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 ddcc2442@gmail.com* 443-254-6298
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
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.
hlhp-105.umd.edu
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.
hlhp-105.umd.edu
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 Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442@gmail.com ddcc2442@gmail.com* 443-254-6298
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 $FREESURFER_HOME/bin (make a backup of the original one though)
On 2/25/19 1:50 PM, Daniel Callow wrote:
External Email - Use CautionHello freesurfer experts,
I am running dt_recon with the following script
dt_recon --sd /Volumes/DANIEL/dti_freesurf/diffusion_recons --i
/Volumes/DANIEL/dti_freesurf/diffusion_recons/${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
that is an error in eddy_correct
On 2/28/19 3:52 PM, Daniel Callow wrote:
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.
hlhp-105.umd.eduhttp://hlhp-105.umd.edu
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.
hlhp-105.umd.eduhttp://hlhp-105.umd.edu
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 Callow PhD Student, Neuroscience and Cognitive Science Exercise for Brain Health Lab University of Maryland, College Park ddcc2442@gmail.commailto:ddcc2442@gmail.com 443-254-6298
On Thu, Feb 28, 2019 at 2:52 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto: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 $FREESURFER_HOME/bin (make a backup of the original one though)
On 2/25/19 1:50 PM, Daniel Callow wrote:
External Email - Use CautionHello freesurfer experts,
I am running dt_recon with the following script
dt_recon --sd /Volumes/DANIEL/dti_freesurf/diffusion_recons --i /Volumes/DANIEL/dti_freesurf/diffusion_recons/${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.commailto:ddcc2442@gmail.com <mailto:ddcc2442@gmail.commailto:ddcc2442@gmail.com>_ 443-254-6298
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Daniel Callow -
Greve, Douglas N.,Ph.D.