#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_ourbrains

# Subject IDs
#
set subjlist = ( p100307 p103414 )
# 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 = $TUTORIAL_DATA/diffusion_ourbrains
set dcmlist = ( p100307/T1w/Diffusion/data.nii
                p103414/T1w/Diffusion/data.nii )

set bveclist = (/diffusion_ourbrains/p100307/T1w/Diffusion/bvecs.txt \
                /diffusion_ourbrains/p103414/T1w/Diffusion/bvecs.txt)

set bvalfile = (/diffusion_ourbrains/p100307/T1w/Diffusion.txt \ 
		/diffusion_ourbrains/p100307/T1w/Diffusion.txt )

set doeddy = 0

set dorotbvecs = 0

set usemaskanat = 1

set thrbet = 0.3

set doregflt = 0
set doregbbr = 1

set doregmni = 0
set doregcvs = 0

#set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz

#set cvstemp = cvs_avg35
#set cvstempdir = $FREESURFER_HOME/subjects

set pathlist = ( lh.cst_AS rh.cst_AS \
                 lh.unc_AS rh.unc_AS \ )

set ncpts = (6 6 5 5)