# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
# set SUBJECTS_DIR=/sc/arion/projects/adineto/ADNI_tracto_1/emrin_choose/TRACULA/DTI_NL_MCI/subjects/003_S_4288

# output directory (same as SUBJECTS_DIR)
set dtroot = /sc/arion/projects/adineto/ADNI_tracto_1/emrin_choose/TRACULA/DTI_NL_MCI/subjects/003_S_4288

# Subject IDs (one per time point per subject)
set subjlist = (003_S_4288_ses-1 003_S_4288_ses-2)

# Longitudinal base template subject IDs (one for each time point above)
set baselist = (003_S_4288_base 003_S_4288_base)

# Default: Run analysis on all time points and subjects
set runlist = (1 2)

# Input diffusion DICOMs (file names relative to dcmroot)
set dcmroot = /sc/arion/projects/adineto/ADNI_tracto_1/emrin_choose/TRACULA/DTI_NL_MCI/subjects
set dcmlist = (003_S_4288/DTI/DTI_ses-1/003_S_4288.nii.gz  003_S_4288/DTI/DTI_ses-2/003_S_4288.nii.gz)


# Diffusion gradient tables (if there is a different one for each scan)
set bveclist = (/sc/arion/projects/adineto/ADNI_tracto_1/emrin_choose/TRACULA/DTI_NL_MCI/subjects/003_S_4288/DTI/DTI_ses-1/003_S_4288.bvec /sc/arion/projects/adineto/ADNI_tracto_1/emrin_choose/TRACULA/DTI_NL_MCI/subjects/003_S_4288/DTI/DTI_ses-2/003_S_4288.bvec)

# Diffusion b-value tables (if there is a different one for each scan)
set bvallist = (/sc/arion/projects/adineto/ADNI_tracto_1/emrin_choose/TRACULA/DTI_NL_MCI/subjects/003_S_4288/DTI/DTI_ses-1/003_S_4288.bval /sc/arion/projects/adineto/ADNI_tracto_1/emrin_choose/TRACULA/DTI_NL_MCI/subjects/003_S_4288/DTI/DTI_ses-2/003_S_4288.bval)


# Perform registration-based eddy-current compensation?
set doeddy = 1

# Rotate diffusion gradient vectors to match eddy-current compensation?
set dorotbvecs = 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 = 0.3

# Perform diffusion-to-T1 registration by flirt?
# Default: 0 (no)
set doregflt = 0

# 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 = /hpc/packages/minerva-common/fsl/6.0.0/fsl/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)

# 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