First version of scripts

Author: scholand

.gitignore

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+# Skip
+*.cfl
+*.hdr
+*.txt
+*.code-workspace
+*.log
+*/out*
+
+# Add anyway
+!*/vertices/*.cfl
+!*/vertices/*.hdr
+!00_gold_standard_nist/ref_values_nist.txt
+!05_IR-bSSFP_NIST/ref_values_nist.txt
+!06_IR-bSSFP_invivo/tables.txt
+!s03_multi_trf_analysis/tables.txt

LICENSE

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+# Quantitative Multi-Parameter Mapping in Magnetic Resonance Imaging
+
+This repository includes the scripts to create the Figures for chapter 5 of
+
+> #### Quantitative Multi-Parameter Mapping in Magnetic Resonance Imaging
+> Scholand, N. Doctoral thesis, 2023.
+> [doi: 10.53846/goediss-10028](http://dx.doi.org/10.53846/goediss-10028)
+
+The scripts for the figures of chapter 4 can be found on [Github](https://github.com/mrirecon/bloch-moba).
+
+## Requirements
+This repository has been tested on Debian 11, but is assumed to work on other Linux-based operating systems, too.
+
+### Reconstruction
+Pre-processing, reconstruction and post-processing is performed with the [BART toolbox](https://github.com/mrirecon/bart).
+The provided scripts are compatible with commit `f1192bc` or later.
+If you experience any compatibility problems with later BART versions please contact us!
+
+[//]: <> (FIXME: Add DOI for BART version including the Bloch model-based reconstruction)
+
+For running the reconstructions access to a GPU is recommended.
+If the CPU should be used, please remove `-g` flags from `bart moba ...`, `bart pics ...` and `bart rtnlinv ...` calls.
+
+### Visualization
+The visualizations have been tested with Python on version 3.9.2 and require numpy, copy, matplotlib, mpl_toolkits, sys, os, math, time, and scipy. Ensure to have set a DISPLAY variable, when the results should be visualized.
+
+## Data
+The data is hosted on [ZENODO](https://zenodo.org/) and must be downloaded first.
+
+* Manual download: https://zenodo.org/record/7837312
+* Download via script: Run the download script in the `./data` folder.
+  * **All** files: `bash load-all.sh`
+  * **Individual** files: `bash load.sh 7654462 <FILENAME> . ` or `bash load.sh 6992763 <FILENAME> . ` for the scripts in the folder `init_test`
+
+Note: The data must be stored in the `./data` folder!
+
+
+## Folders
+Each folder contains a README file explaining how the figure can be reproduced.
+
+
+[//]: <> (FIXME: Add Runtime!)
+
+## Feedback
+Please feel free to send us feedback about this scripts!
+We would be happy to learn how to improve this and future script publications.
+
+
+## License
+This work is licensed under a **Creative Commons Attribution 4.0 International License**.
+You should have received a copy of the license along with this
+work. If not, see <https://creativecommons.org/licenses/by/4.0/>.

README.md

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+To run a reconstruction with a specific model run `./run_reco.sh <MODEL>`.
+
+All reconstruction can be run using `./run.sh`.
+
+For running all models and creating the final figure enter `./run_figs.sh`.
+
+You might want to specify the reconstruction parameters in `func/opts.sh`.
+
+To clean up the folder run `./clean_up.sh`.

b0_invivo/README.mkd

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+#!/bin/bash
+
+# B0 Mapping with Siemens Sequence "gre_field_mapping" based on
+# Nayak, K.S. and Nishimura, D.G. (2000),
+# Automatic field map generation and off-resonance correction for projection reconstruction imaging.
+# Magn. Reson. Med., 43: 151-154.
+# https://doi.org/10.1002/(SICI)1522-2594(200001)43:1<151::AID-MRM19>3.0.CO;2-K
+
+# Estimate relative paths
+FULL_PATH=$(realpath ${0})
+REL_PATH=$(dirname ${FULL_PATH})
+
+TE1=0.00492	# Early TE
+TE2=0.00738	# Late TE
+
+# Load data
+# bart twixread -A /home/ague/archive/vol/2023-03-14_MRTG-BLMB-0008/raw/meas_MID00043_FID06084_gre_field_mapping_BR256_S01.dat raw
+bart copy ${REL_PATH}/../data/ksp_b0map raw
+
+# Estimate Coil sensitivities
+bart ecalib -c 0 -m 1 raw sens
+
+# Phase preserving PI reconstruction
+bart pics -g -e -S -d 5 raw sens _reco
+rm {sens,raw}.{cfl,hdr}
+
+SAMPLES=$(bart show -d 0 _reco)
+bart resize -c 0 $((SAMPLES/2)) _reco reco
+
+bart slice 5 0 reco te1
+bart slice 5 1 reco te2
+rm {,_}reco.{cfl,hdr}
+
+# Estimate B0 = phase(reco(TE2) * conj(reco(TE2))) / (TE2 - TE1)
+# Nayak & Nishimura, MRM, 2000.
+
+bart conj te1 te1c
+bart fmac te2 te1c prod
+bart carg prod ph
+bart scale -- $(echo $TE1 $TE2 | awk '{printf "%f\n", -1/($2-$1)}') ph _b0map # [rad/s] 
+rm {ph,te1,te1c,te2,prod}.{cfl,hdr}
+
+# Resize for input in moba
+bart resize -c 0 $SAMPLES 1 $SAMPLES _b0map __b0map
+bart transpose 0 1 __b0map b0map
+rm {_,}_b0map.{cfl,hdr}

b0_invivo/b0map/load_b0map.sh

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+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+@author: nscho
+"""
+import sys
+import os
+sys.path.insert(0, os.path.join(os.environ['TOOLBOX_PATH'], 'python'))
+import cfl
+
+import numpy as np
+
+
+if __name__ == "__main__":
+
+	#Error if wrong number of parameters
+	if( len(sys.argv) != 3):
+		print( "arccos(input)" )
+		print( "#-----------------------------------------------" )
+		print( "Usage: arccos.py <input> <output>" )
+		exit()
+
+	sysargs = sys.argv
+
+	out = np.arccos(cfl.readcfl(sysargs[1]).squeeze())
+
+	# Load input
+	cfl.writecfl(sysargs[2], out)
+	

b0_invivo/b1map/arccos.py

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+#!/bin/bash
+
+# B1+ Mapping with Siemens Sequence "tfl_b1map" based on
+# Chung, S., Kim, D., Breton, E. and Axel, L. (2010),
+# Rapid B1+ mapping using a preconditioning RF pulse with TurboFLASH readout.
+# Magn. Reson. Med., 64: 439-446.
+# https://doi.org/10.1002/mrm.22423
+
+set -eux
+
+# Estimate relative paths
+FULL_PATH=$(realpath ${0})
+REL_PATH=$(dirname ${FULL_PATH})
+
+# Load b1 raw data
+# bart twixread -A /home/ague/archive/vol/2023-03-14_MRTG-BLMB-0008/raw/meas_MID00044_FID06085_B1Map_for_MRF_BR256.dat raw_asym
+bart copy ${REL_PATH}/../data/ksp_b1map raw_asym
+
+# Compensate for asymetric echo
+## Mirror kspace to fill missing lines
+FREQ_ASYM=$(bart show -d 0 raw_asym)
+PHASE=$(bart show -d 1 raw_asym)
+DIFF=$(($((PHASE*2))-FREQ_ASYM))
+
+bart extract 0 $((FREQ_ASYM-DIFF)) $FREQ_ASYM raw_asym miss
+bart flip $(bart bitmask 0) raw_asym tmp
+bart join -a 0 tmp miss _raw
+bart flip $(bart bitmask 0) _raw raw
+
+rm {raw_asym,miss,tmp,_raw}.{cfl,hdr}
+
+
+# Estimate Coil sensitivities
+bart ecalib -c 0 -m 1 raw sens
+
+# Phase preserving PI reconstruction
+bart pics -g -e -S -d 5 raw sens _reco
+
+SAMPLES=$(bart show -d 0 _reco)
+
+bart resize -c 0 $PHASE _reco reco
+
+rm {raw,sens,_reco}.{cfl,hdr}
+
+bart slice 11 0 reco pd
+bart slice 11 1 reco pre
+
+rm reco.{cfl,hdr}
+
+# Calculate: SSPre / PD
+bart invert pd pdi
+bart fmac pre pdi tmp
+
+# Calculate: arccos(SSPre / PD)
+python3 ${REL_PATH}/arccos.py tmp acos
+
+FA_NOM=80 # [deg] Just from raw data..., IDEA internal... -> vim *.dat and /PrepFlipAngle
+
+# Calculate: kappa = arccos(SSPre / PD) / FA_NOM = b1map
+bart scale -- $(echo $FA_NOM | awk '{printf "%f\n", 1/(3.141592653589793 * $1 / 180)}') acos _b1map
+
+rm {pd,pdi,pre,tmp,acos}.{cfl,hdr}
+
+
+# Resize for input in moba
+bart resize -c 0 $SAMPLES 1 $SAMPLES _b1map __b1map
+bart transpose 0 1 __b1map b1map
+
+rm _{,_}b1map.{cfl,hdr}

b0_invivo/b1map/load_b1map.sh

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+#!/bin/bash
+
+[ -d out ] && rm -rf out
+# [ -d mask ] && rm -rf mask

b0_invivo/clean_up.sh

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+#!/bin/bash
+
+
+# Estimate absolute paths
+
+FULL_PATH=$(realpath ${0})
+ABS_PATH=$(dirname ${FULL_PATH})
+
+
+# Get and rename data for this analysis
+## FIXME: remove rename and load data directly
+
+FILES=(
+	data_invivo_b0map
+	data_invivo_b1map
+	data_invivo_irflash
+	data_invivo_irbssfp
+	data_invivo_irbssfp_shim
+	)
+
+OUT=(
+	ksp_b0map
+	ksp_b1map
+	ksp_flash
+	ksp_bssfp
+	ksp_bssfp_shim
+	)
+
+for (( i=0; i<${#FILES[@]}; i++ ));
+do
+	if [[ ! -f "${ABS_PATH}/${OUT[$i]}.cfl" ]];
+	then
+
+		bart copy ${ABS_PATH}/../../data/${FILES[$i]} ${ABS_PATH}/${OUT[$i]}
+
+		echo "Generated output file: ${ABS_PATH}/${OUT[$i]}.{cfl,hdr}" >&2
+	fi
+done