External Email - Use Caution
Hello,
I am still trying to run dt_recon and am having issues.
The code I am running is attached...and an abbreviated version is below.
foreach subj (`ls -d /Volumes/DANIEL/AES101 | sed 's/// /g' | awk '{print $3}'`)
foreach cond (Ex Rest)
echo "subj = " ${subj} ", cond = " ${cond}
cd /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/
mri_convert image000001.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/dwi.nii.gz
dt_recon --sd /Volumes/DANIEL/tutorial_data/diffusion_recons/ --i /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/image000001.dcm --s ${subj}.${cond} --b dwi.bvals dwi.voxel_space.bvecs --o /Volumes/DANIEL/tutorial_data/dtrecon/${subj}.${cond}.
and the following is the output and errors I am getting from running the above code. I have also attached a screenshot of the path and folder with the various file inputs and outputs.
subj = AES101 , cond = Ex
mkdir: /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex: File exists
mri_convert.bin image000001.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/dwi.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from image000001.dcm...
Getting Series No
Scanning Directory
INFO: Found 71 files in /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex
INFO: Scanning for Series Number 171
INFO: found 65 files in series
INFO: loading series header info.
INFO: sorting.
RunNo = 170
WARNING: Run 1 appears to be truncated
Files Found: 65, Files Expected (lRep+1): 1
FileName /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm
Identification
NumarisVer syngo MR B17
ScannerModel TrioTim
PatientName AES101
Date and time
StudyDate 20170409
StudyTime 105710.343000
SeriesTime 120657.984000
AcqTime 120650.230000
Acquisition parameters
PulseSeq *ep_b0
Protocol ep2d_diff_mddw_D64
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 106
InversionTime -1
RepetitionTime 6300
PhEncFOV 210
ReadoutFOV 210
Image information
RunNo 170
SeriesNo 171
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 65
SliceArraylSize 35
IsMosaic 1
ImgPos 630.8714 646.6747 -31.8394
VolRes 1.6406 1.6406 3.6000
VolDim 128 128 35
Vc -1.0000 -0.0000 0.0000
Vr -0.0000 -1.0000 0.0000
Vs -0.0000 -0.0000 1.0000
VolCenter 0.0000 0.0000 0.0000
TransferSyntaxUID 1.2.840.10008.1.2.1
INFO: (128 128 35), nframes = 65, ismosaic=1
sdfi->UseSliceScaleFactor 0
datatype = 4, short=4, float=3
Could not parse NUMARIS version string syngo MR B17
found in dicom tag 18,1020 (len = 3 != 6)
Repetition Time = 6300, TR = 6300 ms
PE Dir COL COL
AutoAlign matrix detected
AutoAlign Matrix ---------------------
1.00000 0.00000 0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000;
0.00000 0.00000 1.00000 0.00000;
0.00000 0.00000 0.00000 1.00000;
FileName /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm
Identification
NumarisVer syngo MR B17
ScannerModel TrioTim
PatientName AES101
Date and time
StudyDate 20170409
StudyTime 105710.343000
SeriesTime 120657.984000
AcqTime 120650.230000
Acquisition parameters
PulseSeq *ep_b0
Protocol ep2d_diff_mddw_D64
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 106
InversionTime -1
RepetitionTime 6300
PhEncFOV 210
ReadoutFOV 210
Image information
RunNo 170
SeriesNo 171
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 65
SliceArraylSize 35
IsMosaic 1
ImgPos 105.8714 121.6747 -31.8394
VolRes 1.6406 1.6406 3.6000
VolDim 128 128 35
Vc -1.0000 -0.0000 0.0000
Vr -0.0000 -1.0000 0.0000
Vs -0.0000 -0.0000 1.0000
VolCenter 0.8714 16.6747 31.1606
TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
IsDWI = 1
sagrev = 0, correv =0, trarev = 0
Vs = -0 -0 1
INFO: no Siemens slice order reversal detected (good!).
TR=6300.00, TE=106.00, TI=-1.00, flip angle=90.00
i_ras = (-1, -0, 0)
j_ras = (-0, -1, 0)
k_ras = (-0, -0, 1)
writing to /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/dwi.nii.gz...
Saving bvals and bvecs
-rwxrwxrwx 1 administrator staff 1276058 Feb 18 10:18 /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm
INFO: SUBJECTS_DIR is /Volumes/DANIEL/tutorial_data/diffusion_recons/
dt_recon logfile
Mon Feb 18 10:19:18 EST 2019
VERSION $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
setenv SUBJECTS_DIR /Volumes/DANIEL/tutorial_data/diffusion_recons/
cd /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex
/Applications/freesurfer//bin/dt_recon --sd /Volumes/DANIEL/tutorial_data/diffusion_recons/ --i /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm --s AES101.Ex --b dwi.bvals dwi.voxel_space.bvecs --o /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex.
hlhp-105.umd.edu
administrator
/usr/local/fsl/bin/eddy_correct
ECRefTP 0
#@#-------------------------------
Converting input
Mon Feb 18 10:19:18 EST 2019
cd /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex
mri_convert /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii
mri_convert.bin /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm...
Getting Series No
INFO: Found 71 files in /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex
INFO: Scanning for Series Number 171
Scanning Directory
INFO: found 65 files in series
INFO: loading series header info.
RunNo = 170
WARNING: Run 1 appears to be truncated
Files Found: 65, Files Expected (lRep+1): 1
FileName /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm
Identification
NumarisVer syngo MR B17
ScannerModel TrioTim
PatientName AES101
Date and time
StudyDate 20170409
StudyTime 105710.343000
SeriesTime 120657.984000
AcqTime 120650.230000
Acquisition parameters
PulseSeq *ep_b0
Protocol ep2d_diff_mddw_D64
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 106
InversionTime -1
RepetitionTime 6300
PhEncFOV 210
ReadoutFOV 210
Image information
RunNo 170
SeriesNo 171
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 65
SliceArraylSize 35
IsMosaic 1
ImgPos 630.8714 646.6747 -31.8394
VolRes 1.6406 1.6406 3.6000
VolDim 128 128 35
Vc -1.0000 -0.0000 0.0000
Vr -0.0000 -1.0000 0.0000
Vs -0.0000 -0.0000 1.0000
VolCenter 0.0000 0.0000 0.0000
TransferSyntaxUID 1.2.840.10008.1.2.1
INFO: sorting.
INFO: (128 128 35), nframes = 65, ismosaic=1
sdfi->UseSliceScaleFactor 0
datatype = 4, short=4, float=3
Could not parse NUMARIS version string syngo MR B17
found in dicom tag 18,1020 (len = 3 != 6)
Repetition Time = 6300, TR = 6300 ms
PE Dir COL COL
AutoAlign matrix detected
AutoAlign Matrix ---------------------
1.00000 0.00000 0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000;
0.00000 0.00000 1.00000 0.00000;
0.00000 0.00000 0.00000 1.00000;
FileName /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm
Identification
NumarisVer syngo MR B17
ScannerModel TrioTim
PatientName AES101
Date and time
StudyDate 20170409
StudyTime 105710.343000
SeriesTime 120657.984000
AcqTime 120650.230000
Acquisition parameters
PulseSeq *ep_b0
Protocol ep2d_diff_mddw_D64
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 106
InversionTime -1
RepetitionTime 6300
PhEncFOV 210
ReadoutFOV 210
Image information
RunNo 170
SeriesNo 171
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 65
SliceArraylSize 35
IsMosaic 1
ImgPos 105.8714 121.6747 -31.8394
VolRes 1.6406 1.6406 3.6000
VolDim 128 128 35
Vc -1.0000 -0.0000 0.0000
Vr -0.0000 -1.0000 0.0000
Vs -0.0000 -0.0000 1.0000
VolCenter 0.8714 16.6747 31.1606
TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
IsDWI = 1
sagrev = 0, correv =0, trarev = 0
Vs = -0 -0 1
INFO: no Siemens slice order reversal detected (good!).
TR=6300.00, TE=106.00, TI=-1.00, flip angle=90.00
i_ras = (-1, -0, 0)
j_ras = (-0, -1, 0)
k_ras = (-0, -0, 1)
writing to /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii...
Saving bvals and bvecs
#@#-------------------------------
Eddy/Motion Correct
Mon Feb 18 10:19:30 EST 2019
cd /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./ectmp
eddy_correct /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii 0
Image Exception : #61 :: Multiple possible filenames detected for basename: /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi
Multiple possible filenames detected for basename: /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi
Image Exception : #61 :: Multiple possible filenames detected for basename: /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi
libc++abi.dylib: terminating with uncaught exception of type armawrap::AWException: Multiple possible filenames detected for basename: /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi
/usr/local/fsl/bin/eddy_correct: line 94: 64175 Abort trap: 6 fslsplit $input ${output}_tmp
Usage: fslmerge <-x/y/z/t/a/tr> <output> <file1 file2 .......> [tr value in seconds]
-t : concatenate images in time
-x : concatenate images in the x direction
-y : concatenate images in the y direction
-z : concatenate images in the z direction
-a : auto-choose: single slices -> volume, volumes -> 4D (time series)
-tr : concatenate images in time and set the output image tr to the final option value
rm: /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp????.*: No such file or directory
rm: /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_ref*: No such file or directory
Any help you could provide for trouble shooting the issue would be greatly appreciated!
Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park dcallow@umd.edu dcallow@gmail.com 443-254-6298
External Email - Use Caution
When performing the above command on a different subject with the same files I get a slightly different error...
subj = AES101 , cond = Rest
mkdir: /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Rest: File exists
mri_convert.bin image000001.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Rest/dwi.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from image000001.dcm...
Getting Series No
Scanning Directory
INFO: Found 68 files in /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Rest
INFO: Scanning for Series Number 171
INFO: found 65 files in series
INFO: loading series header info.
INFO: sorting.
RunNo = 170
WARNING: Run 1 appears to be truncated
Files Found: 65, Files Expected (lRep+1): 1
FileName /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Rest/image000001.dcm
Identification
NumarisVer syngo MR B17
ScannerModel TrioTim
PatientName AES101
Date and time
StudyDate 20170402
StudyTime 104810.015000
SeriesTime 120532.312000
AcqTime 120524.237500
Acquisition parameters
PulseSeq *ep_b0
Protocol ep2d_diff_mddw_D64
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 106
InversionTime -1
RepetitionTime 6300
PhEncFOV 210
ReadoutFOV 210
Image information
RunNo 170
SeriesNo 171
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 65
SliceArraylSize 35
IsMosaic 1
ImgPos 631.7400 647.7831 -33.5438
VolRes 1.6406 1.6406 3.6000
VolDim 128 128 35
Vc -1.0000 -0.0000 0.0000
Vr -0.0000 -1.0000 0.0000
Vs -0.0000 -0.0000 1.0000
VolCenter 0.0000 0.0000 0.0000
TransferSyntaxUID 1.2.840.10008.1.2.1
INFO: (128 128 35), nframes = 65, ismosaic=1
sdfi->UseSliceScaleFactor 0
datatype = 4, short=4, float=3
Could not parse NUMARIS version string syngo MR B17
found in dicom tag 18,1020 (len = 3 != 6)
Repetition Time = 6300, TR = 6300 ms
PE Dir COL COL
AutoAlign matrix detected
AutoAlign Matrix ---------------------
1.00000 0.00000 0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000;
0.00000 0.00000 1.00000 0.00000;
0.00000 0.00000 0.00000 1.00000;
FileName /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Rest/image000001.dcm
Identification
NumarisVer syngo MR B17
ScannerModel TrioTim
PatientName AES101
Date and time
StudyDate 20170402
StudyTime 104810.015000
SeriesTime 120532.312000
AcqTime 120524.237500
Acquisition parameters
PulseSeq *ep_b0
Protocol ep2d_diff_mddw_D64
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 106
InversionTime -1
RepetitionTime 6300
PhEncFOV 210
ReadoutFOV 210
Image information
RunNo 170
SeriesNo 171
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 65
SliceArraylSize 35
IsMosaic 1
ImgPos 106.7400 122.7831 -33.5438
VolRes 1.6406 1.6406 3.6000
VolDim 128 128 35
Vc -1.0000 -0.0000 0.0000
Vr -0.0000 -1.0000 0.0000
Vs -0.0000 -0.0000 1.0000
VolCenter 1.7400 17.7831 29.4562
TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
IsDWI = 1
sagrev = 0, correv =0, trarev = 0
Vs = -0 -0 1
INFO: no Siemens slice order reversal detected (good!).
TR=6300.00, TE=106.00, TI=-1.00, flip angle=90.00
i_ras = (-1, -0, 0)
j_ras = (-0, -1, 0)
k_ras = (-0, -0, 1)
writing to /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Rest/dwi.nii.gz...
Saving bvals and bvecs
-rwxrwxrwx 1 administrator staff 1276090 Feb 18 10:19 /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Rest/image000001.dcm
INFO: SUBJECTS_DIR is /Volumes/DANIEL/tutorial_data/diffusion_recons/
dt_recon logfile
Mon Feb 18 10:20:05 EST 2019
VERSION $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
setenv SUBJECTS_DIR /Volumes/DANIEL/tutorial_data/diffusion_recons/
cd /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Rest
/Applications/freesurfer//bin/dt_recon --sd /Volumes/DANIEL/tutorial_data/diffusion_recons/ --i /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Rest/image000001.dcm --s AES101.Rest --b dwi.bvals dwi.voxel_space.bvecs --o /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest.
hlhp-105.umd.edu
administrator
/usr/local/fsl/bin/eddy_correct
ECRefTP 0
#@#-------------------------------
Converting input
Mon Feb 18 10:20:05 EST 2019
cd /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Rest
mri_convert /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Rest/image000001.dcm /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi.nii
mri_convert.bin /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Rest/image000001.dcm /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Rest/image000001.dcm...
Getting Series No
INFO: Found 71 files in /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Rest
INFO: Scanning for Series Number 171
Scanning Directory
INFO: found 65 files in series
INFO: loading series header info.
RunNo = 170
WARNING: Run 1 appears to be truncated
Files Found: 65, Files Expected (lRep+1): 1
FileName /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Rest/image000001.dcm
Identification
NumarisVer syngo MR B17
ScannerModel TrioTim
PatientName AES101
Date and time
StudyDate 20170402
StudyTime 104810.015000
SeriesTime 120532.312000
AcqTime 120524.237500
Acquisition parameters
PulseSeq *ep_b0
Protocol ep2d_diff_mddw_D64
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 106
InversionTime -1
RepetitionTime 6300
PhEncFOV 210
ReadoutFOV 210
Image information
RunNo 170
SeriesNo 171
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 65
SliceArraylSize 35
IsMosaic 1
ImgPos 631.7400 647.7831 -33.5438
VolRes 1.6406 1.6406 3.6000
VolDim 128 128 35
Vc -1.0000 -0.0000 0.0000
Vr -0.0000 -1.0000 0.0000
Vs -0.0000 -0.0000 1.0000
VolCenter 0.0000 0.0000 0.0000
TransferSyntaxUID 1.2.840.10008.1.2.1
INFO: sorting.
INFO: (128 128 35), nframes = 65, ismosaic=1
sdfi->UseSliceScaleFactor 0
datatype = 4, short=4, float=3
Could not parse NUMARIS version string syngo MR B17
found in dicom tag 18,1020 (len = 3 != 6)
Repetition Time = 6300, TR = 6300 ms
PE Dir COL COL
AutoAlign matrix detected
AutoAlign Matrix ---------------------
1.00000 0.00000 0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000;
0.00000 0.00000 1.00000 0.00000;
0.00000 0.00000 0.00000 1.00000;
FileName /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Rest/image000001.dcm
Identification
NumarisVer syngo MR B17
ScannerModel TrioTim
PatientName AES101
Date and time
StudyDate 20170402
StudyTime 104810.015000
SeriesTime 120532.312000
AcqTime 120524.237500
Acquisition parameters
PulseSeq *ep_b0
Protocol ep2d_diff_mddw_D64
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 106
InversionTime -1
RepetitionTime 6300
PhEncFOV 210
ReadoutFOV 210
Image information
RunNo 170
SeriesNo 171
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 65
SliceArraylSize 35
IsMosaic 1
ImgPos 106.7400 122.7831 -33.5438
VolRes 1.6406 1.6406 3.6000
VolDim 128 128 35
Vc -1.0000 -0.0000 0.0000
Vr -0.0000 -1.0000 0.0000
Vs -0.0000 -0.0000 1.0000
VolCenter 1.7400 17.7831 29.4562
TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
IsDWI = 1
sagrev = 0, correv =0, trarev = 0
Vs = -0 -0 1
INFO: no Siemens slice order reversal detected (good!).
TR=6300.00, TE=106.00, TI=-1.00, flip angle=90.00
i_ras = (-1, -0, 0)
j_ras = (-0, -1, 0)
k_ras = (-0, -0, 1)
writing to /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi.nii...
Saving bvals and bvecs
#@#-------------------------------
Eddy/Motion Correct
Mon Feb 18 10:20:17 EST 2019
cd /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./ectmp
eddy_correct /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi.nii /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec.nii 0
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0000
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0001
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0002
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0003
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0004
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0005
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0006
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0007
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0008
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0009
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0010
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0011
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0012
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0013
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0014
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0015
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0016
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0017
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0018
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0019
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0020
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0021
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0022
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0023
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0024
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0025
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0026
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0027
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0028
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0029
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0030
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0031
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0032
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0033
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0034
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0035
./dt_recon.sh
subj = AES101 , cond = Ex
mkdir: /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex: File exists
mri_convert.bin image000001.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/dwi.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from image000001.dcm...
Getting Series No
Scanning Directory
INFO: Found 71 files in /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex
INFO: Scanning for Series Number 171
INFO: found 65 files in series
INFO: loading series header info.
INFO: sorting.
RunNo = 170
WARNING: Run 1 appears to be truncated
Files Found: 65, Files Expected (lRep+1): 1
FileName /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm
Identification
NumarisVer syngo MR B17
ScannerModel TrioTim
PatientName AES101
Date and time
StudyDate 20170409
StudyTime 105710.343000
SeriesTime 120657.984000
AcqTime 120650.230000
Acquisition parametprocessing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0036
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0037
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0038
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0039
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0040
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0041
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0042
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0043
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0044
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0045
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0046
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0047
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0048
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0049
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0050
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0051
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0052
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0053
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0054
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0055
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0056
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0057
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0058
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0059
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0060
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0061
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0062
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0063
processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec_tmp0064
#@#-------------------------------
Fitting Tensors
Mon Feb 18 10:29:31 EST 2019
gzip /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi.nii
gzip /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec.nii
cd /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Rest
mri_glmfit --y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec.nii.gz --glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest. --dti dwi.bvals dwi.voxel_space.bvecs
$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
cwd /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Rest
cmdline mri_glmfit.bin --y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec.nii.gz --glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest. --dti dwi.bvals dwi.voxel_space.bvecs
sysname Darwin
hostname hlhp-105.umd.edu
machine x86_64
user administrator
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec.nii.gz
logyflag 1
usedti 1
glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest.
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest.
Loading y from /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./dwi-ec.nii.gz
... done reading.
Using DTI
Loading BValues from dwi.bvals
Found 65 bvalues
Loading BVectors from dwi.voxel_space.bvecs
Found 65 bvectorss
Detected BVec file as MGH formatted
Saving design matrix to /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./Xg.dat
Computing normalized matrix
Normalized matrix condition is 275.544
Matrix condition is 2.14029e+07
Pruning voxels by thr: 1.175494e-38
Found 163931 voxels in mask
Saving mask to /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./mask.nii.gz
search space = 1588481.750000
Computing natural log of input
DOF = 58
Starting fit and test
Fit completed in 0.1058 minutes
Writing results
Saving DTI Analysis
Computing fa
Computing ra
Computing vr
Computing radial diffusivity
Computing adc
Computing ivc
Computing dwisynth
Computing dwires
Computing dwi rvar
mri_glmfit done
#@#-------------------------------
Registration
Mon Feb 18 10:30:08 EST 2019
setenv SUBJECTS_DIR /Volumes/DANIEL/tutorial_data/diffusion_recons/
cd /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Rest
bbregister --s AES101.Rest --mov /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./lowb.nii.gz --init-fsl --lta /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./register.lta --bold
tmp /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./tmp.bbregister.64570
Log file is /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./register.dat.log
Mon Feb 18 10:30:09 EST 2019
setenv SUBJECTS_DIR /Volumes/DANIEL/tutorial_data/diffusion_recons/
cd /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Rest
/Applications/freesurfer//bin/bbregister --s AES101.Rest --mov /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./lowb.nii.gz --init-fsl --lta /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./register.lta --bold
$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
Darwin hlhp-105.umd.edu 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 10 20:06:00 PDT 2018; root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64
FREESURFER_HOME /Applications/freesurfer/
mri_convert /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./lowb.nii.gz /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./tmp.bbregister.64570/template.nii
mri_convert.bin /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./lowb.nii.gz /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./tmp.bbregister.64570/template.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./lowb.nii.gz...
TR=6300.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, -1, 0)
k_ras = (0, 0, 1)
writing to /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./tmp.bbregister.64570/template.nii...
fslregister --s AES101.Rest --mov /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./tmp.bbregister.64570/template.nii --reg /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./tmp.bbregister.64570/reg.init.dat --niters 1 --maxangle 90 --tmp /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./tmp.bbregister.64570/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov
Log file is /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./tmp.bbregister.64570/reg.init.dat.fslregister.log
Mon Feb 18 10:30:09 EST 2019
--s AES101.Rest --mov /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./tmp.bbregister.64570/template.nii --reg /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./tmp.bbregister.64570/reg.init.dat --niters 1 --maxangle 90 --tmp /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Rest./tmp.bbregister.64570/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov
$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
hlhp-105.umd.edu
Darwin hlhp-105.umd.edu 16.7.0 Darwin Kernel Version 16.7.0: Wed Oct 10 20:06:00 PDT 2018; root:xnu-3789.73.24~1/RELEASE_X86_64 x86_64
nIters 1
ERROR: cannot find /Volumes/DANIEL/tutorial_data/diffusion_recons//AES101.Rest/mri/brainmask
[hlhp-105:DANIEL/scripts/dti_freesurfer] administrator% p_b0
Protocol ./dt_recon.sh
subj = AES101 , cond = Ex
mkdir: /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex: File exists
mri_convert.bin image000001.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/dwi.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from image000001.dcm...
Getting Series No
Scanning Directory
INFO: Found 71 files in /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex
INFO: Scanning for Series Number 171
INFO: found 65 files in series
INFO: loading series header info.
INFO: sorting.
RunNo = 170
WARNING: Run 1 appears to be truncated
Files Found: 65, Files Expected (lRep+1): 1
FileName /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm
Identification
NumarisVer syngo MR B17
ScannerModel TrioTim
PatientName AES101
Date and time
StudyDate 20170409
StudyTime 105710.343000
SeriesTime 120657.984000
AcqTime 120650.230000
Acquisition parameters
PulseSeq *ep_b0
Protocol ep2d_diff_mddw_D64
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 106
InversionTime -1
RepetitionTime 6300
PhEncFOV 210
ReadoutFOV 210
Image information
RunNo 170
SeriesNo 171
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 65
SliceArraylSize 35
IsMosaic 1
ImgPos 630.8714 646.6747 -31.8394
VolRes 1.6406 1.6406 3.6000
VolDim 128 128 35
Vc -1.0000 -0.0000 0.0000
Vr -0.0000 -1.0000 0.0000
Vs -0.0000 -0.0000 1.0000
VolCenter 0.0000 0.0000 0.0000
TransferSyntaxUID 1.2.840.10008.1.2.1
INFO: (128 128 35), nframes = 65, ismosaic=1
sdfi->UseSliceScaleFactor 0
datatype = 4, short=4, float=3
Could not parse NUMARIS version string syngo MR B17
found in dicom tag 18,1020 (len = 3 != 6)
Repetition Time = 6300, TR = 6300 ms
PE Dir COL COL
AutoAlign matrix detected
AutoAlign Matrix ---------------------
1.00000 0.00000 0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000;
0.00000 0.00000 1.00000 0.00000;
0.00000 0.00000 0.00000 1.00000;
FileName /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm
Identification
NumarisVer syngo MR B17
ScannerModel TrioTim
PatientName AES101
Date and time
StudyDate 20170409
StudyTime 105710.343000
SeriesTime 120657.984000
AcqTime 120650.230000
Acquisition parameters
PulseSeq *ep_b0
Protocol ep2d_diff_mddw_D64
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 106
InversionTime -1
RepetitionTime 6300
PhEncFOV 210
ReadoutFOV 210
Image information
RunNo 170
SeriesNo 171
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 65
SliceArraylSize 35
IsMosaic 1
ImgPos 105.8714 121.6747 -31.8394
VolRes 1.6406 1.6406 3.6000
VolDim 128 128 35
Vc -1.0000 -0.0000 0.0000
Vr -0.0000 -1.0000 0.0000
Vs -0.0000 -0.0000 1.0000
VolCenter 0.8714 16.6747 31.1606
TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
IsDWI = 1
sagrev = 0, correv =0, trarev = 0
Vs = -0 -0 1
INFO: no Siemens slice order reversal detected (good!).
TR=6300.00, TE=106.00, TI=-1.00, flip angle=90.00
i_ras = (-1, -0, 0)
j_ras = (-0, -1, 0)
k_ras = (-0, -0, 1)
writing to /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/dwi.nii.gz...
Saving bvals and bvecs
-rwxrwxrwx 1 administrator staff 1276058 Feb 18 10:30 /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm
INFO: SUBJECTS_DIR is /Volumes/DANIEL/tutorial_data/diffusion_recons/
dt_recon logfile
Mon Feb 18 10:30:36 EST 2019
VERSION $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
setenv SUBJECTS_DIR /Volumes/DANIEL/tutorial_data/diffusion_recons/
cd /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex
/Applications/freesurfer//bin/dt_recon --sd /Volumes/DANIEL/tutorial_data/diffusion_recons/ --i /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm --s AES101.Ex --b dwi.bvals dwi.voxel_space.bvecs --o /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex.
hlhp-105.umd.edu
administrator
/usr/local/fsl/bin/eddy_correct
ECRefTP 0
#@#-------------------------------
Converting input
Mon Feb 18 10:30:36 EST 2019
cd /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex
mri_convert /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii
mri_convert.bin /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm...
Getting Series No
INFO: Found 71 files in /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex
INFO: Scanning for Series Number 171
Scanning Directory
INFO: found 65 files in series
INFO: loading series header info.
RunNo = 170
WARNING: Run 1 appears to be truncated
Files Found: 65, Files Expected (lRep+1): 1
FileName /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm
Identification
NumarisVer syngo MR B17
ScannerModel TrioTim
PatientName AES101
Date and time
StudyDate 20170409
StudyTime 105710.343000
SeriesTime 120657.984000
AcqTime 120650.230000
Acquisition parameters
PulseSeq *ep_b0
Protocol ep2d_diff_mddw_D64
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 106
InversionTime -1
RepetitionTime 6300
PhEncFOV 210
ReadoutFOV 210
Image information
RunNo 170
SeriesNo 171
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 65
SliceArraylSize 35
IsMosaic 1
ImgPos 630.8714 646.6747 -31.8394
VolRes 1.6406 1.6406 3.6000
VolDim 128 128 35
Vc -1.0000 -0.0000 0.0000
Vr -0.0000 -1.0000 0.0000
Vs -0.0000 -0.0000 1.0000
VolCenter 0.0000 0.0000 0.0000
TransferSyntaxUID 1.2.840.10008.1.2.1
INFO: sorting.
INFO: (128 128 35), nframes = 65, ismosaic=1
sdfi->UseSliceScaleFactor 0
datatype = 4, short=4, float=3
Could not parse NUMARIS version string syngo MR B17
found in dicom tag 18,1020 (len = 3 != 6)
Repetition Time = 6300, TR = 6300 ms
PE Dir COL COL
AutoAlign matrix detected
AutoAlign Matrix ---------------------
1.00000 0.00000 0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000;
0.00000 0.00000 1.00000 0.00000;
0.00000 0.00000 0.00000 1.00000;
FileName /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm
Identification
NumarisVer syngo MR B17
ScannerModel TrioTim
PatientName AES101
Date and time
StudyDate 20170409
StudyTime 105710.343000
SeriesTime 120657.984000
AcqTime 120650.230000
Acquisition parameters
PulseSeq *ep_b0
Protocol ep2d_diff_mddw_D64
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 106
InversionTime -1
RepetitionTime 6300
PhEncFOV 210
ReadoutFOV 210
Image information
RunNo 170
SeriesNo 171
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 65
SliceArraylSize 35
IsMosaic 1
ImgPos 105.8714 121.6747 -31.8394
VolRes 1.6406 1.6406 3.6000
VolDim 128 128 35
Vc -1.0000 -0.0000 0.0000
Vr -0.0000 -1.0000 0.0000
Vs -0.0000 -0.0000 1.0000
VolCenter 0.8714 16.6747 31.1606
TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
IsDWI = 1
sagrev = 0, correv =0, trarev = 0
Vs = -0 -0 1
INFO: no Siemens slice order reversal detected (good!).
TR=6300.00, TE=106.00, TI=-1.00, flip angle=90.00
i_ras = (-1, -0, 0)
j_ras = (-0, -1, 0)
k_ras = (-0, -0, 1)
writing to /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii...
Saving bvals and bvecs
#@#-------------------------------
Eddy/Motion Correct
Mon Feb 18 10:30:48 EST 2019
cd /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./ectmp
eddy_correct /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii 0
Image Exception : #61 :: Multiple possible filenames detected for basename: /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi
Multiple possible filenames detected for basename: /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi
Image Exception : #61 :: Multiple possible filenames detected for basename: /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi
libc++abi.dylib: terminating with uncaught exception of type armawrap::AWException: Multiple possible filenames detected for basename: /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi
/usr/local/fsl/bin/eddy_correct: line 94: 64863 Abort trap: 6 fslsplit $input ${output}_tmp
Usage: fslmerge <-x/y/z/t/a/tr> <output> <file1 file2 .......> [tr value in seconds]
-t : concatenate images in time
-x : concatenate images in the x direction
-y : concatenate images in the y direction
-z : concatenate images in the z direction
-a : auto-choose: single slices -> volume, volumes -> 4D (time series)
-tr : concatenate images in time and set the output image tr to the final option value
Does anyone have an idea of why I am getting this error as well?
Thank you, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park dcallow@umd.edu dcallow@gmail.com 443-254-6298
On Mon, Feb 18, 2019 at 10:36 AM Daniel Davidson Callow dcallow@umd.edu wrote:
Hello,
I am still trying to run dt_recon and am having issues.
The code I am running is attached...and an abbreviated version is below.
foreach subj (`ls -d /Volumes/DANIEL/AES101 | sed 's/// /g' | awk '{print $3}'`)
foreach cond (Ex Rest)
echo "subj = " ${subj} ", cond = " ${cond}
cd /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/
mri_convert image000001.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/dwi.nii.gz
dt_recon --sd /Volumes/DANIEL/tutorial_data/diffusion_recons/ --i /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/image000001.dcm --s ${subj}.${cond} --b dwi.bvals dwi.voxel_space.bvecs --o /Volumes/DANIEL/tutorial_data/dtrecon/${subj}.${cond}.
and the following is the output and errors I am getting from running the above code. I have also attached a screenshot of the path and folder with the various file inputs and outputs.
subj = AES101 , cond = Ex
mkdir: /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex: File exists
mri_convert.bin image000001.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/dwi.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from image000001.dcm...
Getting Series No
Scanning Directory
INFO: Found 71 files in /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex
INFO: Scanning for Series Number 171
INFO: found 65 files in series
INFO: loading series header info.
INFO: sorting.
RunNo = 170
WARNING: Run 1 appears to be truncated
Files Found: 65, Files Expected (lRep+1): 1
FileName /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm
Identification
NumarisVer syngo MR B17
ScannerModel TrioTim
PatientName AES101
Date and time
StudyDate 20170409
StudyTime 105710.343000
SeriesTime 120657.984000
AcqTime 120650.230000
Acquisition parameters
PulseSeq *ep_b0
Protocol ep2d_diff_mddw_D64
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 106
InversionTime -1
RepetitionTime 6300
PhEncFOV 210
ReadoutFOV 210
Image information
RunNo 170
SeriesNo 171
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 65
SliceArraylSize 35
IsMosaic 1
ImgPos 630.8714 646.6747 -31.8394
VolRes 1.6406 1.6406 3.6000
VolDim 128 128 35
Vc -1.0000 -0.0000 0.0000
Vr -0.0000 -1.0000 0.0000
Vs -0.0000 -0.0000 1.0000
VolCenter 0.0000 0.0000 0.0000
TransferSyntaxUID 1.2.840.10008.1.2.1
INFO: (128 128 35), nframes = 65, ismosaic=1
sdfi->UseSliceScaleFactor 0
datatype = 4, short=4, float=3
Could not parse NUMARIS version string syngo MR B17
found in dicom tag 18,1020 (len = 3 != 6)
Repetition Time = 6300, TR = 6300 ms
PE Dir COL COL
AutoAlign matrix detected
AutoAlign Matrix ---------------------
1.00000 0.00000 0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000;
0.00000 0.00000 1.00000 0.00000;
0.00000 0.00000 0.00000 1.00000;
FileName /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm
Identification
NumarisVer syngo MR B17
ScannerModel TrioTim
PatientName AES101
Date and time
StudyDate 20170409
StudyTime 105710.343000
SeriesTime 120657.984000
AcqTime 120650.230000
Acquisition parameters
PulseSeq *ep_b0
Protocol ep2d_diff_mddw_D64
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 106
InversionTime -1
RepetitionTime 6300
PhEncFOV 210
ReadoutFOV 210
Image information
RunNo 170
SeriesNo 171
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 65
SliceArraylSize 35
IsMosaic 1
ImgPos 105.8714 121.6747 -31.8394
VolRes 1.6406 1.6406 3.6000
VolDim 128 128 35
Vc -1.0000 -0.0000 0.0000
Vr -0.0000 -1.0000 0.0000
Vs -0.0000 -0.0000 1.0000
VolCenter 0.8714 16.6747 31.1606
TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
IsDWI = 1
sagrev = 0, correv =0, trarev = 0
Vs = -0 -0 1
INFO: no Siemens slice order reversal detected (good!).
TR=6300.00, TE=106.00, TI=-1.00, flip angle=90.00
i_ras = (-1, -0, 0)
j_ras = (-0, -1, 0)
k_ras = (-0, -0, 1)
writing to /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/dwi.nii.gz...
Saving bvals and bvecs
-rwxrwxrwx 1 administrator staff 1276058 Feb 18 10:18 /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm
INFO: SUBJECTS_DIR is /Volumes/DANIEL/tutorial_data/diffusion_recons/
dt_recon logfile
Mon Feb 18 10:19:18 EST 2019
VERSION $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
setenv SUBJECTS_DIR /Volumes/DANIEL/tutorial_data/diffusion_recons/
cd /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex
/Applications/freesurfer//bin/dt_recon --sd /Volumes/DANIEL/tutorial_data/diffusion_recons/ --i /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm --s AES101.Ex --b dwi.bvals dwi.voxel_space.bvecs --o /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex.
hlhp-105.umd.edu
administrator
/usr/local/fsl/bin/eddy_correct
ECRefTP 0
#@#-------------------------------
Converting input
Mon Feb 18 10:19:18 EST 2019
cd /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex
mri_convert /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii
mri_convert.bin /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm...
Getting Series No
INFO: Found 71 files in /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex
INFO: Scanning for Series Number 171
Scanning Directory
INFO: found 65 files in series
INFO: loading series header info.
RunNo = 170
WARNING: Run 1 appears to be truncated
Files Found: 65, Files Expected (lRep+1): 1
FileName /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm
Identification
NumarisVer syngo MR B17
ScannerModel TrioTim
PatientName AES101
Date and time
StudyDate 20170409
StudyTime 105710.343000
SeriesTime 120657.984000
AcqTime 120650.230000
Acquisition parameters
PulseSeq *ep_b0
Protocol ep2d_diff_mddw_D64
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 106
InversionTime -1
RepetitionTime 6300
PhEncFOV 210
ReadoutFOV 210
Image information
RunNo 170
SeriesNo 171
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 65
SliceArraylSize 35
IsMosaic 1
ImgPos 630.8714 646.6747 -31.8394
VolRes 1.6406 1.6406 3.6000
VolDim 128 128 35
Vc -1.0000 -0.0000 0.0000
Vr -0.0000 -1.0000 0.0000
Vs -0.0000 -0.0000 1.0000
VolCenter 0.0000 0.0000 0.0000
TransferSyntaxUID 1.2.840.10008.1.2.1
INFO: sorting.
INFO: (128 128 35), nframes = 65, ismosaic=1
sdfi->UseSliceScaleFactor 0
datatype = 4, short=4, float=3
Could not parse NUMARIS version string syngo MR B17
found in dicom tag 18,1020 (len = 3 != 6)
Repetition Time = 6300, TR = 6300 ms
PE Dir COL COL
AutoAlign matrix detected
AutoAlign Matrix ---------------------
1.00000 0.00000 0.00000 0.00000;
0.00000 1.00000 0.00000 0.00000;
0.00000 0.00000 1.00000 0.00000;
0.00000 0.00000 0.00000 1.00000;
FileName /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm
Identification
NumarisVer syngo MR B17
ScannerModel TrioTim
PatientName AES101
Date and time
StudyDate 20170409
StudyTime 105710.343000
SeriesTime 120657.984000
AcqTime 120650.230000
Acquisition parameters
PulseSeq *ep_b0
Protocol ep2d_diff_mddw_D64
PhEncDir COL
EchoNo 1
FlipAngle 90
EchoTime 106
InversionTime -1
RepetitionTime 6300
PhEncFOV 210
ReadoutFOV 210
Image information
RunNo 170
SeriesNo 171
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 65
SliceArraylSize 35
IsMosaic 1
ImgPos 105.8714 121.6747 -31.8394
VolRes 1.6406 1.6406 3.6000
VolDim 128 128 35
Vc -1.0000 -0.0000 0.0000
Vr -0.0000 -1.0000 0.0000
Vs -0.0000 -0.0000 1.0000
VolCenter 0.8714 16.6747 31.1606
TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
IsDWI = 1
sagrev = 0, correv =0, trarev = 0
Vs = -0 -0 1
INFO: no Siemens slice order reversal detected (good!).
TR=6300.00, TE=106.00, TI=-1.00, flip angle=90.00
i_ras = (-1, -0, 0)
j_ras = (-0, -1, 0)
k_ras = (-0, -0, 1)
writing to /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii...
Saving bvals and bvecs
#@#-------------------------------
Eddy/Motion Correct
Mon Feb 18 10:19:30 EST 2019
cd /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./ectmp
eddy_correct /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii 0
Image Exception : #61 :: Multiple possible filenames detected for basename: /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi
Multiple possible filenames detected for basename: /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi
Image Exception : #61 :: Multiple possible filenames detected for basename: /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi
libc++abi.dylib: terminating with uncaught exception of type armawrap::AWException: Multiple possible filenames detected for basename: /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi
/usr/local/fsl/bin/eddy_correct: line 94: 64175 Abort trap: 6 fslsplit $input ${output}_tmp
Usage: fslmerge <-x/y/z/t/a/tr> <output> <file1 file2 .......> [tr value in seconds]
-t : concatenate images in time -x : concatenate images in the x direction -y : concatenate images in the y direction -z : concatenate images in the z direction -a : auto-choose: single slices -> volume, volumes -> 4D (timeseries)
-tr : concatenate images in time and set the output image tr to thefinal option value
rm: /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp????.*: No such file or directory
rm: /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_ref*: No such file or directory
Any help you could provide for trouble shooting the issue would be greatly appreciated!
Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park dcallow@umd.edu dcallow@gmail.com 443-254-6298
freesurfer@nmr.mgh.harvard.edu
-
Daniel Davidson Callow