Hi Ashley - You need to specify a gradient table and b-value table. You
can find more information on how to do this in the tutorial here:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
Hope this helps,
a.y
On Mon, 29 Dec 2014, Ashley Hannah wrote:
Hello,
I keep receiving an error when I try to run 'trac-all -prep -c dmric.trac'
The error I receive says that dwi_orig_flip.mghdti.bvecs can not be moved but
in the code it is never created. Is there a way to manually
create this file? I have tried to manually run the code and edit the dmric file
but nothing is working.
Below I have the error message and dmric.trac file.
Thank you,
Ashley
[hannahas@gauss MCIStudy]$ trac-all -prep -c dmric.trac
INFO: SUBJECTS_DIR is /extern/research/PI/training/hannahas/MCIStudy
INFO: Diffusion root is /extern/research/PI/training/hannahas/MCIStudy
Actual FREESURFER_HOME /extern/soft/tools/freesurfer-5.3.0
trac-preproc -c
/extern/research/PI/training/hannahas/MCIStudy/NAP_002/scripts/dmrirc.local -log
/extern/research/PI/training/hannahas/MCIStudy/NAP_002/scripts/trac-all.log -cmd
/extern/research/PI/training/hannahas/MCIStudy/NAP_002/scripts/trac-all.cmd
#-------------------------------------
/extern/soft/tools/freesurfer/bin/trac-preproc
#-------------------------------------
#@# Image corrections Mon Dec 29 11:28:47 EST 2014
mri_convert
/extern/research/PI/training/hannahas/MCIStudy/NAP_002/dtiwholebrain/MRDC.00001
/extern/research/PI/training/hannahas/MCIStudy/NAP_002/dmri/dwi_orig.nii.gz
mri_convert
/extern/research/PI/training/hannahas/MCIStudy/NAP_002/dtiwholebrain/MRDC.00001
/extern/research/PI/training/hannahas/MCIStudy/NAP_002/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from
/extern/research/PI/training/hannahas/MCIStudy/NAP_002/dtiwholebrain/MRDC.00001...
Starting DICOMRead2()
dcmfile =
/extern/research/PI/training/hannahas/MCIStudy/NAP_002/dtiwholebrain/MRDC.00001
dcmdir = /extern/research/PI/training/hannahas/MCIStudy/NAP_002/dtiwholebrain
Ref Series No = 5
Found 1250 files, checking for dicoms
Found 1248 dicom files in series.
First Sorting
Computing Slice Direction
Vs: 0 0 2.4
Vs: 0 0 1
Second Sorting
Counting frames
nframes = 26
nslices = 48
ndcmfiles = 1248
PE Dir = COL (dicom read)
TransferSyntaxUID: --1.2.840.10008.1.2.1--
Loading pixel data
TR=13700.00, TE=79.70, TI=0.00, flip angle=90.00
i_ras = (-1, 0, 0)
j_ras = (0, -1, 0)
k_ras = (-0, -0, 1)
writing to
/extern/research/PI/training/hannahas/MCIStudy/NAP_002/dmri/dwi_orig.nii.gz...
mri_probedicom --i
/extern/research/PI/training/hannahas/MCIStudy/NAP_002/dtiwholebrain/MRDC.00001
>
/extern/research/PI/training/hannahas/MCIStudy/NAP_002/dmri/dcminfo.dat
flip4fsl
/extern/research/PI/training/hannahas/MCIStudy/NAP_002/dmri/dwi_orig.nii.gz
/extern/research/PI/training/hannahas/MCIStudy/NAP_002/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 7.09026
fslswapdim
/extern/research/PI/training/hannahas/MCIStudy/NAP_002/dmri/dwi_orig.nii.gz x
-y z
/extern/research/PI/training/hannahas/MCIStudy/NAP_002/dmri/dwi_orig_flip.nii.gz
INFO: left-right orientation was flipped by fslswapdim
fslorient -forceradiological
/extern/research/PI/training/hannahas/MCIStudy/NAP_002/dmri/dwi_orig_flip.nii.gz
mv -f
/extern/research/PI/training/hannahas/MCIStudy/NAP_002/dmri/dwi_orig_flip.mghdti.bvecs
/extern/research/PI/training/hannahas/MCIStudy/NAP_002/dmri/bvecs
mv: cannot stat
`/extern/research/PI/training/hannahas/MCIStudy/NAP_002/dmri/dwi_orig_flip.mghdti.bvecs':
No such file or directory
Linux gauss.rad.msu.edu 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25
UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Mon Dec 29 11:29:14 EST 2014
_______________
# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
#
setenv SUBJECTS_DIR /extern/research/PI/training/hannahas/MCIStudy
# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#
set dtroot = /extern/research/PI/training/hannahas/MCIStudy
# Subject IDs
#
set subjlist = (NAP_002 NAP_003)
# In case you want to analyze only Huey and Louie
# Default: Run analysis on all subjects
#
#set runlist = (1 2)
# 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 = /extern/research/PI/training/hannahas/MCIStudy
set dcmlist = (NAP_002/dtiwholebrain/MRDC.00001
NAP_003/dtiwholebrain/MRDC.00001)
# Diffusion gradient tables (if there is a different one for each scan)
# Must be specified if inputs are not MGH DICOMs
# The tables must have either three columns, where each row is a gradient vector
# or three rows, where each column is a gradient vector
# There must be as many gradient vectors as volumes in the diffusion data set
# Default: Read from DICOM header
#
set bveclist = (/NAP_002/FSL_DTI_analy_RAD_final/dtifit/bvecs.txt \
/NAP_003/FSL_DTI_analy_RAD_final/dtifit/bvecs.txt)
# Diffusion gradient table (if using the same one for all scans)
# Must be specified if inputs are not MGH DICOMs
# The table must have either three columns, where each row is a gradient vector
# or three rows, where each column is a gradient vector
# There must be as many gradient vectors as volumes in the diffusion data set
# Default: Read from DICOM header (Removed so that it would run as default)
#
# Diffusion b-value table
# Must be specified if inputs are not MGH DICOMs
# There must be as many b-values as volumes in the diffusion data set
# Default: Read from DICOM header (removed so that it would run as default)
#
# Perform registration-based B0-inhomogeneity compensation?
# Default: 0 (no)
#
set dob0 = 0
# Input B0 field map magnitude DICOMs (file names relative to dcmroot)
# Only used if dob0 = 1
# Default: None
#
set b0mlist = (NAP_002/dtiwholebrain/MRDC.00001
NAP_003/dtiwholebrain/MRDC.00001)
# Input B0 field map phase DICOMs (file names relative to dcmroot)
# Only used if dob0 = 1
# Default: None
#
set b0plist = (NAP_002/dtiwholebrain/MRDC.00001
NAP_003/dtiwholebrain/MRDC.00001)
# 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 = 0.5
# 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 =
/extern/research/PI/training/hannahas/MCIStudy/MNI152_T1_2mm_brain.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 = /extern/research/PI/training/hannahas/MCIStudy/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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