# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
#_____________________________________________________
setenv SUBJECTS_DIR /cluster/guptagp/Emad/3LT/subjDir
setenv RAW_DATA /cluster/guptagp/Emad/3LT/rawData
#_____________________________________________________

# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#
#set dtroot = /path/to/tracts/of/ducks

# Subject IDs (one per time point per subject)
#_____________________________________________________
set subjlist = ( 2a \
                 2b \
                 3a \
                 3b )
#_____________________________________________________

# Longitudinal base template subject IDs (one for each time point above)
#_____________________________________________________
set baselist = ( 2tem \
                 2tem \
                 3tem \
                 3tem )
#_____________________________________________________

# In case you want to analyze only Huey and Louie
# Default: Run analysis on all time points and subjects
#
#set runlist = (1 2 5 6)

# Input diffusion DICOMs (file names relative to dcmroot)
# 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 dcmroot = $RAW_DATA
set dcmlist = ( 2a/Diffusion/IM-0001-0001.dcm \
                2b/Diffusion/IM-0001-0001.dcm \
                3a/Diffusion/IM-0001-0001.dcm \
                3b/Diffusion/IM-0003-0001.dcm )
#_____________________________________________________

# Diffusion gradient tables (if there is a different one for each scan)
# Must be specified if inputs are not MGH DICOMs
# 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
# Default: Read from DICOM header
#_____________________________________________________
set bveclist = (/cluster/guptagp/Emad/3LT/subjDir/codes/bvecXinv.txt \
                /cluster/guptagp/Emad/3LT/subjDir/codes/bvecXinv.txt \
                /cluster/guptagp/Emad/3LT/subjDir/codes/bvecXinv.txt \
                /cluster/guptagp/Emad/3LT/subjDir/codes/bvecXinv.txt)
#_____________________________________________________

# Diffusion gradient table (if using the same one for all scans)
# Must be specified if inputs are not MGH DICOMs
# The table 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
# Default: Read from DICOM header
#_____________________________________________________
#set bvecfile = /cluster/guptagp/Emad/3LT/subjDir/codes/bvecXinv.txt
#_____________________________________________________

# Diffusion b-value table
# Must be specified if inputs are not MGH DICOMs
# There must be as many b-values as volumes in the diffusion data set
# Default: Read from DICOM header
#_____________________________________________________
set bvalfile = /cluster/guptagp/Emad/3LT/subjDir/codes/bval.txt
#_____________________________________________________

# Perform registration-based B0-inhomogeneity compensation?
# Default: 0 (no)
#
#set dob0 = 1

# Input B0 field map magnitude DICOMs (file names relative to dcmroot)
# Only used if dob0 = 1
# Default: None
#
#set b0mlist = ( huey/year1/fmag/XXX-1.dcm \
                huey/year2/fmag/XXX-1.dcm \
                dewey/year1/fmag/XXX-1.dcm \
                dewey/year2/fmag/XXX-1.dcm \
                louie/year1/fmag/XXX-1.dcm \
                louie/year2/fmag/XXX-1.dcm )

# Input B0 field map phase DICOMs (file names relative to dcmroot)
# Only used if dob0 = 1
# Default: None
#
#set b0plist = ( huey/year1/fphas/XXX-1.dcm \
                huey/year2/fphas/XXX-1.dcm \
                dewey/year1/fphas/XXX-1.dcm \
                dewey/year2/fphas/XXX-1.dcm \
                louie/year1/fphas/XXX-1.dcm \
                louie/year2/fphas/XXX-1.dcm )

# Echo spacing for field mapping sequence (from sequence printout)
# Only used if dob0 = 1
# Default: None
#
#set echospacing = 0.7

# Perform registration-based eddy-current compensation?
# Default: 1 (yes)
#
#set doeddy = 1

# Rotate diffusion gradient vectors to match eddy-current compensation?
# Only used if doeddy = 1
# Default: 1 (yes)
#
#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 = 0.5

# Perform diffusion-to-T1 registration by flirt?
# Default: 0 (no)
#
set doregflt = 1

# Perform diffusion-to-T1 registration by bbregister?
# Default: 1 (yes)
#
set doregbbr = 0

# 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 = /path/to/mni_template.nii.gz

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

# CVS template subject ID
# Only used if doregcvs = 1
# Default: cvs_avg35
#
#set cvstemp = donald

# Parent directory of the CVS template subject
# Only used if doregcvs = 1
# Default: $FREESURFER_HOME/subjects
#
#set cvstempdir = /path/to/cvs/atlases/of/ducks

# 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