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
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