I'm guessing that this shows up in the scripts/trac-all.log of a
particular subject? Then it applies to that subject.
On Mon, 10 Dec 2012, s0675204 wrote:
Hello
My trac- preproc has completed. However, I am confused about the
status message. It says:
#-------------------------------------
trac-preproc finished without error at Mon Dec 10 16:32:20 EST 2012
ERROR: cannot find /home/canlilab/SBU/data/recon_output/00387
Does this mean it was completed succesfully for everyone or everyone
but that 00387 person?
Is there any way I can verify this?
thank you so much for your help
best wishes,
Prerona
On 8 December 2012 13:38, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
In your dmrirc, you define multiple subjects, but only one bvecfile and one
bvalfile that are used for all subjects.
On Sat, 8 Dec 2012, s0675204 wrote:
the values are the same but each subject has an individual bvec & bval
file. so it depends on how the script will read it?
On 8 December 2012 00:03, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
Are the bvecs/bvals not the same for all subjects?
On Fri, 7 Dec 2012, s0675204 wrote:
oh! i thought this was how these were meant to be! i will do that.
sadly i left the lab and came home for the day but i will try it as
soon as i am back and let you know!
thank you so much! do we have to do this for each subject or just one
time?
On 7 December 2012 23:51, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
I see. Can you try formatting them in columns (1 column for the bvals
and
3
columns for the bvecs)?
On Fri, 7 Dec 2012, s0675204 wrote:
yes! these are the original files
well these are the files i pointed to in my config file. and i think
the script copies them over to the dmrirc folder?
best wishes,
Prerona
On 7 December 2012 23:38, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
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 <s0675...@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
<ayend...@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
<ayend...@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
==============================================
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