External Email - Use Caution
Thanks for the reply Doug,
I changed the dt_recon file to what you included in the link and got the following output and error message (I then ran with the original copy of dt_recon and got no error). Is there is an issue calling eddy_correct? What do you make of this issue?
mri_convert.bin image000001.dcm /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES113.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 74 files in /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES113.Rest
INFO: Scanning for Series Number 170
INFO: found 65 files in series
INFO: loading series header info.
INFO: sorting.
RunNo = 169
WARNING: Run 1 appears to be truncated
Files Found: 65, Files Expected (lRep+1): 1
FileName /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES113.Rest/image000001.dcm
Identification
NumarisVer syngo MR B17
ScannerModel TrioTim
PatientName AES113
Date and time
StudyDate 20170203
StudyTime 142632.625000
SeriesTime 160622.218000
AcqTime 160613.950000
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 169
SeriesNo 170
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 65
SliceArraylSize 35
IsMosaic 1
ImgPos 630.9305 648.8915 -20.1985
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/dti_freesurf/diffusion_recons/AES113.Rest/image000001.dcm
Identification
NumarisVer syngo MR B17
ScannerModel TrioTim
PatientName AES113
Date and time
StudyDate 20170203
StudyTime 142632.625000
SeriesTime 160622.218000
AcqTime 160613.950000
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 169
SeriesNo 170
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 65
SliceArraylSize 35
IsMosaic 1
ImgPos 105.9305 123.8916 -20.1985
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 0.9305 18.8916 42.8015
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/dti_freesurf/diffusion_recons/AES113.Rest/dwi.nii.gz...
Saving bvals and bvecs
-rwxrwxrwx 1 administrator staff 1276096 Feb 28 15:06 /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES113.Rest/image000001.dcm
INFO: SUBJECTS_DIR is /Volumes/DANIEL/dti_freesurf/diffusion_recons
dt_recon logfile
Thu Feb 28 15:07:48 EST 2019
VERSION $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
setenv SUBJECTS_DIR /Volumes/DANIEL/dti_freesurf/diffusion_recons
cd /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES113.Rest
/Applications/dt_recon_new --sd /Volumes/DANIEL/dti_freesurf/diffusion_recons --i /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES113.Rest/image000001.dcm --s AES113.Rest --b dwi.bvals dwi.voxel_space.bvecs --o /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest.
administrator
/usr/local/fsl/bin/eddy_correct
ECRefTP 0
#@#-------------------------------
Converting input
Thu Feb 28 15:07:48 EST 2019
cd /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES113.Rest
mri_convert /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES113.Rest/image000001.dcm /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi.nii.gz
mri_convert.bin /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES113.Rest/image000001.dcm /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES113.Rest/image000001.dcm...
Getting Series No
INFO: Found 74 files in /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES113.Rest
INFO: Scanning for Series Number 170
Scanning Directory
INFO: found 65 files in series
INFO: loading series header info.
RunNo = 169
WARNING: Run 1 appears to be truncated
Files Found: 65, Files Expected (lRep+1): 1
FileName /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES113.Rest/image000001.dcm
Identification
NumarisVer syngo MR B17
ScannerModel TrioTim
PatientName AES113
Date and time
StudyDate 20170203
StudyTime 142632.625000
SeriesTime 160622.218000
AcqTime 160613.950000
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 169
SeriesNo 170
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 65
SliceArraylSize 35
IsMosaic 1
ImgPos 630.9305 648.8915 -20.1985
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/dti_freesurf/diffusion_recons/AES113.Rest/image000001.dcm
Identification
NumarisVer syngo MR B17
ScannerModel TrioTim
PatientName AES113
Date and time
StudyDate 20170203
StudyTime 142632.625000
SeriesTime 160622.218000
AcqTime 160613.950000
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 169
SeriesNo 170
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 65
SliceArraylSize 35
IsMosaic 1
ImgPos 105.9305 123.8916 -20.1985
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 0.9305 18.8916 42.8015
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/dti_freesurf/dtrecon/AES113.Rest./dwi.nii.gz...
Saving bvals and bvecs
#@#-------------------------------
Eddy/Motion Correct
Thu Feb 28 15:08:06 EST 2019
cd /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./ectmp
eddy_correct /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi.nii.gz /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec.nii.gz 0
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0000
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0001
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0002
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0003
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0004
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0005
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0006
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0007
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0008
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0009
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0010
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0011
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0012
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0013
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0014
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0015
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0016
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0017
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0018
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0019
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0020
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0021
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0022
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0023
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0024
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0025
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0026
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0027
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0028
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0029
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0030
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0031
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0032
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0033
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0034
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0035
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0036
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0037
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0038
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0039
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0040
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0041
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0042
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0043
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0044
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0045
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0046
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0047
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0048
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0049
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0050
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0051
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0052
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0053
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0054
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0055
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0056
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0057
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0058
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0059
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0060
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0061
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0062
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0063
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0064
Image Exception : #22 :: Failed to read volume /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0002
Error : Error: short read, file may be truncated
libc++abi.dylib: terminating with uncaught exception of type armawrap::AWException: Failed to read volume /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0002
Error : Error: short read, file may be truncated
/usr/local/fsl/bin/eddy_correct: line 103: 27997 Abort trap: 6 fslmerge -t $output $full_list
ERROR: when running eddy_correct
[hlhp-105:/Volumes/DANIEL/dti_freesurf] administrator% ./dt_recon.sh
subj = AES113 , cond = Rest
mkdir: /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES113.Rest: File exists
mri_convert.bin image000001.dcm /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES113.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 74 files in /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES113.Rest
INFO: Scanning for Series Number 170
INFO: found 65 files in series
INFO: loading series header info.
INFO: sorting.
RunNo = 169
WARNING: Run 1 appears to be truncated
Files Found: 65, Files Expected (lRep+1): 1
FileName /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES113.Rest/image000001.dcm
Identification
NumarisVer syngo MR B17
ScannerModel TrioTim
PatientName AES113
Date and time
StudyDate 20170203
StudyTime 142632.625000
SeriesTime 160622.218000
AcqTime 160613.950000
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 169
SeriesNo 170
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 65
SliceArraylSize 35
IsMosaic 1
ImgPos 630.9305 648.8915 -20.1985
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/dti_freesurf/diffusion_recons/AES113.Rest/image000001.dcm
Identification
NumarisVer syngo MR B17
ScannerModel TrioTim
PatientName AES113
Date and time
StudyDate 20170203
StudyTime 142632.625000
SeriesTime 160622.218000
AcqTime 160613.950000
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 169
SeriesNo 170
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 65
SliceArraylSize 35
IsMosaic 1
ImgPos 105.9305 123.8916 -20.1985
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 0.9305 18.8916 42.8015
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/dti_freesurf/diffusion_recons/AES113.Rest/dwi.nii.gz...
Saving bvals and bvecs
-rwxrwxrwx 1 administrator staff 1276096 Feb 28 15:24 /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES113.Rest/image000001.dcm
INFO: SUBJECTS_DIR is /Volumes/DANIEL/dti_freesurf/diffusion_recons
dt_recon logfile
Thu Feb 28 15:26:13 EST 2019
VERSION $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
setenv SUBJECTS_DIR /Volumes/DANIEL/dti_freesurf/diffusion_recons
cd /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES113.Rest
/Applications/freesurfer//bin/dt_recon --sd /Volumes/DANIEL/dti_freesurf/diffusion_recons --i /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES113.Rest/image000001.dcm --s AES113.Rest --b dwi.bvals dwi.voxel_space.bvecs --o /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest.
administrator
/usr/local/fsl/bin/eddy_correct
ECRefTP 0
#@#-------------------------------
Converting input
Thu Feb 28 15:26:13 EST 2019
cd /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES113.Rest
mri_convert /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES113.Rest/image000001.dcm /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi.nii.gz
mri_convert.bin /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES113.Rest/image000001.dcm /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES113.Rest/image000001.dcm...
Getting Series No
INFO: Found 74 files in /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES113.Rest
INFO: Scanning for Series Number 170
Scanning Directory
INFO: found 65 files in series
INFO: loading series header info.
RunNo = 169
WARNING: Run 1 appears to be truncated
Files Found: 65, Files Expected (lRep+1): 1
FileName /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES113.Rest/image000001.dcm
Identification
NumarisVer syngo MR B17
ScannerModel TrioTim
PatientName AES113
Date and time
StudyDate 20170203
StudyTime 142632.625000
SeriesTime 160622.218000
AcqTime 160613.950000
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 169
SeriesNo 170
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 65
SliceArraylSize 35
IsMosaic 1
ImgPos 630.9305 648.8915 -20.1985
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/dti_freesurf/diffusion_recons/AES113.Rest/image000001.dcm
Identification
NumarisVer syngo MR B17
ScannerModel TrioTim
PatientName AES113
Date and time
StudyDate 20170203
StudyTime 142632.625000
SeriesTime 160622.218000
AcqTime 160613.950000
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 169
SeriesNo 170
ImageNo 1
NImageRows 768
NImageCols 768
NFrames 65
SliceArraylSize 35
IsMosaic 1
ImgPos 105.9305 123.8916 -20.1985
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 0.9305 18.8916 42.8015
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/dti_freesurf/dtrecon/AES113.Rest./dwi.nii.gz...
Saving bvals and bvecs
#@#-------------------------------
Eddy/Motion Correct
Thu Feb 28 15:26:31 EST 2019
cd /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./ectmp
eddy_correct /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi.nii.gz /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec.nii.gz 0
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0000
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0001
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0002
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0003
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0004
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0005
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0006
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0007
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0008
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0009
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0010
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0011
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0012
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0013
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0014
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0015
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0016
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0017
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0018
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0019
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0020
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0021
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0022
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0023
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0024
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0025
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0026
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0027
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0028
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0029
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0030
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0031
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0032
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0033
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0034
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0035
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0036
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0037
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0038
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0039
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0040
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0041
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0042
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0043
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0044
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0045
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0046
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0047
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0048
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0049
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0050
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0051
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0052
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0053
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0054
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0055
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0056
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0057
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0058
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0059
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0060
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0061
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0062
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0063
processing /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0064
Image Exception : #22 :: Failed to read volume /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0021
Error : Error: short read, file may be truncated
libc++abi.dylib: terminating with uncaught exception of type armawrap::AWException: Failed to read volume /Volumes/DANIEL/dti_freesurf/dtrecon/AES113.Rest./dwi-ec_tmp0021
Error : Error: short read, file may be truncated
/usr/local/fsl/bin/eddy_correct: line 103: 30200 Abort trap: 6 fslmerge -t $output $full_list
ERROR: when running eddy_correct
Daniel CallowPhD Student, Neuroscience and Cognitive ScienceExercise for Brain Health LabUniversity of Maryland, College Park443-254-6298
On Thu, Feb 28, 2019 at 2:52 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> wrote:
Did you check the registration? My guess is that the registration failed
because the initial FSL registration failed. I've put a new version here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/dt_recon
it has a better initializer. Just copy it over the one in
$FREESURFER_HOME/bin (make a backup of the original one though)
On 2/25/19 1:50 PM, Daniel Callow wrote:
>
> External Email - Use Caution
>
> Hello freesurfer experts,
>
> I am running dt_recon with the following script
>
> dt_recon --sd /Volumes/DANIEL/dti_freesurf/diffusion_recons --i
> /Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/image000001.dcm
> --s ${subj}.${cond} --b dwi.bvals dwi.voxel_space.bvecs --o
> /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}.
>
>
> and mri_vol2vol to get the wmparc and aseg.mgz files in my lowb space
> with the script below
>
> mri_vol2vol --mov $subj_dir/dtrecon/${subj}.${cond}./lowb.nii.gz
> --targ $subj_dir/diffusion_recons/${subj}.${cond}/mri/wmparc.mgz --inv
> --interp nearest --o
> /Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/mri/wmparc2diff.mgz
> --reg $subj_dir/dtrecon/${subj}.${cond}./register.dat --no-save-reg
>
>
> mri_vol2vol --mov $subj_dir/dtrecon/${subj}.${cond}./lowb.nii.gz
> --targ $subj_dir/diffusion_recons/${subj}.${cond}/mri/aseg.mgz --inv
> --interp nearest --o
> $subj_dir/dtrecon/${subj}.${cond}./aseg2diff.nii.gz --reg
> $subj_dir/dtrecon/${subj}.${cond}./register.dat --no-save-reg
>
>
> However, one of my subjects shows a major issue with the mri_vol2vol
> registration (for most of the subject scans it seems to work no
> problem). When looking at the wmparc2diff.mgz I created (screenshot
> attached), it is apparent that the registration of the wmparc to
> wmparc2diff space actually causes wmparc2diff.mgz to be further from
> the lowb than wmparc is. This same registration issue occurs for aseg.mgz.
>
>
> I assume this means there is an issue with the register.dat file for
> this subject? If so is there any way to troubleshoot the issue and get
> a correct register.dat file?
>
>
> For reference, the following commands and registration steps have
> worked for other subjects, as well as this same subject's scans under
> another condition.
>
>
> Any advice with troubleshooting would be greatly appreciated.
>
>
> Best,
>
> *Daniel Callow*
> /PhD Student, Neuroscience and Cognitive Science/
> Exercise for Brain Health Lab
> University of Maryland, College Park
> _ddcc2442@gmail.com <mailto:ddcc2442@gmail.com>_
> 443-254-6298
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer