# FreeSurfer SUBJECTS_DIR
# Outputs of recon-all are expected to be here
#
setenv SUBJECTS_DIR /home/gabriellam/Desktop/soggetto_prova_007_S_6341/prova_tracula/fs/

# TRACULA output directory
#
set dtroot = (/home/gabriellam/Desktop/soggetto_prova_007_S_6341/prova_tracula/trc)

# Subject IDs
#
set subjlist = (007_S_6341)

# Input DWI volumes (file names relative to dcmroot)
#
set dcmroot = (/home/gabriellam/Desktop/soggetto_prova_007_S_6341/prova_tracula/bids)
set dcmlist = (007_S_6341/dwi/eddy.nii.gz)

# Input gradient tables (file names relative to dcmroot)
#
set bveclist = (007_S_6341/dwi/sub-007_S_6341_dwi.bvec)

# Input b-value tables (file names relative to dcmroot)
#
set bvallist = (007_S_6341/dwi/sub-007_S_6341_dwi.bval)

# Perform correction for B0 inhomogeneity distortions? (0 = no correction)
set dob0 = 0

# Perform eddy correction (0 no correction)
set doeddy = 0

# Rotate diffusion gradient vectors to match eddy-current compensation
set dorotbvecs = 0

# Intra-subject reg method (lascio quello che fa di default: affine with boundary-based cost)

# Inter-subject registration method
set interreg=1

# Utilizzare segmentazione talamica (0 = NO)
set usethalnuc = 1
