# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
set SUBJECTS_DIR=/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D

# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#
set dtroot=/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D

##Subject IDs
#

set runlist=( 1 )
set subjlist=( timePoint1  )
# Input diffusion DICOMs (file names relative to dcmroot)
# If original DICOMs don't exist, these can be in other image format
# but then bvecfile and bvalfile must be specified
#
set dcmroot=/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/DTI
set dcmlist=( timePoint1/1.3.12.2.1107.5.2.7.20118.30000011122311175865600000353.dcm )
set dob0=0
set b0mlist=( B0mag/timePoint1/1.3.12.2.1107.5.2.7.20118.30000011122311175865600000185.dcm )
set b0plist=( B0phase/timePoint1/1.3.12.2.1107.5.2.7.20118.30000011122311175865600000185.dcm )
set echospacing=0.7
set bvecfile=/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/bvecs.txt
set bvalfile=/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/bvals.txt
set doregbbr=1
set thrbet=0.3
set nstick=2
set nburnin=200
set nsample=7500
set nkeep=5
set pathlist=( lh.cst_AS rh.cst_AS fmajor_PP lh.atr_PP rh.atr_PP fminor_PP )
set ncpts=( 6 6 9 5 5 9 )