# Rotate diffusion gradient vectors to match eddy-current compensation?
# Only used if doeddy = 1 or 2
# Default: 1 (yes)
#
set dorotbvecs = 1
# Intra-subject (diffusion-to-T1) registration method
# 1: Affine with a correlation ratio cost
# 2: Affine with a mutual information cost
# 3: Affine with a boundary-based cost (default)
#
set intrareg = 3
# Degrees of freedom for intra-subject registration
# Can be 6 (rigid), 9 (rigid+scaling), or 12 (full affine)
# Default: 6 for infants, 9 otherwise
#
set intradof = 9
# Maximum rotation angle (degrees) for intra-subject registration
# Default: 3 for infants, 90 otherwise
#
set intrarot = 90
# Inter-subject registration method
# 1: Affine T1-to-T1 with a correlation ratio cost
# 2: Affine T1-to-T1 with a mutual information cost
# 3: Affine T1-to-T1 with a robust cost (default for infants)
# 4: Nonlinear T1-to-T1 with CVS
# 5: Nonlinear FA-to-FA with SyN (default)
#
set interreg = 5
# Target brain for inter-subject registration
# Default for affine T1-to-T1:
# $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
# Default for nonlinear T1-to-T1:
# $FREESURFER_HOME/subjects/cvs_avg35/
# Default for nonlinear FA-to-FA:
# $FREESURFER_HOME/trctrain/hcp/MGH35_HCP_FA_template.nii.gz
#
# I think this fixed my issue with syntax
#
set intertrg = /proj/mihaliklab/usasoc/FREESURFER_HOME_LOC/trctrain/hcp/MGH35_HCP_FA_template.nii.gz
# Whole-brain segmentation used to extract the anatomical neighborhood priors
# of the pathways of interest
# Must exist in each subject's FreeSurfer recon directory, under:
# $SUBJECTS_DIR/$subjid/mri/$segname.mgz
# Default: aparc+aseg
#
set segname = aparc+aseg
# Use the thalamic nuclei segmentation?
# This is highly recommended to use for any pathways that terminate in
# or neighbor the thalamus
# When used, it is merged with the whole-brain segmentation above
# Must exist in each subject's FreeSurfer recon directory, under:
# $SUBJECTS_DIR/$subjid/mri/ThalamicNuclei.v12.T1.FSvoxelSpace.mgz
# Default: 1 (yes)
#
set usethalnuc = 0
# Use brain mask extracted from T1 image instead of low-b diffusion image?
# Has no effect if there is no T1 data
# Default: 1 (yes)
#
set usemaskanat = 1
# Fractional intensity threshold for BET mask extraction from low-b images
# This mask is used only if usemaskanat = 0
# Default: 0.3
#
#set thrbet = 0.5
# Paths to reconstruct
# Default: All paths in $FREESURFER_HOME/trctrain/hcp/pathlist.txt
#
set pathlist = /proj/mihaliklab/usasoc/FREESURFER_HOME_LOC/trctrain/hcp/pathlist.txt
# Number of path control points
# It can be a single number for all paths or a different number for each of the
# paths specified in pathlist (recommended, with more points for longer paths)
# Default: As in $FREESURFER_HOME/trctrain/hcp/pathlist.txt
#
set ncpts = /proj/mihaliklab/usasoc/FREESURFER_HOME_LOC/trctrain/hcp/pathlist.txt
# List of training subjects
# This text file lists the locations of training subject directories
# Default: $FREESURFER_HOME/trctrain/trainlist.txt
#
set trainfile = /proj/mihaliklab/usasoc/FREESURFER_HOME_LOC/trctrain/hcp/trainlist.txt
# Number of "sticks" (anisotropic diffusion compartments) in the bedpostx
# ball-and-stick model
# Default: 2
#
set nstick = 2
# Number of MCMC burn-in iterations
# (Path samples drawn initially by MCMC algorithm and discarded)
# Default: 200
#
set nburnin = 200
# Number of MCMC iterations
# (Path samples drawn by MCMC algorithm and used to estimate path distribution)
# Default: 7500
#
set nsample = 7500
# Frequency with which MCMC path samples are retained for path distribution
# Default: 5 (keep every 5th sample)
#
set nkeep = 5
# Reinitialize path reconstruction?
# This is an option of last resort, to be used only if one of the reconstructed
# pathway distributions looks like a single curve. This is a sign that the
# initial guess for the pathway was problematic, perhaps due to poor alignment
# between the individual and the atlas. Setting the reinit parameter to 1 and
# rerunning "trac-all -prior" and "trac-all -path", only for the specific
# subjects and pathways that had this problem, will attempt to reconstruct them
# with a different initial guess.
# Default: 0 (do not reinitialize)
#
set reinit = 0