Hw4

example_solution/scripts/README.md

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+# Example HW4 solution
+
+On HPC:
+
+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`
+

example_solution/scripts/inputs.txt

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+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

example_solution/scripts/run_all.sh

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+#!/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:$j_topup sbatch_eddy_mp.sh )
+j_dtifit=$( sbatch --dependency=afterok:$j_eddy sbatch_dtifit.sh )
+j_bedpostprep=$( sbatch --dependency=afterok:$j_eddy sbatch_bedpost_pre.sh )
+j_bedpost=$( sbatch --dependency=afterok:$j_bedpostprep sbatch_bedpost.sh )
+sbatch --dependency=afterok:$j_bedpost sbatch_bedpost_post.sh
+

example_solution/scripts/run_bedpost.sh

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+#!/bin/bash
+cd /bind/data_out
+bedpostx_single_slice.sh bedpostX $1 --nf=2 --fudge=1 --bi=1000 --nj=1250 --se=25 --model=2 --cnonlinear  --rician
+

example_solution/scripts/run_bedpost_post.sh

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+#!/bin/bash
+cd /bind/data_out
+bedpostx_postproc.sh bedpostX.bedpostX
+

example_solution/scripts/run_bedpost_pre.sh

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+#!/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
+bedpostx_preproc.sh bedpostX
+#make the required directories
+mkdir -p bedpostX.bedpostX/logs/monitor

example_solution/scripts/run_dtifit.sh

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+#!/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
+
+
+

example_solution/scripts/run_eddy.sh

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+#!/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_cropped \
+--bvecs=bvecs \
+--bvals=bvals \
+--out=corrected \
+--mb=3 \
+--mb_offs=1 \
+--ol_type=gw \
+--cnr_maps \
+--repol \
+--topup=topup

example_solution/scripts/run_eddy_mp.sh

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+#!/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

example_solution/scripts/run_topup.sh

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+#!/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
+
+#clean up
+rm ${OUTDIR}/index.txt
+rm ${OUTDIR}/acqparams.txt
+
+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
+	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
+		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="paste -d ' ' "
+cmd_merge_bvec="paste -d ' ' "
+
+
+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]}"
+	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 "\${acq}"
+	let offset=offset+`fslnvols $prefix`
+done <<< "$(cat $inputs)"
+
+`$cmd_merge_dwi`
+eval "$cmd_merge_bvec" > ${OUTDIR}/bvecs
+eval "$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
+
+
+

example_solution/scripts/sbatch_bedpost.sh

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+#!/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=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
+#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=$USER
+PROJECT=martin
+
+export DIR_BASE=/scratch/${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 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

example_solution/scripts/sbatch_bedpost_post.sh

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+#!/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=$USER
+PROJECT=martin
+
+export DIR_BASE=/scratch/${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 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

example_solution/scripts/sbatch_bedpost_pre.sh

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+#!/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=$USER
+PROJECT=martin
+
+export DIR_BASE=/scratch/${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 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

example_solution/scripts/sbatch_dtifit.sh

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+#!/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=00:10:00				# 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=1			#<= cpus-per-task
+export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1	#<= cpus-per-task
+##### END OF JOB DEFINITION  #####
+
+#Define user paths
+NETID=$USER
+PROJECT=martin
+
+export DIR_BASE=/scratch/${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 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