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

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

# Subject IDs
#
set subjlist = (40 39 36)
           
# 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 = Users/jasminalves/Desktop/data/DTI
set dcmlist = (40/DTI.nii.gz DTI.bvec DTI.bval 39/DTI.nii.gz DTI.bvec DTI.bval 36/DTI.nii.gz DTI.bvec DTI.bval)

set bveclist = (Users/jasminalves/Desktop/data/DTI/40/DTI.bvec Users/jasminalves/Desktop/data/DTI/39/DTI.bvec Users/jasminalves/Desktop/data/DTI/36/DTI.bvec)

set bvecfile = (Users/jasminalves/Desktop/data/DTI/40/DTI.bvec Users/jasminalves/Desktop/data/DTI/39/DTI.bvec Users/jasminalves/Desktop/data/DTI/36/DTI.bvec)

set bvalfile = (Users/jasminalves/Desktop/data/DTI/40/DTI.bval Users/jasminalves/Desktop/data/DTI/39/DTI.bval Users/jasminalves/Desktop/data/DTI/36/DTI.bval)

set dob0 = 0

set doeddy = 1

set dorotbvecs = 1

set thrbet = 0.5

set doregflt = 0

set doregbbr = 1

set doregmni = 1

set mnitemp = /Applications/Utilities/fsl/data/standard/MNI152_T1_2mm_brain.nii.gz

set doregcvs = 0

set usemaskanat = 1

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 )

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

set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt

set nstick = 2

set nburnin = 200

set nsample = 7500

set nkeep = 5

set reinit = 0