DETAILS

7 Dec 2012

      Yes, I can see that each of the bvecs/bvals files is one long line. Was 
that the case for the original files that you specified in the dmrirc?
On Fri, 7 Dec 2012, s0675204 wrote:
...
Hi Anastasia
I had attached the files, but maybe they did not go through to the
mailing list? So I am sending them to your email id. Hope this is okay
best wishes,
Prerona
---------- Forwarded message ----------
From: s0675204 s0675204@sms.ed.ac.uk
Date: 7 December 2012 19:44
Subject: Re: [Freesurfer] Running Tracula: trac-preproc exited with ERRORS
To: freesurfer@nmr.mgh.harvard.edu
Hello
I think I spoke to soon!
It ended with errors again.
I get the error message: "bvecs and bvals don't have the same number of entries"
I saw on some older messages on the mail-base you said that we need to
check that the number of entries in the bvals is same as and bvecs is
3 times as much as the number of volumes. I have checked that this is
the case
I am wondering if it is some formatting problem? there are no spaces
at the end of the file. and there are no end of line markers either.
Please could you advise me? I have attached the files and also pasted
the contents below
My config file is still the same (as pasted below) except I tried changing
nb0 to 2
(# Number of low-b images
# Must be specified if inputs are not DICOM
# Default: Read from DICOM header
#
set nb0 = 2)
best wishes,
Prerona
=========================================================
bvals:
0 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800 800
800 800 800 0 800 800 800 800 800 800 800 800 800 800 800 800 800 800
800 800 800 800 800 800
bvecs:
0 0.99864840507507 0.01463935524225 0.01274211052805 0.85177010297775
0.86449736356735 0.85295587778091 0.83894062042236 0.7912425994873
0.51641523838043 0.46147873997688 0.54209464788436 0.44143822789192
0.52723878622055 0.4250853061676 0.51590526103973 0.43744987249374
0.50455766916275 0.05208261311054 0.06073396280407 0.00979638285934 0
0.99864840507507 0.01463935524225 0.01274211052805 0.85177010297775
0.86449736356735 0.85295587778091 0.83894062042236 0.7912425994873
0.51641523838043 0.46147873997688 0.54209464788436 0.44143822789192
0.52723878622055 0.4250853061676 0.51590526103973 0.43744987249374
0.50455766916275 0.05208261311054 0.06073396280407 0.00979638285934 0
-0.00687454920262 0.96709138154983 0.62002921104431 0.52092331647872
0.18501849472522 -0.42448142170906 -0.44344407320022 0.15539556741714
0.60610836744308 0.88347893953323 0.71210372447967 0.30400663614273
-0.23736105859279 -0.70398008823394 -0.85636389255523
-0.73376137018203 -0.22848516702652 -0.00803200621157 0.51328992843627
0.93218487501144 0 -0.00687454920262 0.96709138154983 0.62002921104431
0.52092331647872 0.18501849472522 -0.42448142170906 -0.44344407320022
0.15539556741714 0.60610836744308 0.88347893953323 0.71210372447967
0.30400663614273 -0.23736105859279 -0.70398008823394 -0.85636389255523
-0.73376137018203 -0.22848516702652 -0.00803200621157 0.51328992843627
0.93218487501144 0 0.05151799321174 -0.2540076971054 -0.78447526693344
0.05591572076082 -0.46734625101089 -0.3037790954113 0.31549325585365
0.5914282798767 0.60493636131286 0.08063688874244 -0.44614082574844
-0.84422290325164 -0.81589156389236 -0.56895911693573
-0.02196817658841 0.51983833312988 0.83259600400924 0.99861049652099
0.85606354475021 0.36184993386268 0 0.05151799321174 -0.2540076971054
-0.78447526693344 0.05591572076082 -0.46734625101089 -0.3037790954113
0.31549325585365 0.5914282798767 0.60493636131286 0.08063688874244
-0.44614082574844 -0.84422290325164 -0.81589156389236
-0.56895911693573 -0.02196817658841 0.51983833312988 0.83259600400924
0.99861049652099 0.85606354475021 0.36184993386268
On 7 December 2012 14:08, Anastasia Yendiki
ayendiki@nmr.mgh.harvard.edu wrote:
...
Great, I love easy problems :)
On Fri, 7 Dec 2012, s0675204 wrote:
...
Thank you! It's chugging away now
best wishes,
Prerona
On 7 December 2012 13:46, Anastasia Yendiki
ayendiki@nmr.mgh.harvard.edu wrote:
...
Hi Prerona - You need to uncomment the bvecfile and bvalfile definitions
in
your configuration file.
Hope this helps,
a.y
On Fri, 7 Dec 2012, s0675204 wrote:
...
Hello
I am trying to run Tracula on a set of dicoms files. I have run
recon-all previously.
I am getting a message trac-preproc exited with ERRORS
Please can anyone advise me on this?
I have listed all the details (command, error/output, config file) below
Thank you so much for your help
best wishes,
Prerona
DETAILS
command used:  trac-all -prep -c ./scripts/dmrirc_single_subject
=========================================
error message
=========================================
canlilab@112-205:~/SBU/data/tracula$ trac-all -prep -c
./scripts/dmrirc_single_subject
INFO: SUBJECTS_DIR is /home/canlilab/SBU/data/recon_output
INFO: Diffusion root is /home/canlilab/SBU/data/tracula
Actual FREESURFER_HOME /home/canlilab/freesurfer
trac-preproc -c
/home/canlilab/SBU/data/tracula/00075/scripts/dmrirc.local -log
/home/canlilab/SBU/data/tracula/00075/scripts/trac-all.log -cmd
/home/canlilab/SBU/data/tracula/00075/scripts/trac-all.cmd
#-------------------------------------
/home/canlilab/freesurfer/bin/trac-preproc
#-------------------------------------
#@# Image corrections Fri Dec  7 10:42:30 EST 2012
mri_convert /home/canlilab/SBU/data/dti_dicoms/00075/data_1.dcm
/home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig.nii.gz
mri_convert /home/canlilab/SBU/data/dti_dicoms/00075/data_1.dcm
/home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from /home/canlilab/SBU/data/dti_dicoms/00075/data_1.dcm...
Getting Series No
INFO: Found 44 files in /home/canlilab/SBU/data/dti_dicoms/00075
INFO: Scanning for Series Number 7
Scanning Directory
INFO: found 42 files in series
INFO: loading series header info.
RunNo = 6
WARNING: Run 1 appears to be truncated
 Files Found: 42, Files Expected (lRep+1): 2
FileName
/home/canlilab/SBU/data/dti_dicoms/00075/data_1.dcm
Identification
        NumarisVer        syngo MR B17
        ScannerModel      TrioTim
        PatientName       S790_P72_TC
Date and time
        StudyDate         20120502
        StudyTime         120741.390000
        SeriesTime        125649.953000
        AcqTime           125626.150000
Acquisition parameters
        PulseSeq          ep_b0
        Protocol          DTI
        PhEncDir          COL
        EchoNo            1
        FlipAngle         90
        EchoTime          93
        InversionTime     -1
        RepetitionTime    5500
        PhEncFOV          220
        ReadoutFOV        220
Image information
        RunNo             6
        SeriesNo          7
        ImageNo           1
        NImageRows        896
        NImageCols        896
        NFrames           42
        SliceArraylSize   40
        IsMosaic          1
        ImgPos            772.3238 773.0634 185.5347
        VolRes              1.7188   1.7188   3.0000
        VolDim            128      128       40
        Vc                 -0.9983   0.0151  -0.0555
        Vr                 -0.0000  -0.9648  -0.2629
        Vs                 -0.0575  -0.2625   0.9632
        VolCenter           0.0000   0.0000   0.0000
        TransferSyntaxUID 1.2.840.10008.1.2.1
INFO: sorting.
INFO: (128 128  40), nframes = 42, ismosaic=1
Could not parse NUMARIS version string syngo MR B17
found in dicom tag 18,1020 (len = 3 != 6)
Repetition Time = 5500, TR = 5500 ms
PE Dir COL COL
AutoAlign matrix detected
AutoAlign Matrix ---------------------
1.000   0.000   0.000   0.000;
0.000   1.000   0.000   0.000;
0.000   0.000   1.000   0.000;
0.000   0.000   0.000   1.000;
FileName
/home/canlilab/SBU/data/dti_dicoms/00075/data_1.dcm
Identification
        NumarisVer        syngo MR B17
        ScannerModel      TrioTim
        PatientName       S790_P72_TC
Date and time
        StudyDate         20120502
        StudyTime         120741.390000
        SeriesTime        125649.953000
        AcqTime           125626.150000
Acquisition parameters
        PulseSeq          ep_b0
        Protocol          DTI
        PhEncDir          COL
        EchoNo            1
        FlipAngle         90
        EchoTime          93
        InversionTime     -1
        RepetitionTime    5500
        PhEncFOV          220
        ReadoutFOV        220
Image information
        RunNo             6
        SeriesNo          7
        ImageNo           1
        NImageRows        896
        NImageCols        896
        NFrames           42
        SliceArraylSize   40
        IsMosaic          1
        ImgPos            113.4156 146.2544 -24.5854
        VolRes              1.7188   1.7188   3.0000
        VolDim            128      128       40
        Vc                 -0.9983   0.0151  -0.0555
        Vr                 -0.0000  -0.9648  -0.2629
        Vs                 -0.0575  -0.2625   0.9632
        VolCenter           0.1478  26.0388  -1.8116
        TransferSyntaxUID 1.2.840.10008.1.2.1
sagrev = 0, correv =0, trarev = 0
Vs = -0.0574949 -0.262456 0.963229
INFO: no Siemens slice order reversal detected (good!).
TR=5500.00, TE=93.00, TI=-1.00, flip angle=90.00
i_ras = (-0.998346, 0.0151149, -0.0554726)
j_ras = (-3.31902e-08, -0.964826, -0.262891)
k_ras = (-0.0574949, -0.262456, 0.963229)
writing to /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig.nii.gz...
mri_probedicom --i /home/canlilab/SBU/data/dti_dicoms/00075/data_1.dcm
...
/home/canlilab/SBU/data/tracula/00075/dmri/dcminfo.dat
flip4fsl /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig.nii.gz
/home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 8.86231
fslswapdim /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig.nii.gz
x -y z /home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig_flip.nii.gz
INFO: left-right orientation was flipped by fslswapdim
fslorient -forceradiological
/home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig_flip.nii.gz
mv -f
/home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig_flip.mghdti.bvecs
/home/canlilab/SBU/data/tracula/00075/dmri/bvecs
mv: cannot stat
`/home/canlilab/SBU/data/tracula/00075/dmri/dwi_orig_flip.mghdti.bvecs':
No such file or directory
Linux 112-205.psy.sunysb.edu 2.6.32-279.5.2.el6.x86_64 #1 SMP Fri Aug
24 01:07:11 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Fri Dec  7 10:42:51 EST 2012
config file:
#
# dmrirc.example
#
# This file contains commands that will be run by trac-all before an
analysis.
# It is used to set all parameters needed for the analysis.
#
# Remove a parameter from your dmrirc file if you want use the default
value.
# Parameters that don't have default values must be specified.
#
# Any other commands that you might want to run before an analysis can
be
added
# to this file.
#
# Original Author: Anastasia Yendiki
# CVS Revision Info:
#    $Author: ayendiki $
#    $Date: 2011/05/24 06:47:12 $
#    $Revision: 1.3.2.3 $
#
# Copyright © 2011 The General Hospital Corporation (Boston MA) "MGH"
#
# Terms and conditions for use reproduction distribution and
contribution
# are found in the 'FreeSurfer Software License Agreement' contained
# in the file 'LICENSE' found in the FreeSurfer distribution and here:
#
# https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense
#
# Reporting: freesurfer@nmr.mgh.harvard.edu
#
#
# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
# setenv SUBJECTS_DIR /path/to/recons/of/ducks
# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#
set dtroot = $pre_data/tracula
# Subject IDs
#
set subjlist = (00075 00104 00122 00200 00308 00369 00387 00400 00422
00452 00518 00568 00587 00624 00636 00686 00698 00727 00909 00926
00933 00943 00983 00992 01049 01121 01329 01450 01509 01531 01678
01735 01746 01809 01843 01917 10039 10056 10089 10165 10171 10227
10238 10263 10314 10320 10326 10349 10407 10431 10435 10458 10477
10499 10500 10636 10750 11209 12210 12357 12472 12645 13493 13958
14302 14481 14530 15329 15345 15864 16654 17267 17478 18337 18422
18530 19259 19377 19725 20071 20383 21413 23846 24115 24531 24781
25962 26314 26475 28822 30510 30571 30927 31034 31049 31237 31437
31471 31531 32131 32162 32222)
# In case you want to analyze only Huey and Louie
# Default: Run analysis on all subjects
#
set runlist = (1       2       3       4       5       6       7
8       9       10      11      12      13      14      15      16
17      18      19      20      21      22      23      24      25
 26      27      28      29      30      31      32      33      34
  35      36      37      38      39      40      41      42      43
   44      45      46      47      48      49      50      51      52
    53      54      55      56      57      58      59      60
61      62      63      64      65      66      67      68      69
70      71      72      73      74      75      76      77      78
 79      80      81      82      83      84      85      86      87
  88      89      90      91      92      93      94      95      96
   97      98      99      100     101     102)
# Input diffusion DICOMs (file names relative to dcmroot)
# If original DICOMs don't exist these can be in other image format
# but then bvecfile bvalfile and nb0 must be specified (see below)
#
set dcmroot = $pre_data/dti_dicoms
set dcmlist = (00075/data_1.dcm \
00104/data_1.dcm \
00122/data_1.dcm \
00200/data_1.dcm \
00308/data_1.dcm \
00369/data_1.dcm \
00387/data_1.dcm \
00400/data_1.dcm \
00422/data_1.dcm \
00452/data_1.dcm \
00518/data_1.dcm \
00568/data_1.dcm \
00587/data_1.dcm \
00624/data_1.dcm \
00636/data_1.dcm \
00686/data_1.dcm \
00698/data_1.dcm \
00727/data_1.dcm \
00909/data_1.dcm \
00926/data_1.dcm \
00933/data_1.dcm \
00943/data_1.dcm \
00983/data_1.dcm \
00992/data_1.dcm \
01049/data_1.dcm \
01121/data_1.dcm \
01329/data_1.dcm \
01450/data_1.dcm \
01509/data_1.dcm \
01531/data_1.dcm \
01678/data_1.dcm \
01735/data_1.dcm \
01746/data_1.dcm \
01809/data_1.dcm \
01843/data_1.dcm \
01917/data_1.dcm \
10039/data_1.dcm \
10056/data_1.dcm \
10089/data_1.dcm \
10165/data_1.dcm \
10171/data_1.dcm \
10227/data_1.dcm \
10238/data_1.dcm \
10263/data_1.dcm \
10314/data_1.dcm \
10320/data_1.dcm \
10326/data_1.dcm \
10349/data_1.dcm \
10407/data_1.dcm \
10431/data_1.dcm \
10435/data_1.dcm \
10458/data_1.dcm \
10477/data_1.dcm \
10499/data_1.dcm \
10500/data_1.dcm \
10636/data_1.dcm \
10750/data_1.dcm \
11209/data_1.dcm \
12210/data_1.dcm \
12357/data_1.dcm \
12472/data_1.dcm \
12645/data_1.dcm \
13493/data_1.dcm \
13958/data_1.dcm \
14302/data_1.dcm \
14481/data_1.dcm \
14530/data_1.dcm \
15329/data_1.dcm \
15345/data_1.dcm \
15864/data_1.dcm \
16654/data_1.dcm \
17267/data_1.dcm \
17478/data_1.dcm \
18337/data_1.dcm \
18422/data_1.dcm \
18530/data_1.dcm \
19259/data_1.dcm \
19377/data_1.dcm \
19725/data_1.dcm \
20071/data_1.dcm \
20383/data_1.dcm \
21413/data_1.dcm \
23846/data_1.dcm \
24115/data_1.dcm \
24531/data_1.dcm \
24781/data_1.dcm \
25962/data_1.dcm \
26314/data_1.dcm \
26475/data_1.dcm \
28822/data_1.dcm \
30510/data_1.dcm \
30571/data_1.dcm \
30927/data_1.dcm \
31034/data_1.dcm \
31049/data_1.dcm \
31237/data_1.dcm \
31437/data_1.dcm \
31471/data_1.dcm \
31531/data_1.dcm \
32131/data_1.dcm \
32162/data_1.dcm \
32222/data_1.dcm)
# 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 = $pre_data/DTI_Analysis/00075/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 = $pre_data/DTI_Analysis/00075/bvals.txt
# Number of low-b images
# Must be specified if inputs are not DICOM
# Default: Read from DICOM header
#
set nb0 = 1
# 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 = (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.dcm)
# 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: 1 (yes)
#
set doregflt = 1
# Perform diffusion-to-T1 registration by bbregister?
# Default: 0 (no)
#
set doregbbr = 0
# MNI template (the only option for inter-subject registration in this
version)
# Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
#
set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
# 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
# Default: 5
#
set ncpts = 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
# Use long (more descriptive) directory hierarchy for saving path
distributions?
# By default paths distributions are saved directly under
$subjectname/dpath
# Default: 0 (no)
#
set dopathsubdirs = 0
# 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: 5000
#
set nsample = 5000
# Frequency with which MCMC path samples are retained for path
distribution
# Default: 5 (keep every 5th sample)
#
set nkeep = 5
==============================================

Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it
is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in
error
but does not contain patient information, please contact the sender and
properly
dispose of the e-mail.

Re: [Freesurfer] Fwd: Running Tracula: trac-preproc exited with ERRORS

DETAILS

trac-preproc exited with ERRORS at Fri Dec 7 10:42:51 EST 2012

config file: