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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