# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
#
setenv SUBJECTS_DIR $TUTORIAL_DATA/diffusion_recons

# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#
set dtroot = $TUTORIAL_DATA/diffusion_tutorial

# Subject IDs
#
set subjlist = ( elmo.2005 \
                 elmo.2008 \
                 elmo.2012 )

# Input diffusion DICOMs
# 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 = $TUTORIAL_DATA/diffusion_tutorial

set dcmlist = ( elmo.2005/orig/656000-11-1.dcm \
                elmo.2008/orig/97000-000017-000001.dcm \
                elmo.2012/orig/MR.1.3.12.2.1107.5.2.32.35006.2012121819455034689828982 )

# Diffusion gradient tables (if there is a different one for each scan)
# Must be specified if they cannot be read from the DICOM headers
# 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 = ( $TUTORIAL_DATA/diffusion_tutorial/elmo.2005/orig/gradients.txt \
                 $TUTORIAL_DATA/diffusion_tutorial/elmo.2008/orig/gradients.txt \
                 $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/orig/gradients.txt )

#set bvecfile = /path/to/bvecs.txt

# Diffusion b-value tables (if there is a different one for each scan)
# Must be specified if they cannot be read from the DICOM headers
# There must be as many b-values as volumes in the diffusion data set
# Default: Read from DICOM header
#
set bvallist = ( $TUTORIAL_DATA/diffusion_tutorial/elmo.2005/orig/bvalues.txt \
                 $TUTORIAL_DATA/diffusion_tutorial/elmo.2008/orig/bvalues.txt \
                 $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/orig/bvalues.txt )

#set bvalfile = /path/to/bvals.txt

set runlist = (1 2 3)

set doeddy = 1

set dorotbvecs = 1

set usemaskanat = 1

set thrbet = 0.3

set doregflt = 0
set doregbbr = 1

set doregmni = 1
set doregcvs = 0

#set mnitemp = /path/to/mni/template
#set cvstemp = /cvs/template/name
#set cvstempdir = /path/to/parent/dir/of/cvstemp

set pathlist = ( lh.cst_AS rh.cst_AS \
                 lh.ilf_AS rh.ilf_AS \
                 lh.unc_AS rh.unc_AS \
                 fmajor_PP fminor_PP \
                 lh.atr_PP rh.atr_PP \
                 lh.cab_PP rh.cab_PP \
                 lh.ccg_PP rh.ccg_PP \
                 lh.slfp_PP rh.slfp_PP \
                 lh.slft_PP rh.slft_PP )

set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)