# FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmentations are expected to be found here # setenv SUBJECTS_DIR /home/costanza/extra/PET/PET # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = /home/costanza/extra/PET/PET # Subject IDs # set subjlist = ( DOD_C01_recon \ DOD_MS01_recon \ DOD_MS03_recon \ DOD_MS06_recon \ DOD_MS07_recon \ DOD_MS08_recon \ DOD_MS09_recon \ DOD_MS10_recon \ DOD_MS12_recon \ DOD_MS14_recon \ DOD_MS16_recon \ DOD_MS18_recon \ Marco_CTRL002_recon \ Marco_CTRL003_recon \ Marco_CTRL009_recon \ Marco_CTRL018_recon \ Marco_CTRL021_recon \ Marco_CTRL022_scan2_recon \ Marco_CTRL033_scan1_recon \ Marco_CTRL035_recon \ MSPET08_recon \ MSPET09_recon \ MSPET10_recon \ MSPET12_recon \ MSPET13_recon_skullfixed \ MSPET14_recon \ MSPET15_recon \ MSPET16_recon \ MSPET17_recon \ MSPET19_recon \ MSPET20_recon \ MSPET_C01_recon \ MSPET_C02_recon \ MSPET_C04_recon \ MSPET_C06_recon \ MSPET_C09_recon \ MSPET_C11_recon \ MSPET_C13_recon ) # In case you want to analyze only Huey and Louie # Default: Run analysis on all subjects # #set runlist = (1 3) # 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 (see below) # #set dcmroot = /path/to/dicoms/of/ducks set dcmlist = ( $SUBJECTS_DIR/DOD_C01_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/DOD_MS01_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/DODMS03_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/DODMS06_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/DODMS07_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/DODMS08_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/DODMS09_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/DODMS10_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/DODMS12_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/DODMS14_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/DODMS16_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/DODMS18_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/Marco_CTRL002_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/Marco_CTRL003_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/Marco_CTRL009_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/Marco_CTRL018_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/Marco_CTRL021_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/Marco_CTRL022_scan2_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/Marco_CTRL033_scan1_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/Marco_CTRL035_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/MSPET08_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/MSPET09_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/MSPET10_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/MSPET12_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/MSPET13_recon_skullfixed/dmri/dwi.nii.gz \ $SUBJECTS_DIR/MSPET14_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/MSPET15_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/MSPET16_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/MSPET17_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/MSPET19_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/MSPET20_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/MSPET_C01_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/MSPET_C02_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/MSPET_C04_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/MSPET_C06_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/MSPET_C09_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/MSPET_C11_recon/dmri/dwi.nii.gz \ $SUBJECTS_DIR/MSPET_C13_recon/dmri/dwi.nii.gz ) # Diffusion gradient tables (if there is a different one for each scan) # Must be specified if inputs are not MGH DICOMs # 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 = ( $SUBJECTS_DIR/DOD_C01_recon/dmri/bvecs \ $SUBJECTS_DIR/DOD_MS01_recon/dmri/bvecs \ $SUBJECTS_DIR/DODMS03_recon/dmri/bvecs \ $SUBJECTS_DIR/DODMS06_recon/dmri/bvecs \ $SUBJECTS_DIR/DODMS07_recon/dmri/bvecs \ $SUBJECTS_DIR/DODMS08_recon/dmri/bvecs \ $SUBJECTS_DIR/DODMS09_recon/dmri/bvecs \ $SUBJECTS_DIR/DODMS10_recon/dmri/bvecs \ $SUBJECTS_DIR/DODMS12_recon/dmri/bvecs \ $SUBJECTS_DIR/DODMS14_recon/dmri/bvecs \ $SUBJECTS_DIR/DODMS16_recon/dmri/bvecs \ $SUBJECTS_DIR/DODMS18_recon/dmri/bvecs \ $SUBJECTS_DIR/Marco_CTRL002_recon/dmri/bvecs \ $SUBJECTS_DIR/Marco_CTRL003_recon/dmri/bvecs \ $SUBJECTS_DIR/Marco_CTRL009_recon/dmri/bvecs \ $SUBJECTS_DIR/Marco_CTRL018_recon/dmri/bvecs \ $SUBJECTS_DIR/Marco_CTRL021_recon/dmri/bvecs \ $SUBJECTS_DIR/Marco_CTRL022_scan2_recon/dmri/bvecs \ $SUBJECTS_DIR/Marco_CTRL033_scan1_recon/dmri/bvecs \ $SUBJECTS_DIR/Marco_CTRL035_recon/dmri/bvecs \ $SUBJECTS_DIR/MSPET08_recon/dmri/bvecs \ $SUBJECTS_DIR/MSPET09_recon/dmri/bvecs \ $SUBJECTS_DIR/MSPET10_recon/dmri/bvecs \ $SUBJECTS_DIR/MSPET12_recon/dmri/bvecs \ $SUBJECTS_DIR/MSPET13_recon_skullfixed/dmri/bvecs \ $SUBJECTS_DIR/MSPET14_recon/dmri/bvecs \ $SUBJECTS_DIR/MSPET15_recon/dmri/bvecs \ $SUBJECTS_DIR/MSPET16_recon/dmri/bvecs \ $SUBJECTS_DIR/MSPET17_recon/dmri/bvecs \ $SUBJECTS_DIR/MSPET19_recon/dmri/bvecs \ $SUBJECTS_DIR/MSPET20_recon/dmri/bvecs \ $SUBJECTS_DIR/MSPET_C01_recon/dmri/bvecs \ $SUBJECTS_DIR/MSPET_C02_recon/dmri/bvecs \ $SUBJECTS_DIR/MSPET_C04_recon/dmri/bvecs \ $SUBJECTS_DIR/MSPET_C06_recon/dmri/bvecs \ $SUBJECTS_DIR/MSPET_C09_recon/dmri/bvecs \ $SUBJECTS_DIR/MSPET_C11_recon/dmri/bvecs \ $SUBJECTS_DIR/MSPET_C13_recon/dmri/bvecs ) # Diffusion gradient table (if using the same one for all scans) # Must be specified if inputs are not MGH DICOMs # The table 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 bvecfile = /path/to/bvecs.txt # Diffusion b-value table # Must be specified if inputs are not MGH DICOMs # There must be as many b-values as volumes in the diffusion data set # Default: Read from DICOM header # #set bvalfile = /path/to/bvals.txt # Perform registration-based B0-inhomogeneity compensation? # Default: 0 (no) # set dob0 = 0 # Input B0 field map magnitude DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # #set b0mlist = (huey/fmag/XXX-1.dcm dewey/fmag/XXX-1.dcm louie/fmag/XXX-1.dcm) # Input B0 field map phase DICOMs (file names relative to dcmroot) # Only used if dob0 = 1 # Default: None # #set b0plist = (huey/fphas/XXX-1.dcm dewey/fphas/XXX-1.dcm louie/fphas/XXX-1.dcm) # Echo spacing for field mapping sequence (from sequence printout) # Only used if dob0 = 1 # Default: None # #set echospacing = 0.7 # Perform registration-based eddy-current compensation? # Default: 1 (yes) # set doeddy = 1 # Rotate diffusion gradient vectors to match eddy-current compensation? # Only used if doeddy = 1 # Default: 1 (yes) # set dorotbvecs = 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 = 0.5 # Perform diffusion-to-T1 registration by flirt? # Default: 0 (no) # set doregflt = 0 # Perform diffusion-to-T1 registration by bbregister? # Default: 1 (yes) # set doregbbr = 1 # Perform registration of T1 to MNI template? # Default: 1 (yes) # set doregmni = 1 # MNI template # Only used if doregmni = 1 # Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz # set mnitemp = /usr/share/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz # Perform registration of T1 to CVS template? # Default: 0 (no) # set doregcvs = 0 # CVS template subject ID # Only used if doregcvs = 1 # Default: cvs_avg35 # #set cvstemp = donald # Parent directory of the CVS template subject # Only used if doregcvs = 1 # Default: $FREESURFER_HOME/subjects # #set cvstempdir = /path/to/cvs/atlases/of/ducks # 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 # Paths to reconstruct # Default: All paths in the atlas # set pathlist = ( lh.cst_AS rh.cst_AS \ lh.unc_AS rh.unc_AS \ lh.ilf_AS rh.ilf_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.ccg_PP rh.ccg_PP \ lh.cab_PP rh.cab_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP ) # 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 # Default: 7 for the forceps major, 6 for the corticospinal tract, # 4 for the angular bundle, and 5 for all other paths # set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5) # List of training subjects # This text file lists the locations of training subject directories # Default: $FREESURFER_HOME/trctrain/trainlist.txt # #set trainfile = $FREESURFER_HOME/trctrain/trainlist.txt # 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 = 200 # 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