Hi Jason - Did this file get created?
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi.nii.gz
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Jason Silva Rudberg
<jason.rudb...@yale.edu>
Sent: Sunday, July 12, 2020 2:45 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] TRACULA preprocessing error
External Email - Use Caution
Hello,
I have been attempting to run TRACULA on the sample practice data using the
sample configuration file listed here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula. I am using Free
Surfer 6.
I receive an error message at the first step of the pre-processing pathway with
subjects elmo.2008 and elmo.2012. It looks like it may be getting hung up at
the Eddy Correction step. Do you know why this might be happening?
Thank you for your help!
Jason
This is the configuration file:
# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
#
setenv SUBJECTS_DIR $TUTORIAL_DATA/diffusion_recons
# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#
set dtroot = $TUTORIAL_DATA/diffusion_tutorial
# Subject IDs
#
set subjlist = ( elmo.2005 \
elmo.2008 \
elmo.2012 )
# Input diffusion DICOMs
# If original DICOMs don't exist, these can be in other image format
# but then the gradient table and b-value table must be specified (see below)
#
set dcmroot = $TUTORIAL_DATA/diffusion_tutorial
set dcmlist = ( elmo.2005/orig/656000-11-1.dcm \
elmo.2008/orig/97000-000017-000001.dcm \
elmo.2012/orig/MR.1.3.12.2.1107.5.2.32.35006.2012121819455034689828982 )
# Diffusion gradient tables (if there is a different one for each scan)
# Must be specified if they cannot be read from the DICOM headers
# 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 = ( $TUTORIAL_DATA/diffusion_tutorial/elmo.2005/orig/gradients.txt
\
$TUTORIAL_DATA/diffusion_tutorial/elmo.2008/orig/gradients.txt
\
$TUTORIAL_DATA/diffusion_tutorial/elmo.2012/orig/gradients.txt
)
#set bvecfile = /path/to/bvecs.txt
# Diffusion b-value tables (if there is a different one for each scan)
# Must be specified if they cannot be read from the DICOM headers
# There must be as many b-values as volumes in the diffusion data set
# Default: Read from DICOM header
#
set bvallist = ( $TUTORIAL_DATA/diffusion_tutorial/elmo.2005/orig/bvalues.txt \
$TUTORIAL_DATA/diffusion_tutorial/elmo.2008/orig/bvalues.txt \
$TUTORIAL_DATA/diffusion_tutorial/elmo.2012/orig/bvalues.txt )
#set bvalfile = /path/to/bvals.txt
set runlist = (2)
set doeddy = 1
set dorotbvecs = 1
set usemaskanat = 1
set thrbet = 0.3
set doregflt = 0
set doregbbr = 1
set doregmni = 1
set doregcvs = 0
#set mnitemp = /path/to/mni/template
#set cvstemp = /cvs/template/name
#set cvstempdir = /path/to/parent/dir/of/cvstemp
set pathlist = ( lh.cst_AS rh.cst_AS \
lh.ilf_AS rh.ilf_AS \
lh.unc_AS rh.unc_AS \
fmajor_PP fminor_PP \
lh.atr_PP rh.atr_PP \
lh.cab_PP rh.cab_PP \
lh.ccg_PP rh.ccg_PP \
lh.slfp_PP rh.slfp_PP \
lh.slft_PP rh.slft_PP )
set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)
This is the attempted run:
[jar269@librapet ~]$ trac-all -corr -c /home1/jar269/Elmo2/dmrirc.tutorial
INFO: SUBJECTS_DIR is /home1/jar269/Elmo2/diffusion_recons
INFO: Diffusion root is /home1/jar269/Elmo2/diffusion_tutorial
Actual FREESURFER_HOME /home1/am2359/freesurfer_6
trac-preproc -c
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/scripts/dmrirc.local -log
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/scripts/trac-all.log -cmd
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/scripts/trac-all.cmd
#-------------------------------------
/home1/am2359/freesurfer_6/bin/trac-preproc
#-------------------------------------
#@# Image corrections Sun Jul 12 14:27:04 EDT 2020
mri_convert --bvec-voxel
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/orig/97000-000017-000001.dcm
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/orig/97000-000017-000001.dcm
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/orig/97000-000017-000001.dcm...
Getting Series No
INFO: Found 74 files in /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/orig
INFO: Scanning for Series Number 17
Scanning Directory
INFO: found 70 files in series
INFO: loading series header info.
RunNo = 16
WARNING: Run 1 appears to be truncated
Files Found: 70, Files Expected (lRep+1): 120
FileName
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/orig/97000-000017-000001.dcm
Identification
NumarisVer syngo MR B15
ScannerModel TrioTim
PatientName CON04_07172008
Date and time
StudyDate 20080717
StudyTime 082602.097000
SeriesTime 091538.382000
AcqTime 091309.512500
Acquisition parameters
PulseSeq ep_b0#1
Protocol DTI
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 84
InversionTime -1
RepetitionTime 9850
PhEncFOV 237
ReadoutFOV 237
Image information
RunNo 16
SeriesNo 17
ImageNo 1
NImageRows 1152
NImageCols 1152
NFrames 70
SliceArraylSize 79
IsMosaic 1
ImgPos 1042.7820 1078.5270 242.5410
VolRes 1.8516 1.8516 1.8500
VolDim 128 128 79
Vc -0.9997 -0.0232 -0.0095
Vr 0.0249 -0.9576 -0.2870
Vs -0.0024 -0.2872 0.9579
VolCenter 0.0000 0.0000 0.0000
TransferSyntaxUID 1.2.840.10008.1.2.1
INFO: sorting.
INFO: (128 128 79), nframes = 70, ismosaic=1
sdfi->UseSliceScaleFactor 0
datatype = 4, short=4, float=3
Could not parse NUMARIS version string syngo MR B15
found in dicom tag 18,1020 (len = 3 != 6)
Repetition Time = 9850, TR = 9850 ms
PE Dir COL COL
AutoAlign matrix detected
AutoAlign Matrix ---------------------
0.99969 -0.02379 0.00778 -0.14012;
0.02316 0.99706 0.07309 -9.34992;
-0.00949 -0.07288 0.99730 -12.79552;
0.00000 0.00000 0.00000 1.00000;
FileName
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/orig/97000-000017-000001.dcm
Identification
NumarisVer syngo MR B15
ScannerModel TrioTim
PatientName CON04_07172008
Date and time
StudyDate 20080717
StudyTime 082602.097000
SeriesTime 091538.382000
AcqTime 091309.512500
Acquisition parameters
PulseSeq ep_b0#1
Protocol DTI
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 84
InversionTime -1
RepetitionTime 9850
PhEncFOV 237
ReadoutFOV 237
Image information
RunNo 16
SeriesNo 17
ImageNo 1
NImageRows 1152
NImageCols 1152
NFrames 70
SliceArraylSize 79
IsMosaic 1
ImgPos 118.6930 148.7646 -38.5453
VolRes 1.8516 1.8516 1.8500
VolDim 128 128 79
Vc -0.9997 -0.0232 -0.0095
Vr 0.0249 -0.9576 -0.2870
Vs -0.0024 -0.2872 0.9579
VolCenter 3.0033 11.5602 -3.6840
TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
IsDWI = 1
sagrev = 0, correv =0, trarev = 0
Vs = -0.00244356 -0.287158 0.95788
INFO: no Siemens slice order reversal detected (good!).
TR=9850.00, TE=84.00, TI=-1.00, flip angle=90.00
i_ras = (-0.999687, -0.0231588, -0.00949289)
j_ras = (0.0249093, -0.957603, -0.287012)
k_ras = (-0.00244356, -0.287158, 0.95788)
writing to
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.nii.gz...
Saving bvals and bvecs
mv -f
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.voxel_space.bvecs
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.bvecs
mri_probedicom --i
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/orig/97000-000017-000001.dcm >
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dcminfo.dat
cp /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/orig/gradients.txt
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.bvecs
cp /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/orig/bvalues.txt
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.bvals
mv -f /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/bvecs.tmp
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.bvecs
mv -f /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/bvals.tmp
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.bvals
orientLAS /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.nii.gz
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig_las.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 6.34232
mri_convert -oni 128 -onj 128 -onk 79 -oid -0.999687 -0.0231588 -0.00949289
-ojd -0.0249093 0.957603 0.287012 -okd -0.00244356 -0.287158 0.95788 -oc
2.95721 13.3333 -3.15258 -rt nearest
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.nii.gz
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig_las.nii.gz
mri_convert.bin -oni 128 -onj 128 -onk 79 -oid -0.999687 -0.0231588 -0.00949289
-ojd -0.0249093 0.957603 0.287012 -okd -0.00244356 -0.287158 0.95788 -oc
2.95721 13.3333 -3.15258 -rt nearest
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.nii.gz
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig_las.nii.gz
normalizing out_i_direction: (-0.999687, -0.0231588, -0.00949289) ->
(-0.999687, -0.0231588, -0.00949289)
normalizing out_j_direction: (-0.0249093, 0.957603, 0.287012) -> (-0.0249093,
0.957603, 0.287012)
normalizing out_k_direction: (-0.00244356, -0.287158, 0.95788) -> (-0.00244356,
-0.287158, 0.95788)
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.nii.gz...
TR=9850.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999687, -0.0231588, -0.00949289)
j_ras = (0.0249093, -0.957603, -0.287012)
k_ras = (-0.00244356, -0.287158, 0.95788)
Reslicing using nearest
writing to
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig_las.nii.gz...
INFO: found
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.bvals, copying
INFO: found
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.bvecs,
converting to LAS
mv -f /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig_las.bvecs
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/bvecs
mv -f /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig_las.bvals
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/bvals
eddy_correct
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig_las.nii.gz
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi.nii.gz 0
processing INTEL
Image Exception : #63 :: No image files match: INTEL
Image Exception : #22 :: Failed to read volume INTEL
Error : No image files match: INTEL
Failed to read volume INTEL
Error : No image files match: INTEL
processing MKL
Image Exception : #63 :: No image files match: MKL
Image Exception : #22 :: Failed to read volume MKL
Error : No image files match: MKL
Failed to read volume MKL
Error : No image files match: MKL
processing ERROR:
Image Exception : #63 :: No image files match: ERROR:
Image Exception : #22 :: Failed to read volume ERROR:
Error : No image files match: ERROR:
Failed to read volume ERROR:
Error : No image files match: ERROR:
processing
/home1/jar269/fsl/fslpython/envs/fslpython/lib/python3.7/site-packages/numpy/core/../../../../libmkl_core.so:
Image Exception : #63 :: No image files match:
/home1/jar269/fsl/fslpython/envs/fslpython/lib/python3.7/site-packages/numpy/core/../../../../libmkl_core.so:
Image Exception : #22 :: Failed to read volume
/home1/jar269/fsl/fslpython/envs/fslpython/lib/python3.7/site-packages/numpy/core/../../../../libmkl_core.so:
Error : No image files match:
/home1/jar269/fsl/fslpython/envs/fslpython/lib/python3.7/site-packages/numpy/core/../../../../libmkl_core.so:
Failed to read volume
/home1/jar269/fsl/fslpython/envs/fslpython/lib/python3.7/site-packages/numpy/core/../../../../libmkl_core.so:
Error : No image files match:
/home1/jar269/fsl/fslpython/envs/fslpython/lib/python3.7/site-packages/numpy/core/../../../../libmkl_core.so:
processing undefined
Image Exception : #63 :: No image files match: undefined
Image Exception : #22 :: Failed to read volume undefined
Error : No image files match: undefined
Failed to read volume undefined
Error : No image files match: undefined
processing symbol:
Image Exception : #63 :: No image files match: symbol:
Image Exception : #22 :: Failed to read volume symbol:
Error : No image files match: symbol:
Failed to read volume symbol:
Error : No image files match: symbol:
processing mkl_pds_lp64_pds_sym_indef_bk_fct_slv_c_seq_nrhs_cmplx.
Image Exception : #63 :: No image files match:
mkl_pds_lp64_pds_sym_indef_bk_fct_slv_c_seq_nrhs_cmplx.
Image Exception : #22 :: Failed to read volume
mkl_pds_lp64_pds_sym_indef_bk_fct_slv_c_seq_nrhs_cmplx.
Error : No image files match:
mkl_pds_lp64_pds_sym_indef_bk_fct_slv_c_seq_nrhs_cmplx.
Failed to read volume mkl_pds_lp64_pds_sym_indef_bk_fct_slv_c_seq_nrhs_cmplx.
Error : No image files match:
mkl_pds_lp64_pds_sym_indef_bk_fct_slv_c_seq_nrhs_cmplx.
processing Intel
Image Exception : #63 :: No image files match: Intel
Image Exception : #22 :: Failed to read volume Intel
Error : No image files match: Intel
Failed to read volume Intel
Error : No image files match: Intel
processing MKL
Image Exception : #63 :: No image files match: MKL
Image Exception : #22 :: Failed to read volume MKL
Error : No image files match: MKL
Failed to read volume MKL
Error : No image files match: MKL
processing FATAL
Image Exception : #63 :: No image files match: FATAL
Image Exception : #22 :: Failed to read volume FATAL
Error : No image files match: FATAL
Failed to read volume FATAL
Error : No image files match: FATAL
processing ERROR:
Image Exception : #63 :: No image files match: ERROR:
Image Exception : #22 :: Failed to read volume ERROR:
Error : No image files match: ERROR:
Failed to read volume ERROR:
Error : No image files match: ERROR:
processing Cannot
Image Exception : #63 :: No image files match: Cannot
Image Exception : #22 :: Failed to read volume Cannot
Error : No image files match: Cannot
Failed to read volume Cannot
Error : No image files match: Cannot
processing load
Image Exception : #63 :: No image files match: load
Image Exception : #22 :: Failed to read volume load
Error : No image files match: load
Failed to read volume load
Error : No image files match: load
processing libmkl_core.so.
Image Exception : #63 :: No image files match: libmkl_core.so.
Image Exception : #22 :: Failed to read volume libmkl_core.so.
Error : No image files match: libmkl_core.so.
Failed to read volume libmkl_core.so.
Error : No image files match: libmkl_core.so.
Image Exception : #63 :: No image files match: INTEL
terminate called after throwing an instance of 'std::runtime_error'
what(): No image files match: INTEL
/home1/jar269/fsl/bin/eddy_correct: line 103: 13578 Aborted
(core dumped) fslmerge -t $output $full_list
mv -f /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/bvecs
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/bvecs.norot
xfmrot /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi.ecclog
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/bvecs.norot
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/bvecs
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R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
ln -sf /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi.nii.gz
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/data.nii.gz
mri_convert --frame 0 1 2 3 4 5 6 7 8 9
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi.nii.gz
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/lowb.nii.gz
mri_convert.bin --frame 0 1 2 3 4 5 6 7 8 9
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi.nii.gz
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/lowb.nii.gz
niiRead(): error opening file
/home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi.nii.gz...
Linux librapet.med.yale.edu<http://librapet.med.yale.edu>
3.10.0-693.5.2.el7.x86_64 #1 SMP Fri Oct 20 20:32:50 UTC 2017 x86_64 x86_64
x86_64 GNU/Linux
trac-preproc exited with ERRORS at Sun Jul 12 14:29:05 EDT 2020
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