Hi, Did you try changing the folder name? tutorial/data/dti/a226A/226A/ Maybe that's what it has to start with a letter? Just guessing. .. On Oct 13, 2013 12:02 AM, "Michael Datko" mikedatko@gmail.com wrote:
Hello, I have been trying to set up a working Tracula configuration file and I keep getting an error:
set: Variable name must begin with a letter
I have searched previous message board questions and it seems that others have seen this same error. I have tried implementing some of their solutions, as well as searching my code for a problem, but I cannot find the source. Any advice? I am trying to get this working for a single subject for now. I used the dmrirc.example file as a template. I am calling trac-all from the tcsh command line with the following: trac-all -c dmrirc.example -prep
The contents of my dmrirc file are below, I have deleted most of the options for which I am just using the default, to make things simpler.
Thank you, Mike
# FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmentations are expected to be found here # setenv SUBJECTS_DIR /Users/mdatko/Desktop/tracula_tutorial/data/freesurfer
# Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = /Users/mdatko/Desktop/tracula_tutorial/data/freesurfer
# Subject IDs # set subjlist = (a226A)
# 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 = /Users/mdatko/Desktop/tracula_tutorial/data/dti set dcmlist = (a226A/226A/data.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 = /Users/mdatko/Desktop/tracula_tutorial/data/dti/a226A/226A/bvecs.txt
# 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 = /Users/mdatko/Desktop/tracula_tutorial/data/dti/a226A/226A/bvals.txt
# Perform registration-based eddy-current compensation? # Default: 1 (yes) # set doeddy = 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
# 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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