# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
setenv SUBJECTS_DIR /data_int/heidi/forHeidi/Preprocessed

# Output directory where trac-all results will be saved
set dtroot = /data_int/heidi/forHeidi/Preprocessed

# Subject IDs
set subjlist = (FS1 FS2 FS3)

# 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 = /data_int/heidi/forHeidi/DWI/dwi
set dcmlist = (dwi_1.nii dwi_2.nii dwi_3.nii)

# Specify diffusion-encoding table 
set bvecfile = /data_int/heidi/forHeidi/DWI/bvecs.txt

# Specify b-value table 
set bvalfile = /data_int/heidi/forHeidi/DWI/bvals.txt

# Eddy-current
set doeddy = 1

# If gradients will be rotated to match eddy-current compensation
set dorotbvecs = 1

# If anatomical brain mask will be used 
set usemaskanat = 1

# Threshold for DWI-based brain mask extraction 
set thrbet = 0.3

# Intra-subject registration method 
set doregflt = 0
set doregbbr = 1

# Inter-subject registration method 
set doregmni = 1
set doregcsv = 0
set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
set doregcvs = 0

# Specify which white-matter pathways to reconstruct 
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 )

# Specify the number of path control points 
set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)