      | 0
 example_solution/scripts/sbatch_bedpost_post.sh | 0
 example_solution/scripts/sbatch_bedpost_pre.sh  | 0
 example_solution/scripts/sbatch_dtifit.sh       | 0
 example_solution/scripts/sbatch_eddy.sh         | 0
 example_solution/scripts/sbatch_eddy_mp.sh      | 0
 example_solution/scripts/sbatch_topup.sh        | 0
 15 files changed, 0 insertions(+), 0 deletions(-)
 mode change 100644 => 100755 example_solution/scripts/run_all.sh
 mode change 100644 => 100755 example_solution/scripts/run_bedpost.sh
 mode change 100644 => 100755 example_solution/scripts/run_bedpost_post.sh
 mode change 100644 => 100755 example_solution/scripts/run_bedpost_pre.sh
 mode change 100644 => 100755 example_solution/scripts/run_dtifit.sh
 mode change 100644 => 100755 example_solution/scripts/run_eddy.sh
 mode change 100644 => 100755 example_solution/scripts/run_eddy_mp.sh
 mode change 100644 => 100755 example_solution/scripts/run_topup.sh
 mode change 100644 => 100755 example_solution/scripts/sbatch_bedpost.sh
 mode change 100644 => 100755 example_solution/scripts/sbatch_bedpost_post.sh
 mode change 100644 => 100755 example_solution/scripts/sbatch_bedpost_pre.sh
 mode change 100644 => 100755 example_solution/scripts/sbatch_dtifit.sh
 mode change 100644 => 100755 example_solution/scripts/sbatch_eddy.sh
 mode change 100644 => 100755 example_solution/scripts/sbatch_eddy_mp.sh
 mode change 100644 => 100755 example_solution/scripts/sbatch_topup.sh

diff --git a/example_solution/scripts/run_all.sh b/example_solution/scripts/run_all.sh
old mode 100644
new mode 100755
diff --git a/example_solution/scripts/run_bedpost.sh b/example_solution/scripts/run_bedpost.sh
old mode 100644
new mode 100755
diff --git a/example_solution/scripts/run_bedpost_post.sh b/example_solution/scripts/run_bedpost_post.sh
old mode 100644
new mode 100755
diff --git a/example_solution/scripts/run_bedpost_pre.sh b/example_solution/scripts/run_bedpost_pre.sh
old mode 100644
new mode 100755
diff --git a/example_solution/scripts/run_dtifit.sh b/example_solution/scripts/run_dtifit.sh
old mode 100644
new mode 100755
diff --git a/example_solution/scripts/run_eddy.sh b/example_solution/scripts/run_eddy.sh
old mode 100644
new mode 100755
diff --git a/example_solution/scripts/run_eddy_mp.sh b/example_solution/scripts/run_eddy_mp.sh
old mode 100644
new mode 100755
diff --git a/example_solution/scripts/run_topup.sh b/example_solution/scripts/run_topup.sh
old mode 100644
new mode 100755
diff --git a/example_solution/scripts/sbatch_bedpost.sh b/example_solution/scripts/sbatch_bedpost.sh
old mode 100644
new mode 100755
diff --git a/example_solution/scripts/sbatch_bedpost_post.sh b/example_solution/scripts/sbatch_bedpost_post.sh
old mode 100644
new mode 100755
diff --git a/example_solution/scripts/sbatch_bedpost_pre.sh b/example_solution/scripts/sbatch_bedpost_pre.sh
old mode 100644
new mode 100755
diff --git a/example_solution/scripts/sbatch_dtifit.sh b/example_solution/scripts/sbatch_dtifit.sh
old mode 100644
new mode 100755
diff --git a/example_solution/scripts/sbatch_eddy.sh b/example_solution/scripts/sbatch_eddy.sh
old mode 100644
new mode 100755
diff --git a/example_solution/scripts/sbatch_eddy_mp.sh b/example_solution/scripts/sbatch_eddy_mp.sh
old mode 100644
new mode 100755
diff --git a/example_solution/scripts/sbatch_topup.sh b/example_solution/scripts/sbatch_topup.sh
old mode 100644
new mode 100755

From ca05e737de9abf12d168a875a9c0ab2a55cbe807 Mon Sep 17 00:00:00 2001
From: rhancockn <rhancock@gmail.com>
Date: Wed, 31 Jan 2018 10:00:59 -0500
Subject: [PATCH 5/7] increasing bedpost time limit

---
 example_solution/scripts/sbatch_bedpost.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/example_solution/scripts/sbatch_bedpost.sh b/example_solution/scripts/sbatch_bedpost.sh
index ea6ccee..5db9eb3 100755
--- a/example_solution/scripts/sbatch_bedpost.sh
+++ b/example_solution/scripts/sbatch_bedpost.sh
@@ -3,7 +3,7 @@
 #SBATCH --mail-user=First.Last@uconn.edu	# Your email address
 #SBATCH --nodes=1					# OpenMP requires a single node
 #SBATCH --mem=2048mb				# Memory limit
-#SBATCH --time=04:00:00				# Time limit hh:mm:ss
+#SBATCH --time=08:00:00				# Time limit hh:mm:ss
 #SBATCH -e error_%A_%a.log				# Standard error
 #SBATCH -o output_%A_%a.log				# Standard output
 #SBATCH --job-name=bedpostx			# Descriptive job name

From 19cae4a93afbf1cd444c5a7766e4fb1bb9bcb59e Mon Sep 17 00:00:00 2001
From: rhancockn <rhancock@gmail.com>
Date: Thu, 1 Feb 2018 13:47:39 -0500
Subject: [PATCH 6/7] Fix eval error in run_topup.sh

---
 example_solution/scripts/run_topup.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/example_solution/scripts/run_topup.sh b/example_solution/scripts/run_topup.sh
index a04f6a2..eac3f5a 100755
--- a/example_solution/scripts/run_topup.sh
+++ b/example_solution/scripts/run_topup.sh
@@ -65,8 +65,8 @@ while read line; do
 done <<< "$(cat $inputs)"
 
 `$cmd_merge_dwi`
-echo "$($cmd_merge_bvec)" > ${OUTDIR}/bvecs
-echo "$($cmd_merge_bval)" > ${OUTDIR}/bvals
+eval "$cmd_merge_bvec" > ${OUTDIR}/bvecs
+eval "$cmd_merge_bval" > ${OUTDIR}/bvals
 
 #merge b0
 fslmerge -t ${OUTDIR}/b0_all ${OUTDIR}/blip_*

From fc62e76aa005dabb26d7448b8dc29872d35d64e7 Mon Sep 17 00:00:00 2001
From: Roeland Hancock <rhancock@gmail.com>
Date: Fri, 2 Feb 2018 13:42:42 -0500
Subject: [PATCH 7/7] Update sbatch_eddy_mp.sh

---
 example_solution/scripts/sbatch_eddy_mp.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/example_solution/scripts/sbatch_eddy_mp.sh b/example_solution/scripts/sbatch_eddy_mp.sh
index 5dfdbf8..53e708d 100755
--- a/example_solution/scripts/sbatch_eddy_mp.sh
+++ b/example_solution/scripts/sbatch_eddy_mp.sh
@@ -12,7 +12,7 @@
 #SBATCH --partition=serial
 
 export OMP_NUM_THREADS=8			#<= cpus-per-task
-export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=18	#<= cpus-per-task
+export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=8	#<= cpus-per-task
 ##### END OF JOB DEFINITION  #####
 
 #Define user paths