# 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 = HD4/DTI

# Subject IDs
#
set subjlist = ( DBK08 \
                 DBK08.2nd \
                 DBK08.3rd \
                 DBK08.4th )

# 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 dcmlist = ( /HD4/DTI/data/DBK08/2011-03-09_090003/DTI_PRODUCT_SEQ_69_DIR_16X16X16_1000B_06F06740 \
                /HD4/DTI/data/DBK08_2nd/2012-04-11_102010/DTI_PRODUCT_SEQ_69_DIR_16X16X16_1000B_261B7A68 \
                /HD4/DTI/data/DBK08_3rd/2012-10-24_101448/DTI_PRODUCT_SEQ_69_DIR_16X16X16_1000B_7BD06410 \
                /HD4/DTI/data/DBK08_4th/2013-08-10_115920/DTI_PRODUCT_SEQ_69_DIR_16X16X16_1000B_A04377CC )

# 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 = ( /HD4/DTI/data/DBK08/2011-03-09_090003/bvec.txt \
                 /HD4/DTI/data/DBK08_2nd/2012-04-11_102010/bvec.txt \
                 /HD4/DTI/data/DBK08_3rd/2012-10-24_101448/bvec.txt \
                 /HD4/DTI/data/DBK08_4th/2013-08-10_115920/bvec.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 = ( /HD4/DTI/data/DBK08/2011-03-09_090003/bval.txt \
                 /HD4/DTI/data/DBK08_2nd/2012-04-11_102010/bval.txt \
                 /HD4/DTI/data/DBK08_3rd/2012-10-24_101448/bval.txt \
                 /HD4/DTI/data/DBK08_4th/2013-08-10_115920/bval.txt )