# T1 images and FreeSurfer segmentations are expected to be found here setenv SUBJECTS_DIR /Users/r0755008/Desktop/mri_data/STRUCT # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = /Users/r0755008/Desktop/mri_data/TRACULA # Subject IDs # Here each subject is listed twice because it has two diffusion scans # set subjlist = (NT001 \ NT001 \ NT002 \ NT002 \ NT003 \ NT003 \ NT004 \ NT004 \ NT005 \ NT005 \ NT006 \ NT006 \ NT007 \ NT007 \ NT009 \ NT009 \ NT010 \ NT010 \ NT011 \ NT011 \ NT012 \ NT012 \ NT013 \ NT013 \ NT014 \ NT014 \ NT015 \ NT015 \ NT016 \ NT016 \ NT017 \ NT017 \ NT018 \ NT018 \ NT020 \ NT020 \ NT021 \ NT021 \ NT024 \ NT024 \ NT025 \ NT025 \ NT026 \ NT026 \ NT027 \ NT027 \ NT028 \ NT028 \ NT029 \ NT029 \ NT030 \ NT030 \ NT032 \ NT032 \ NT033 \ NT033 \ NT034 \ NT034 \ NT035 \ NT035 \ NT036 \ NT036 \ NT037 \ NT037 \ NT038 \ NT038 \ NT039 \ NT039 \ NT040 \ NT040 \ PT002 \ PT002 \ PT003 \ PT003 \ PT004 \ PT004 \ PT005 \ PT005 \ PT007 \ PT007 \ PT008 \ PT008 \ PT010 \ PT010 \ PT011 \ PT011 \ PT013 \ PT013 \ PT014 \ PT014 \ PT015 \ PT015 \ PT016 \ PT017 \ PT018 \ PT018 \ PT019 \ PT019 \ PT020 \ PT020 \ PT021 \ PT021 \ PT022 \ PT022 \ PT023 \ PT023 \ PT024 \ PT024 \ PT025 \ PT025 \ PT026 \ PT026 \ PT027 \ PT027 \ PT028 \ PT028 \ PT029 \ PT029 \ PT030 \ PT030 \ PT030 \ PT031 \ PT031 \ PT032 \ PT032 \ PT033 \ PT033 \ PT034 \ PT034 \ PT035 \ PT035 \ PT036 \ PT036 \ PT037 \ PT037 \ PT038 \ PT038 \ PT039 \ PT039 \ PT040 \ PT040) # 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) #note change to own files set dcmroot = /Users/r0755008/Desktop/mri_data/DIFFUSION set dcmlist = (NT001/front.nii \ NT001/reverse.nii \ NT002/front.nii \ NT002/reverse.nii \ NT003/front.nii \ NT003/reverse.nii \ NT004/front.nii \ NT004/reverse.nii \ NT005/front.nii \ NT005/reverse.nii \ NT006/front.nii \ NT006/reverse.nii \ NT007/front.nii \ NT007/reverse.nii \ NT009/front.nii \ NT009/reverse.nii \ NT010/front.nii \ NT010/reverse.nii \ NT011/front.nii \ NT011/reverse.nii \ NT012/front.nii \ NT012/reverse.nii \ NT013/front.nii \ NT013/reverse.nii \ NT014/front.nii \ NT014/reverse.nii \ NT015/front.nii \ NT015/reverse.nii \ NT016/front.nii \ NT016/reverse.nii \ NT017/front.nii \ NT017/reverse.nii \ NT018/front.nii \ NT018/reverse.nii \ NT020/front.nii \ NT020/reverse.nii \ NT021/front.nii \ NT021/reverse.nii \ NT024/front.nii \ NT024/reverse.nii \ NT025/front.nii \ NT025/reverse.nii \ NT026/front.nii \ NT026/reverse.nii \ NT027/front.nii \ NT027/reverse.nii \ NT028/front.nii \ NT028/reverse.nii \ NT029/front.nii \ NT029/reverse.nii \ NT030/front.nii \ NT030/reverse.nii \ NT032/front.nii \ NT032/reverse.nii \ NT033/front.nii \ NT033/reverse.nii \ NT034/front.nii \ NT034/reverse.nii \ NT035/front.nii \ NT035/reverse.nii \ NT036/front.nii \ NT036/reverse.nii \ NT037/front.nii \ NT037/reverse.nii \ NT038/front.nii \ NT038/reverse.nii \ NT039/front.nii \ NT039/reverse.nii \ NT040/front.nii \ NT040/reverse.nii \ PT002/front.nii \ PT002/reverse.nii \ PT003/front.nii \ PT003/reverse.nii \ PT004/front.nii \ PT004/reverse.nii \ PT005/front.nii \ PT005/reverse.nii \ PT007/front.nii \ PT007/reverse.nii \ PT008/front.nii \ PT008/reverse.nii \ PT010/front.nii \ PT010/reverse.nii \ PT011/front.nii \ PT011/reverse.nii \ PT013/front.nii \ PT013/reverse.nii \ PT014/front.nii \ PT014/reverse.nii \ PT015/front.nii \ PT015/reverse.nii \ PT016/front.nii \ PT016/reverse.nii \ PT017/front.nii \ PT017/reverse.nii \ PT018/front.nii \ PT018/reverse.nii \ PT019/front.nii \ PT019/reverse.nii \ PT020/front.nii \ PT020/reverse.nii \ PT021/front.nii \ PT021/reverse.nii \ PT022/front.nii \ PT022/reverse.nii \ PT023/front.nii \ PT023/reverse.nii \ PT024/front.nii \ PT024/reverse.nii \ PT025/front.nii \ PT025/reverse.nii \ PT026/front.nii \ PT027/reverse.nii \ PT028/front.nii \ PT028/reverse.nii \ PT029/front.nii \ PT029/reverse.nii \ PT030/front.nii \ PT030/reverse.nii \ PT031/front.nii \ PT031/reverse.nii \ PT032/front.nii \ PT032/reverse.nii \ PT033/front.nii \ PT033/reverse.nii \ PT034/front.nii \ PT034/reverse.nii \ PT035/front.nii \ PT035/reverse.nii \ PT036/front.nii \ PT036/reverse.nii \ PT037/front.nii \ PT037/reverse.nii \ PT038/front.nii \ PT038/reverse.nii \ PT039/front.nii \ PT039/reverse.nii \ PT040/front.nii \ PT040/reverse.nii) # 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 = (NT001/front.bvec \ NT001/reverse.bvec \ NT002/front.bvec \ NT002/reverse.bvec \ NT003/front.bvec \ NT003/reverse.bvec \ NT004/front.bvec \ NT004/reverse.bvec \ NT005/front.bvec \ NT005/reverse.bvec \ NT006/front.bvec \ NT006/reverse.bvec \ NT007/front.bvec \ NT007/reverse.bvec \ NT009/front.bvec \ NT009/reverse.bvec \ NT010/front.bvec \ NT010/reverse.bvec \ NT011/front.bvec \ NT011/reverse.bvec \ NT012/front.bvec \ NT012/reverse.bvec \ NT013/front.bvec \ NT013/reverse.bvec \ NT014/front.bvec \ NT014/reverse.bvec \ NT015/front.bvec \ NT015/reverse.bvec \ NT016/front.bvec \ NT016/reverse.bvec \ NT017/front.bvec \ NT017/reverse.bvec \ NT018/front.bvec \ NT018/reverse.bvec \ NT020/front.bvec \ NT020/reverse.bvec \ NT021/front.bvec \ NT021/reverse.bvec \ NT024/front.bvec \ NT024/reverse.bvec \ NT025/front.bvec \ NT025/reverse.bvec \ NT026/front.bvec \ NT026/reverse.bvec \ NT027/front.bvec \ NT027/reverse.bvec \ NT028/front.bvec \ NT028/reverse.bvec \ NT029/front.bvec \ NT029/reverse.bvec \ NT030/front.bvec \ NT030/reverse.bvec \ NT032/front.bvec \ NT032/reverse.bvec \ NT033/front.bvec \ NT033/reverse.bvec \ NT034/front.bvec \ NT034/reverse.bvec \ NT035/front.bvec \ NT035/reverse.bvec \ NT036/front.bvec \ NT036/reverse.bvec \ NT037/front.bvec \ NT037/reverse.bvec \ NT038/front.bvec \ NT038/reverse.bvec \ NT039/front.bvec \ NT039/reverse.bvec \ NT040/front.bvec \ NT040/reverse.bvec \ PT002/front.bvec \ PT002/reverse.bvec \ PT003/front.bvec \ FT003/reverse.bvec \ PT004/front.bvec \ PT004/reverse.bvec \ PT005/front.bvec \ PT005/reverse.bvec \ PT007/front.bvec \ PT007/reverse.bvec \ PT008/front.bvec \ PT008/reverse.bvec \ PT010/front.bvec \ PT010/reverse.bvec \ PT011/front.bvec \ PT011/reverse.bvec \ PT013/front.bvec \ PT013/reverse.bvec \ PT014/front.bvec \ PT014/reverse.bvec \ PT015/front.bvec \ PT015/reverse.bvec \ PT016/front.bvec \ PT016/reverse.bvec \ PT017/front.bvec \ PT018/reverse.bvec \ PT019/front.bvec \ PT019/reverse.bvec \ PT020/front.bvec \ PT020/reverse.bvec \ PT021/front.bvec \ PT021/reverse.bvec \ PT022/front.bvec \ PT022/reverse.bvec \ PT023/front.bvec \ PT023/reverse.bvec \ PT024/front.bvec \ PT024/reverse.bvec \ PT025/front.bvec \ PT025/reverse.bvec \ PT026/front.bvec \ PT026/reverse.bvec \ PT027/front.bvec \ PT027/reverse.bvec \ PT028/front.bvec \ PT028/reverse.bvec \ PT029/front.bvec \ PT029/reverse.bvec \ PT030/front.bvec \ PT030/reverse.bvec \ PT031/front.bvec \ PT031/reverse.bvec \ PT032/front.bvec \ PT032/reverse.bvec \ PT033/front.bvec \ PT033/reverse.bvec \ PT034/front.bvec \ PT034/reverse.bvec \ PT035/front.bvec \ PT035/reverse.bvec \ PT036/front.bvec \ PT036/reverse.bvec \ PT037/front.bvec \ PT037/reverse.bvec \ PT038/front.bvec \ PT038/reverse.bvec \ PT039/front.bvec \ PT039/reverse.bvec \ PT040/front.bvec \ PT040/reverse.bvec) # 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 = (NT001/front.bval \ NT001/reverse.bval \ NT002/front.bval \ NT002/reverse.bval \ NT003/front.bval \ NT003/reverse.bval \ NT004/front.bval \ NT004/reverse.bval \ NT005/front.bval \ NT005/reverse.bval \ NT006/front.bval \ NT006/reverse.bval \ NT007/front.bval \ NT007/reverse.bval \ NT009/front.bval \ NT009/reverse.bval \ NT010/front.bval \ NT010/reverse.bval \ NT011/front.bval \ NT011/reverse.bval \ NT012/front.bval \ NT012/reverse.bval \ NT013/front.bval \ NT013/reverse.bval \ NT014/front.bval \ NT014/reverse.bval \ NT015/front.bval \ NT015/reverse.bval \ NT016/front.bval \ NT016/reverse.bval \ NT017/front.bval \ NT017/reverse.bval \ NT018/front.bval \ NT018/reverse.bval \ NT020/front.bval \ NT020/reverse.bval \ NT021/front.bval \ NT021/reverse.bval \ NT024/front.bval \ NT024/reverse.bval \ NT025/front.bval \ NT025/reverse.bval \ NT026/front.bval \ NT026/reverse.bval \ NT027/front.bval \ NT027/reverse.bval \ NT028/front.bval \ NT028/reverse.bval \ NT029/front.bval \ NT029/reverse.bval \ NT030/front.bval \ NT030/reverse.bval \ NT032/front.bval \ NT032/reverse.bval \ NT033/front.bval \ NT033/reverse.bval \ NT034/front.bval \ NT034/reverse.bval \ NT035/front.bval \ NT035/reverse.bval \ NT036/front.bval \ NT036/reverse.bval \ NT037/front.bval \ NT037/reverse.bval \ NT038/front.bval \ NT038/reverse.bval \ NT039/front.bval \ NT039/reverse.bval \ NT040/front.bval \ NT040/reverse.bval \ PT002/front.bval \ PT002/reverse.bval \ PT003/front.bval \ PT003/reverse.bval \ PT004/front.bval \ PT004/reverse.bval \ PT005/front.bval \ PT005/reverse.bval \ PT007/front.bval \ PT007/reverse.bval \ PT008/front.bval \ PT008/reverse.bval \ PT010/front.bval \ PT010/reverse.bval \ PT011/front.bval \ PT011/reverse.bval \ PT013/front.bval \ PT013/reverse.bval \ PT014/front.bval \ PT014/reverse.bval \ PT015/front.bval \ PT015/reverse.bval \ PT016/front.bval \ PT016/reverse.bval \ PT017/front.bval \ PT017/reverse.bval \ PT018/front.bval \ PT018/reverse.bval \ PT019/front.bval \ PT019/reverse.bval \ PT020/front.bval \ PT020/reverse.bval \ PT021/front.bval \ PT021/reverse.bval \ PT022/front.bval \ PT023/reverse.bval \ PT024/front.bval \ PT024/reverse.bval \ PT025/front.bval \ PT025/reverse.bval \ PT026/front.bval \ PT026/reverse.bval \ PT027/front.bval \ PT027/reverse.bval \ PT028/front.bval \ PT028/reverse.bval \ PT029/front.bval \ PT029/reverse.bval \ PT030/front.bval \ PT030/reverse.bval \ PT031/front.bval \ PT031/reverse.bval \ PT032/front.bval \ PT032/reverse.bval \ PT033/front.bval \ PT033/reverse.bval \ PT034/front.bval \ PT034/reverse.bval \ PT035/front.bval \ PT035/reverse.bval \ PT036/front.bval \ PT036/reverse.bval \ PT037/front.bval \ PT037/reverse.bval \ PT038/front.bval \ PT038/reverse.bval \ PT039/front.bval \ PT039/reverse.bval \ PT040/front.bval \ PT040/reverse.bval) # Perform correction for B0 inhomogeneity distortions? # 0: No correction (default) # 1: Perform correction based on a field map # Requires additional inputs (see below): b0mlist, b0plist, echospacing # 2: Perform correction based on reverse-polarity images # Requires additional inputs (see below): echospacing, pedir, epifactor # set dob0 = 2 # Echo spacing (this is found in the scanner protocol printout) # Only used if dob0 = 1 or 2 # Default: None # set echospacing = 0.227045 # Phase-encode direction (this is found in the scanner protocol printout) # One for each diffusion scan above (must differ between runs in a session) # In this example, each session contains an AP- and a PA-encoded diffusion scan # Only used if dob0 = 2 # Default: None # set pedir = (AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA AP PA) # EPI factor (this is found in the scanner protocol printout) # Only used if dob0 = 2 # Default: None # set epifactor = 57 # 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 = 2 # Rotate diffusion gradient vectors to match eddy-current compensation? # Only used if doeddy = 1 or 2 # Default: 1 (yes) # set dorotbvecs = 1 # Intra-subject (diffusion-to-T1) registration method # 1: Affine with a correlation ratio cost # 2: Affine with a mutual information cost # 3: Affine with a boundary-based cost (default) # set intrareg = 3 # 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 # Inter-subject registration method # 1: Affine T1-to-T1 with a correlation ratio cost # 2: Affine T1-to-T1 with a mutual information cost # 3: Affine T1-to-T1 with a robust cost (default for infants) # 4: Nonlinear T1-to-T1 with CVS # 5: Nonlinear FA-to-FA with SyN (default) # set interreg = 5 # Whole-brain segmentation used to extract the anatomical neighborhood priors # of the pathways of interest # Must exist in each subject's FreeSurfer recon directory, under: # $SUBJECTS_DIR/$subjid/mri/$segname.mgz # Default: aparc+aseg # set segname = aparc+aseg # 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) # set usethalnuc = 1 # Use brain mask extracted from T1 image instead of low-b diffusion image? # Has no effect if there is no T1 data # Default: 1 (yes) # set usemaskanat = 1 # Fractional intensity threshold for BET mask extraction from low-b images # This mask is used only if usemaskanat = 0 # Default: 0.3 # set thrbet = 0.3 # Paths to reconstruct # Default: All paths in $FREESURFER_HOME/trctrain/hcp/pathlist.txt # set pathlist = (lh.uf rh.uf lh.ilf rh.ilf lh.slf1 rh.slf1 lh.slf2 rh.slf2 lh.slf3 rh.slf3) # Number of path control points # It can be a single number for all paths or a different number for each of the # paths specified in pathlist (recommended, with more points for longer paths) # Default: As in $FREESURFER_HOME/trctrain/hcp/pathlist.txt # #set ncpts = ( 7 7 5 ) # Number of "sticks" (anisotropic diffusion compartments) in the bedpostx # ball-and-stick model # Default: 2 # set nstick = 2 # Number of MCMC burn-in iterations # (Path samples drawn initially by MCMC algorithm and discarded) # Default: 200 # set nburnin = 500 # Number of MCMC iterations # (Path samples drawn by MCMC algorithm and used to estimate path distribution) # Default: 7500 # set nsample = 7500 # Frequency with which MCMC path samples are retained for path distribution # Default: 5 (keep every 5th sample) # set nkeep = 5 # Reinitialize path reconstruction? # This is an option of last resort, to be used only if one of the reconstructed # pathway distributions looks like a single curve. This is a sign that the # initial guess for the pathway was problematic, perhaps due to poor alignment # between the individual and the atlas. Setting the reinit parameter to 1 and # rerunning "trac-all -prior" and "trac-all -path", only for the specific # subjects and pathways that had this problem, will attempt to reconstruct them # with a different initial guess. # Default: 0 (do not reinitialize) # set reinit = 0