I have been trying to run tracula with a config file but keep getting the same error message when I use the trac-all command for pre-processing
"set: Variable name must begin with a letter"
It has become very, very annoying. PLEASE SOMEONE HELP!!!
Andrew
------ # FreeSurfer SUBJECTS_DIR # /home/baileype/Desktop/JG005/freesurfer/mri # setenv SUBJECTS_DIR /home/baileype/Desktop/JG005
# Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = /home/baileype/Desktop/JG005
# Subject IDs # set subjlist = (freesurfer)
# In case you want to analyze only Huey and Louie # Default: Run analysis on all subjects # set runlist = (1)
# 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 = /home/baileype/Desktop/JG005 set dcmlist = (DKI.nii.gz)
# Diffusion gradient table # Must be specified if inputs are not MGH DICOMs # Three-column format, one row for each volume in the diffusion data set # Default: Read from DICOM header # set bvecfile = /home/baileype/Desktop/JG005/bvecs
# Diffusion b-value table # Must be specified if inputs are not MGH DICOMs # Single-column format, one value for each volume in the diffusion data set # Default: Read from DICOM header # set bvalfile = /home/baileype/Desktop/JG005/bvals
# Perform registration-based B0-inhomogeneity compensation? # Default: 0 (no) # # set dob0 = 1
# 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
# 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 = 0.2
# 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 = /path/to/mni_template.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