HI All,
I'm fairly new to Tracula but am getting the error message seen way below
here when I run the trac-prep script. It seems that it has a problem with
opening the bvals file within the dmri folder that it creates (the values
seem to be changed back to rows instead of columns) unlike what we created
in the testbvals file.
This does not seem to be a problem with my machine or with permissions
since I can open the bvals file within dmri so I think it may be an issue
with the actual trac -prep script. The complete log of the processing and
the error message is below. I'm also attaching the trac-prep script and
the bvals file it creates within the dmri folder, along with the original
testbvals file that we used in our drmrirc file.
The trac-prep script also creates two folders: dlabel and dmri.
1)Within dlabel is the diff folder within which we only get the
lowb_brain_mask file
2) Within dmri, we get an empty xfms folder as well as the following files:
bvals, bvecs, bvecs.norot, data.nii.gz, dcminfo.dat, dwiecclog, dwi.nii.gz,
dwi_orig.mghdti.bvals, dwi_orig.mghdti.bvecs, dwi_orig.nii.gz,
dwi_orig_fli-p.nii.gz, lowb.nii.gz, lowb_brain.nii.gz
Just checking to see if trac -prep is supposed to create any other files?
Thanks so much! We appreciate any help you can give us with this.
Cheers,
-Karuna
INFO: SUBJECTS_DIR is /home/karunas/Desktop/bin/freesurfer/subjects
INFO: Diffusion root is /home/karunas/Desktop/bin/freesurfer/subjects
Actual FREESURFER_HOME /home/karunas/Desktop/bin/freesurfer
ERROR: cannot find /home/karunas/Desktop/bin/freesurfer/subjects/203
INFO: SUBJECTS_DIR is /home/karunas/Desktop/bin/freesurfer/subjects
INFO: Diffusion root is /home/karunas/Desktop/bin/freesurfer/subjects
Actual FREESURFER_HOME /home/karunas/Desktop/bin/freesurfer
trac-preproc -c
/home/karunas/Desktop/bin/freesurfer/subjects/203/scripts/dmrirc.local -log
/home/karunas/Desktop/bin/freesurfer/subjects/203/scripts/trac-all.log -cmd
/home/karunas/Desktop/bin/freesurfer/subjects/203/scripts/trac-all.cmd
#-------------------------------------
/home/karunas/Desktop/bin/freesurfer/bin/trac-preproc
#-------------------------------------
#@# Image corrections Wed Sep 23 12:33:46 PDT 2015
mri_convert /data/bil-mb7/fMRI/MESSI/HC2/testtrac/203/E1S16I1.dcm
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig.nii.gz
mri_convert /data/bil-mb7/fMRI/MESSI/HC2/testtrac/203/E1S16I1.dcm
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from /data/bil-mb7/fMRI/MESSI/HC2/testtrac/203/E1S16I1.dcm...
crypt_gkey = FSre8SL5LUSmU
Getting Series No
INFO: Found 61 files in /data/bil-mb7/fMRI/MESSI/HC2/testtrac/203
INFO: Scanning for Series Number 16
Scanning Directory
INFO: found 35 files in series
INFO: loading series header info.
RunNo = 15
WARNING: Run 1 appears to be truncated
Files Found: 35, Files Expected (lRep+1): 1
FileName /data/bil-mb7/fMRI/MESSI/HC2/testtrac/203/E1S16I1.dcm
Identification
NumarisVer syngo MR B15
ScannerModel TrioTim
PatientName vinlab_ER_4_8_2011
Date and time
StudyDate 20110408
StudyTime 162622.453000
SeriesTime 180250.125000
AcqTime 175951.002500
Acquisition parameters
PulseSeq *ep_b0
Protocol dti_35dir
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 84
InversionTime -1
RepetitionTime 9000
PhEncFOV 256
ReadoutFOV 256
Image information
RunNo 15
SeriesNo 16
ImageNo 1
NImageRows 1152
NImageCols 1152
NFrames 35
SliceArraylSize 72
IsMosaic 1
ImgPos 1012.3245 1267.7782 -174.7016
VolRes 2.0000 2.0000 2.0000
VolDim 128 128 72
Vc -0.9892 -0.0962 0.1107
Vr 0.0985 -0.9950 0.0158
Vs 0.1086 0.0266 0.9937
VolCenter 0.0000 0.0000 0.0000
TransferSyntaxUID 1.2.840.10008.1.2.2
INFO: sorting.
INFO: (128 128 72), nframes = 35, ismosaic=1
Could not parse NUMARIS version string syngo MR B15
found in dicom tag 18,1020 (len = 3 != 6)
Repetition Time = 9000, TR = 9000 ms
PE Dir COL COL
AutoAlign matrix detected
AutoAlign Matrix ---------------------
0.98919 -0.12584 -0.07527 8.62242;
0.09619 0.94432 -0.31466 -12.16901;
0.11068 0.30402 0.94621 25.01079;
0.00000 0.00000 0.00000 1.00000;
FileName /data/bil-mb7/fMRI/MESSI/HC2/testtrac/203/E1S16I1.dcm
Identification
NumarisVer syngo MR B15
ScannerModel TrioTim
PatientName vinlab_ER_4_8_2011
Date and time
StudyDate 20110408
StudyTime 162622.453000
SeriesTime 180250.125000
AcqTime 175951.002500
Acquisition parameters
PulseSeq *ep_b0
Protocol dti_35dir
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 84
InversionTime -1
RepetitionTime 9000
PhEncFOV 256
ReadoutFOV 256
Image information
RunNo 15
SeriesNo 16
ImageNo 1
NImageRows 1152
NImageCols 1152
NFrames 35
SliceArraylSize 72
IsMosaic 1
ImgPos 100.2677 150.4042 -45.1647
VolRes 2.0000 2.0000 2.0000
VolDim 128 128 72
Vc -0.9892 -0.0962 0.1107
Vr 0.0985 -0.9950 0.0158
Vs 0.1086 0.0266 0.9937
VolCenter -5.9201 12.6446 42.5760
TransferSyntaxUID 1.2.840.10008.1.2.2
UseSliceScaleFactor 0 (slice 0: 1)
sagrev = 0, correv =0, trarev = 0
Vs = 0.108601 0.0265576 0.993731
INFO: no Siemens slice order reversal detected (good!).
TR=9000.00, TE=84.00, TI=-1.00, flip angle=90.00
i_ras = (-0.989192, -0.0961755, 0.110675)
j_ras = (0.0985118, -0.99501, 0.0158258)
k_ras = (0.108601, 0.0265576, 0.993731)
writing to
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig.nii.gz...
crypt_gkey = FSre8SL5LUSmU
mri_probedicom --i /data/bil-mb7/fMRI/MESSI/HC2/testtrac/203/E1S16I1.dcm >
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dcminfo.dat
cp testbvecs.txt
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig.mghdti.bvecs
cp testbvals.txt
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig.mghdti.bvals
mv -f /home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/bvecs.tmp
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig.mghdti.bvecs
mv -f /home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/bvals.tmp
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig.mghdti.bvals
flip4fsl
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig.nii.gz
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 8
fslswapdim
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig.nii.gz x -y
z
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig_flip.nii.gz
INFO: left-right orientation was flipped by fslswapdim
fslorient -forceradiological
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig_flip.nii.gz
INFO: found
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig.mghdti.bvals,
converting to FSL format
INFO: found
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig.mghdti.bvecs,
converting to FSL format
mv -f
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig_flip.mghdti.bvecs
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/bvecs
mv -f
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig_flip.mghdti.bvals
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/bvals
eddy_correct
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig_flip.nii.gz
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi.nii.gz 0
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0000
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0001
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0002
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0003
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0004
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0005
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0006
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0007
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0008
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0009
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0010
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0011
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0012
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0013
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0014
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0015
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0016
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0017
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0018
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0019
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0020
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0021
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0022
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0023
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0024
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0025
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0026
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0027
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0028
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0029
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0030
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0031
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0032
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0033
processing
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_tmp0034
mv -f /home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/bvecs
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/bvecs.norot
xfmrot /home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi.ecclog
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/bvecs.norot
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/bvecs
ln -sf /home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi.nii.gz
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/data.nii.gz
mri_convert --frame 0 1 2 3 4
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi.nii.gz
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/lowb.nii.gz
mri_convert --frame 0 1 2 3 4
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi.nii.gz
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/lowb.nii.gz
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi.nii.gz...
crypt_gkey = FSre8SL5LUSmU
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.989192, -0.0961755, 0.110675)
j_ras = (-0.0985118, 0.99501, -0.0158258)
k_ras = (0.108601, 0.0265576, 0.993731)
keeping frames 0 1 2 3 4
writing to
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/lowb.nii.gz...
crypt_gkey = FSre8SL5LUSmU
mri_concat --i
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/lowb.nii.gz --mean
--o /home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/lowb.nii.gz
ninputs = 1
Checking inputs
nframestot = 5
Allocing output
Done allocing
nframes = 5
Computing mean across frames
Writing to
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/lowb.nii.gz
bet /home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/lowb.nii.gz
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/lowb_brain.nii.gz -m
-f 0.3
mv -f
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/lowb_brain_mask.nii.gz
/home/karunas/Desktop/bin/freesurfer/subjects/203/dlabel/diff
#-------------------------------------
#@# Image quality assessment Wed Sep 23 12:44:54 PDT 2015
/home/karunas/Desktop/bin/freesurfer/bin/dmri_motion --dwi
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig.nii.gz
--mat /home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi.ecclog
--bval /home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/bvals --out
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_motion.txt
cwd /data/bil-mb7/fMRI/MESSI/HC2/testtrac/203
cmdline /home/karunas/Desktop/bin/freesurfer/bin/dmri_motion --dwi
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig.nii.gz
--mat /home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi.ecclog
--bval /home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/bvals --out
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_motion.txt
sysname Linux
hostname manas.radiology.ucsf.edu
machine x86_64
user karunas
Output motion measure file:
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_motion.txt
Input transform file:
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi.ecclog
Input DWI file:
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig.nii.gz
Input b-value table:
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/bvals
Low-b image intensity threshold: 100
Nominal diffusivity: 0.001
Loading volume-to-baseline affine transformations
Computing between-volume head motion measures
INFO: Processed transforms for 35 volumes
Loading DWI volume series from
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/dwi_orig.nii.gz
Loading b-value table from
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/bvals
ERROR: Could not open
/home/karunas/Desktop/bin/freesurfer/subjects/203/dmri/bvals for reading
Linux manas.radiology.ucsf.edu 2.6.18-406.el5 #1 SMP Fri May 1 10:37:57 EDT
2015 x86_64 x86_64 x86_64 GNU/Linux
