That probably means you're not running a C shell. That's fine, can you instead try running trac-all and see if it prints out the value of dcmlist now that you've added that line?

I'll repeat my other question: What program are you using to view the text file?

On Mon, 1 Jul 2013, Gundran, Andrew wrote:

Whoops. It doesn't read like that every # is a new line along with each "set"

I did that and the error was

Line13: syntax error near unexpected token `(' Line 13: `set subjlist = (freesurfer)

-----Original Message----- From: Anastasia Yendiki [mailto:ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 01, 2013 3:09 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula/ config file error

What program are you viewing it in? If you add a line at the end of config.txt that says "echo $dcmlist" (without the quotation marks) and then run "source config.txt" on the command line, does it print out "DKI.nii.gz"?

On Mon, 1 Jul 2013, Gundran, Andrew wrote:

...

It reads like

# 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)

-----Original Message----- From: Anastasia Yendiki [mailto:ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 01, 2013 2:48 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula/ config file error

Can you see that this is all one line?

# 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)

On Mon, 1 Jul 2013, Gundran, Andrew wrote:

...

Yes, the text was saved on a unix system

-----Original Message----- From: Anastasia Yendiki [mailto:ayendiki@nmr.mgh.harvard.edu] Sent: Monday, July 01, 2013 2:34 PM To: Gundran, Andrew Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula/ config file error

Hi Andrew - I'm sorry that you're annoyed. I can feel your pain. Take a deep breath and let it all go.

More to the point, when I view the text file that you sent, I see that several of the lines are joined together, so both the dcmroot and dcmlist variables appear commented out. Is this intentional? Was this text file saved on a unix system?

a.y

On Mon, 1 Jul 2013, Gundran, Andrew wrote:

...

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

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