Hi Anastasia,
I've attached my configuration file, and below is pasted the contents of
the error log. Below that, I've pasted the last few lines of the trac-all
log (not the error log), because it says something about a "dyld" that
cannot be loaded...might be related to the problem.
Thanks,
Mike
from error log:
------------------------------
SUBJECT 226A
DATE Tue Oct 15 18:38:18 PDT 2013
USER mdatko
HOST captain-cosine.local
PROCESSOR i386
OS Darwin
Darwin captain-cosine.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7
16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
$Id: trac-preproc,v 1.17.2.8 2013/02/16 20:57:05 ayendiki Exp $
/Applications/freesurfer/bin/trac-preproc
PWD /Users/mdatko/Desktop
CMD mri_probedicom --i /Users/mdatko/Desktop/226A/dti/i00001.CFMRI.1
Last few lines from non-error log:
mri_probedicom --i /Users/mdatko/Desktop/226A/dti/i00001.CFMRI.1 >
/Users/mdatko/Desktop/tracula_tutorial/data/freesurfer/226A/dmri/dcminfo.dat
dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib
Referenced from: /Applications/freesurfer/bin/mri_probedicom
Reason: image not found
Darwin captain-cosine.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7
16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
trac-preproc exited with ERRORS at Tue Oct 15 18:38:18 PDT 2013
On Tue, Oct 22, 2013 at 8:04 AM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:
>
> Hi Mike - I'll need to see the configuration file and trac-all.log.
>
> Thanks,
> a.y
>
> On Mon, 21 Oct 2013, Michael Datko wrote:
>
> Hello,I am running into a tracula error very early in the preprocessing
>> steps.
>>
>> I have data that was already somewhat preprocessed (reconstruction, eddy
>> correction and magnetic field inhomogeneity correction) that I'm trying
>> to use
>> as an input. I have turned off those steps in the tracula configuration
>> file.
>> Tracula seems to find these files and starts making a few of the dwi
>> output
>> files in the subject's freesurfer/dmri folder. However, it then says
>> something about not having the correct "frames" and it can't find the file
>> dwi_frames.nii.gz. I'm not sure what this error is referring to. I
>> attempted
>> to run the same subject's data from their raw dicoms instead of the
>> slightly-preprocessed file and also ran into errors. If it makes a
>> difference, the subject had recon-all performed with freesurfer version
>> 5.0
>> and I am now using version 5.3. Perhaps the subject is missing some
>> necessary
>> recon-all output that is only created with 5.3? Any advice?
>>
>> Thanks,
>> Mike Datko
>>
>>
>>
>>
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# 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 = (226A)
# 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/226A
set dcmlist = ( dti/i00001.CFMRI.1 )
# 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/226A/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/226A/226A/bvals.txt
# 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 = ( fm_dti/i00001.CFMRI.1 )
# Input B0 field map phase DICOMs (file names relative to dcmroot)
# Only used if dob0 = 1
# Default: None
#
#set b0plist = ( fm_dti/i00001.CFMRI.1 )
# Echo spacing for field mapping sequence (from sequence printout)
# Only used if dob0 = 1
# Default: None
#
# set echospacing = 2
# 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 = 0.5
# 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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