QSM reconstruction using Total Generalized Variation (TGV-QSM) Kristian Bredies and Christian Langkammer Version from June 2016 www.neuroimaging.at

=== NEW ===

• It is a python package now which simplifies installation
• Orientation fixed: image data does NOT have to be transversal any longer (thx Daniel!)

=== Installation === python setup.py install (in case of problems such as Ubuntu 18.04+ try installing an older version of cython with pip install Cython==0.19.2 - Thanks Andrej!)

=== Command line options ===

usage: tgv_qsm [-h] -p PHASE -m MASK [-o OUTPUT_SUFFIX] [--alpha ALPHA ALPHA | --factors FACTORS [FACTORS ...]] [-e EROSIONS] [-i ITERATIONS [ITERATIONS ...]] [-f FIELDSTRENGTH] [-t ECHOTIME] [-s] [--ignore-orientation] [--save-laplacian] [--output-physical] [--no-resampling] [--vis] [-v]

remarks for options: -t TE in seconds -f fieldstrength in Tesla -s autoscaling for SIEMENS phase data

test data: tgv_qsm -p epi3d_test_phase.nii.gz -m epi3d_test_mask.nii.gz -f 2.89 -t 0.027 -o epi3d_test_QSM

=== bet brain masking ===

for high res data (~0.5 mm iso) this does quite a good job: bet magni.nii.gz mask -n -m -R -f 0.1 -g 0.0 (in case something is lost, vary parameter g minimally)