# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
#
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects


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

# Subject IDs
#
set subjlist = ( IXI_25_Guys_T1 \
                 IXI_28_Guys_T1 \
                 IXI_46_Guys_T1 \
		 IXI_53_Guys_T1 )

# 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 = ( /media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/NIfTI/IXI025-Guys-0852-DTI-00.nii.gz \
		/media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/NIfTI/IXI028-Guys-0852-DTI-00.nii.gz \
		/media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/NIfTI/IXI046-Guys-0852-DTI-00.nii.gz \
		/media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/NIfTI/IXI053-Guys-0852-DTI-00.nii.gz )
# 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 = ( /media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/bvec/gradients.txt /
		 /media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/28_Guys/DTI/bvec/gradients.txt /
                 /media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/46_Guys/DTI/bvec/gradients.txt /
		 /media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/53_Guys/DTI/bvec/gradients.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 = (/media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/25_Guys/DTI/bval/bvalues.txt /
                /media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/28_Guys/DTI/bval/bvalues.txt / 
                /media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/46_Guys/DTI/bval/bvalues.txt /
                /media/andraderenew/backup/image_databases/IXI_dataset/guest-20191220_131017/53_Guys/DTI/bval/bvalues.txt )




set runlist = (1 2 3 4)


set doeddy = 1

set dorotbvecs = 1

set usemaskanat = 1

set thrbet = 0.3

set doregflt = 0
set doregbbr = 1

set doregmni = 1
set doregcvs = 0

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 )

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