# practice config file for TRACULA
# txt file with tcsh commands

# T1 images and FreeSurfer segmentations are expected to be found here
#
setenv SUBJECTS_DIR /projects/dsnlab/shared/tag/bids_data/derivatives/LongFreeSurfer/freesurf_7.2.0/

# Output directory where trac-all results will be saved
#
set dtroot = /projects/dsnlab/shared/tag/nonbids_data/dMRI/tracula

# Subject IDs (one per time point per subject)
# (ie what the subject was named when ran recon-all)
#
set subjlist = sub-001w01


# Input diffusion DICOMs (file names relative to dcmroot)
# 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 = /projects/dsnlab/shared/tag/nonbids_data/dMRI/topup_eddy
set dcmlist = 001/wave1/001_wave1_eddy_corrected_data_repol.nii.gz


# Diffusion gradient tables (file names can be relative to dcmroot)
# Must be specified only 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 = 001/wave1/bvecs_65_rotated.txt


# Diffusion b-value tables (file names can be relative to dcmroot)
# Must be specified only 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 = 001/wave1/bvals_65.txt

# Perform correction for eddy-current distortions?
# 0: No correction
# 1: Perform registration-based correction with eddy_correct
# 2: Perform model-based correction with eddy (default)
#
set doeddy = 0



# Degrees of freedom for intra-subject registration
# Can be 6 (rigid), 9 (rigid+scaling), or 12 (full affine)
# Default: 6 for infants, 9 otherwise
#
set intradof = 9

# Maximum rotation angle (degrees) for intra-subject registration
# Default: 3 for infants, 90 otherwise
#
set intrarot = 90

# Target brain for inter-subject registration
# Default for affine T1-to-T1: 
#   $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
# Default for nonlinear T1-to-T1: 
#   $FREESURFER_HOME/subjects/cvs_avg35/
# Default for nonlinear FA-to-FA: 
#   $FREESURFER_HOME/trctrain/hcp/MGH35_HCP_FA_template.nii.gz
#
set intertrg = $FREESURFER_HOME/trctrain/hcp/MGH35_HCP_FA_template.nii.gz


# Use the thalamic nuclei segmentation?
# This is highly recommended to use for any pathways that terminate in
# or neighbor the thalamus
# When used, it is merged with the whole-brain segmentation above
# Must exist in each subject's FreeSurfer recon directory, under:
#   $SUBJECTS_DIR/$subjid/mri/ThalamicNuclei.v12.T1.FSvoxelSpace.mgz
# Default: 1 (yes)
#
# still running... will use in later versions of config
set usethalnuc = 0