# TRACULA configuration text file

# Set subject directory, which contains T1 segmentation outputs
setenv SUBJECTS_DIR $bids_dir/derivatives/t1prep

# Set output directory
set dtroot = $bids_dir/derivatives/tracula

# Specify subject list
set subjlist = (  sub-0003107 )

# Specify input dti data
# If original DICOMs don't exist, these can be in other image format, but then the gradient table and b-value table must be specified (see below)
set dcmlist = ( "$bids_dir"/derivatives/dtiprep/sub-0003107/sub-0003107_eddy_undist.nii.gz )

# Specify diffusion gradient tables
# The tables must have either three columns, where each row is a gradient vector or three rows, where each column is a gradient vector
# There must be as many gradient vectors as volumes in the diffusion data set
set bveclist = ( "$bids_dir"/derivatives/tracula/config/bvecs/sub-0003107_eddy_undist.eddy_rotated_bvecs.txt )

# Specify diffusion b-value tables
# Each b-value table must be a simple text file, with one value for each volume in the corresponding DWI scan
# There must be as many b-values as volumes in the diffusion data set
set bvallist = ( "$bids_dir"/derivatives/tracula/config/bvals/sub-0003107_dwi.bval.txt )

# Specify a method for compensating for B0 inhomogeneity distortions
# set to none -- already preprocessed
set dob0 = 0

# Specify a method for compensating for eddy-current distortions
# set to none -- already preprocessed
set doeddy = 0

# Specify the intra-subject registration method
# set intrareg =
# the default is option 3, bbregister (affine DWI to T1 with boundary based cost)

# Specify the inter-subject registration method
# set interreg =
# the default is option 5, nonlinear FA to FA with symmetric normalization from ANTs

# Specify the whole-brain segmentation
# set segname =
# default is aparc+aseg from recon-all

# Specify the thalamic nuclei segmentation
# set usethalnuc =
# default is yes

# Specify T1 as brain mask
# set usemaskanat =
# default is yes

# Specify which white-matter pathways to reconstruct
# set pathlist =
# default is all 42 pathways

# Specify the number of path control points
# set ncpts =
# default is 7500