Re: [Freesurfer] Tracula/ config file error - Freesurfer

3 Jul 2013


      What is the trac-all command line that you're running?
On Wed, 3 Jul 2013, Gundran, Andrew wrote:
...
I dont seem to have a trac-all.log file in the scripts directory. I do however have a recon-all.log. I'll attach
________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu]
Sent: Wednesday, July 03, 2013 2:42 PM
To: Gundran, Andrew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Tracula/ config file error
Can you please send the trac-all.log file from the scripts directory?
On Wed, 3 Jul 2013, Gundran, Andrew wrote:
...
That'd be a yes to both your questions.
-----Original Message-----
From: Anastasia Yendiki [mailto:ayendiki@nmr.mgh.harvard.edu]
Sent: Wednesday, July 03, 2013 2:33 PM
To: Gundran, Andrew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Tracula/ config file error
You're very welcome. Is your freesurfer recon-all output for this subject under /home/baileype/Desktop/JG005/freesurfer? Does the file mri/aparc+aseg.mgz exist?
I'm cc-ing the freesurfer list so that our conversation is archived, other users benefit from it, and we avoid replication of questions.
On Wed, 3 Jul 2013, Gundran, Andrew wrote:
...
I've reattched the actual file so it might be easier.
Thanks for all the help.
________________________________________
From: Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu]
Sent: Monday, July 01, 2013 3:38 PM
To: Gundran, Andrew
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Tracula/ config file error
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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