struct_pipe_params.cfg

[DEFAULT]
mabs_mask_nproc: 8
fusion:
debug: False
reg_method: rigid


[StructMask]
mask_method: HD-BET
csvFile:
ref_img:
ref_mask:
hdbet_mode:

[N4BiasCorrect]


[Freesurfer]
t1_mask_method: registration
t1_csvFile: 
t1_ref_img: *_desc-Xc_T2w.nii.gz
t1_ref_mask: *_desc-T2wXcMabsQc_mask.nii.gz

t2_mask_method: MABS
t2_csvFile: /data/pnl/U01_HCP_Psychosis/data_processing/TrainingMaskData/trainingDataT2Masks-hdr.csv
t2_ref_img:
t2_ref_mask:

freesurfer_nproc: 4
expert_file:
no_hires: True
no_skullstrip: True
no_rand: False
subfields: True
fs_dirname: fs7.1.0