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
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 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


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