#!/bin/tcsh
set workingDIR = "/data/blt/TRACULA"
set SUBJECTS_DIR = $workingDIR/diffusion_recons
setenv SUBJECTS_DIR $workingDIR/diffusion_recons

setenv FREESURFER_HOME /usr/local/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.csh

set dtroot =  $workingDIR/tractography_output

set subjlist = ( BL01_1 \
BL01_2 )

set baselist= ( BL01_1 \
BL01_2 )

set dcmlist = ( $dcmroot/BL01_1.long.BL01_1/dmri/dwi.nii.gz \
$dcmroot/BL01_2.long.BL01_2/dmri/dwi.nii.gz )

set bveclist = ( /data/blt/TRACULA/tractography_output/BL01_1.long.BL01_1/dmri/bvecs \
/data/blt/TRACULA/tractography_output/BL01_2.long.BL01_2/dmri/bvecs )

set bvalfile = /data/blt/TRACULA/tractography_output/BL01_1.long.BL01_1/dmri/bvals

# Perform diffusion-to-T1 registration by bbregister?
# Default: 1 (yes)
#
set doregbbr = 1

# Perform registration of T1 to MNI template?
# Default: 1 (yes)
#
set doregmni = 1

# MNI template
# Only used if doregmni = 1
# Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
#
set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz

# Perform registration of T1 to CVS template?
# Default: 0 (no)
#
set doregcvs = 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

# Paths to reconstruct
# Default: All paths in the atlas
#
set pathlist = ( lh.cst_AS rh.cst_AS \
                 lh.unc_AS rh.unc_AS \
                 lh.ilf_AS rh.ilf_AS \
                 fmajor_PP fminor_PP \
                 lh.atr_PP rh.atr_PP \
                 lh.ccg_PP rh.ccg_PP \
                 lh.cab_PP rh.cab_PP \
                 lh.slfp_PP rh.slfp_PP \
                 lh.slft_PP rh.slft_PP )

# 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
# Default: 7 for the forceps major, 6 for the corticospinal tract,
#          4 for the angular bundle, and 5 for all other paths
#
set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)

# List of training subjects
# This text file lists the locations of training subject directories
# Default: $FREESURFER_HOME/trctrain/trainlist.txt
#
set trainfile = $FREESURFER_HOME/trctrain/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