Depends on FSL, Freesurfer, AFNI - please acquire relevant licenses and cite appropriately Singularity image neurodoc.sif can be generated with neurodocker or singularity calls can be replaced with direct fsl commands Creates reports for comparing SWI sequence outputs from the Cornell & Berkeley QSM processing code courtesy of Berkin Bilgic (https://nmr.mgh.harvard.edu/~berkin/index.html), please request this code.

Follows structure used in https://github.com/mrfil/7T-mri-pipeline-hpc, see https://github.com/mrfil/7T-mri-pipeline-hpc/blob/main/setup/file_structure_gen.sh for setup.

Before running this report generator, run steps 1 and 2 of https://github.com/mrfil/7T-mri-pipeline-hpc, followed by https://github.com/mrfil/7T-mri-pipeline-hpc/blob/main/slurm_orig_qsm_stats_rage.sh and https://github.com/mrfil/7T-mri-pipeline-hpc/blob/main/slurm_qsm_stats_rage.sh

usage: ./qsm_method_comparison_report.sh -p -s <session ID without "ses-"> -z <subject ID without "sub-"> -b -t