Miscellaneous scripts

Repository for scripts that are too small for their own repo, but useful enough for sharing.

bto_dualecho_fieldmap.sh

Example:

bto_dualecho_fieldmap.sh --mag1=sub-01_ses-01_acq-GRE_run-1_echo-1_part-mag_T2starw.nii.gz --mag2=sub-01_ses-01_acq-GRE_run-1_echo-2_part-mag_T2starw.nii.gz --phs1=sub-01_ses-01_acq-GRE_run-1_echo-1_part-phase_T2starw.nii.gz --phs2=sub-01_ses-01_acq-GRE_run-1_echo-2_part-phase_T2starw.nii.gz --out=sub-01_ses-01_acq-GRE_run-1_Fieldmap_in_Radians.nii.gz

bto_dualecho_fieldmap_fsl.sh

Same script as bto_dualecho_fieldmap.sh except using bet instead of mri_synthstrip to get the brain mask so that all steps are adapted from FSL tools. Example:

bto_dualecho_fieldmap_fsl.sh --mag1=sub-01_ses-01_acq-GRE_run-1_echo-1_part-mag_T2starw.nii.gz --mag2=sub-01_ses-01_acq-GRE_run-1_echo-2_part-mag_T2starw.nii.gz --phs1=sub-01_ses-01_acq-GRE_run-1_echo-1_part-phase_T2starw.nii.gz --phs2=sub-01_ses-01_acq-GRE_run-1_echo-2_part-phase_T2starw.nii.gz --out=sub-01_ses-01_acq-GRE_run-1_Fieldmap_in_Radians.nii.gz