Hi Mike - Good to know. This would make perfect sense b/c in 5.1 trac-all
required a variable to be defined that isn't used any more in 5.3.
a.y
On Tue, 15 Oct 2013, Michael Datko wrote:
Hi Anastasia,I updated freesurfer from 5.1 to 5.3 and that fixed the
problem! Thanks for taking a look at my file.
Mike
On Tue, Oct 15, 2013 at 1:49 PM, Michael Datko <mikeda...@gmail.com> wrote:
I tried making the subjects directory line in the configuration
file point to somewhere that didn't actually exist. I got the
same error as you, where it says that SUBJECTS_DIR doesn't
exist. Then I changed it to point to the real folder, and I am
back at the "set: variable name must begin with a letter" error.
I have now tried this on two different computers with similar
but not identical setups, and get the same error. I am using
freesurfer 5.1 now, but the original data was processed with
version 5.0, if that makes a difference.
Mike
On Mon, Oct 14, 2013 at 6:04 PM, Michael Datko <mikeda...@gmail.com>
wrote:
Very strange...I'm running this on a 2009 macbook pro,
with OSX 10.6.8 (Snow Leopard). I've never had this sort
of problem with command-line programs like AFNI or
freesurfer.
On Mon, Oct 14, 2013 at 2:37 PM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
Hi Michael - It doesn't look like the configuration
file is the problem, or at least I cannot replicate
it. I ran "trac-all -c dmrirc.txt -prep" on a mac
and a linux machine and the only error I got was
that the SUBJECTS_DIR doesn't exist (as expected
since I don't have your directory structure). What
system are you running this on?
a.y
On Mon, 14 Oct 2013, Michael Datko wrote:
Hi Anastasia,No log files were created,
it seems like the program does not even
begin to run. I get that
error immediately upon calling trac-all.
I pasted the entire configuration file
into the original
message, but I attach it here as well.
Thanks,
Mike
On Mon, Oct 14, 2013 at 1:55 PM,
Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
Hi Michael - It's hard to tell at
which point it fails. Is there any
output, is there a
trac-all.log? If so, can you
please attach the entire file, as well
as the entire
configuration file?
Thanks,
a.y
On Sat, 12 Oct 2013, Michael Datko
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
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