Hello,

I am still trying to run dt_recon and am having issues.

The code I am running is attached...and an abbreviated version is below. 

foreach subj (`ls -d /Volumes/DANIEL/AES101 | sed 's/\// /g' | awk '{print $3}'`)

foreach cond (Ex Rest)

echo "subj = " ${subj} ", cond = " ${cond}

cd /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/

mri_convert image000001.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/dwi.nii.gz

dt_recon --sd /Volumes/DANIEL/tutorial_data/diffusion_recons/ --i /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/image000001.dcm --s ${subj}.${cond} --b dwi.bvals dwi.voxel_space.bvecs --o /Volumes/DANIEL/tutorial_data/dtrecon/${subj}.${cond}.

and the following is the output and errors I am getting from running the above code. I have also attached a screenshot of the path and folder with the various file inputs and outputs.

subj =  AES101 , cond =  Ex

mkdir: /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex: File exists

mri_convert.bin image000001.dcm /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/dwi.nii.gz 

$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $

reading from image000001.dcm...

Getting Series No 

Scanning Directory 

INFO: Found 71 files in /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex

INFO: Scanning for Series Number 171

INFO: found 65 files in series

INFO: loading series header info.

INFO: sorting.

RunNo = 170

WARNING: Run 1 appears to be truncated

  Files Found: 65, Files Expected (lRep+1): 1

FileName /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm

Identification

NumarisVer        syngo MR B17

ScannerModel      TrioTim 

PatientName       AES101

Date and time

StudyDate         20170409

StudyTime         105710.343000 

SeriesTime        120657.984000 

AcqTime           120650.230000 

Acquisition parameters

PulseSeq          *ep_b0

Protocol          ep2d_diff_mddw_D64

PhEncDir          COL

EchoNo            1

FlipAngle         90

EchoTime          106

InversionTime     -1

RepetitionTime    6300

PhEncFOV          210

ReadoutFOV        210

Image information

RunNo             170

SeriesNo          171

ImageNo           1

NImageRows        768

NImageCols        768

NFrames           65

SliceArraylSize   35

IsMosaic          1

ImgPos            630.8714 646.6747 -31.8394 

VolRes              1.6406   1.6406   3.6000 

VolDim            128      128       35 

Vc                 -1.0000  -0.0000   0.0000 

Vr                 -0.0000  -1.0000   0.0000 

Vs                 -0.0000  -0.0000   1.0000 

VolCenter           0.0000   0.0000   0.0000 

TransferSyntaxUID 1.2.840.10008.1.2.1

INFO: (128 128  35), nframes = 65, ismosaic=1

sdfi->UseSliceScaleFactor 0

datatype = 4, short=4, float=3

Could not parse NUMARIS version string syngo MR B17

found in dicom tag 18,1020 (len = 3 != 6)

Repetition Time = 6300, TR = 6300 ms

PE Dir COL COL

AutoAlign matrix detected 

AutoAlign Matrix --------------------- 

 1.00000   0.00000   0.00000   0.00000;

 0.00000   1.00000   0.00000   0.00000;

 0.00000   0.00000   1.00000   0.00000;

 0.00000   0.00000   0.00000   1.00000;

FileName /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm

Identification

NumarisVer        syngo MR B17

ScannerModel      TrioTim 

PatientName       AES101

Date and time

StudyDate         20170409

StudyTime         105710.343000 

SeriesTime        120657.984000 

AcqTime           120650.230000 

Acquisition parameters

PulseSeq          *ep_b0

Protocol          ep2d_diff_mddw_D64

PhEncDir          COL

EchoNo            1

FlipAngle         90

EchoTime          106

InversionTime     -1

RepetitionTime    6300

PhEncFOV          210

ReadoutFOV        210

Image information

RunNo             170

SeriesNo          171

ImageNo           1

NImageRows        768

NImageCols        768

NFrames           65

SliceArraylSize   35

IsMosaic          1

ImgPos            105.8714 121.6747 -31.8394 

VolRes              1.6406   1.6406   3.6000 

VolDim            128      128       35 

Vc                 -1.0000  -0.0000   0.0000 

Vr                 -0.0000  -1.0000   0.0000 

Vs                 -0.0000  -0.0000   1.0000 

VolCenter           0.8714  16.6747  31.1606 

TransferSyntaxUID 1.2.840.10008.1.2.1

UseSliceScaleFactor 0 (slice 0: 1)

IsDWI = 1

sagrev = 0, correv =0, trarev = 0

Vs = -0 -0 1

INFO: no Siemens slice order reversal detected (good!). 

TR=6300.00, TE=106.00, TI=-1.00, flip angle=90.00

i_ras = (-1, -0, 0)

j_ras = (-0, -1, 0)

k_ras = (-0, -0, 1)

writing to /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/dwi.nii.gz...

Saving bvals and bvecs

-rwxrwxrwx  1 administrator  staff  1276058 Feb 18 10:18 /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm

INFO: SUBJECTS_DIR is /Volumes/DANIEL/tutorial_data/diffusion_recons/

dt_recon logfile

Mon Feb 18 10:19:18 EST 2019

VERSION $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $

setenv SUBJECTS_DIR /Volumes/DANIEL/tutorial_data/diffusion_recons/

cd /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex

/Applications/freesurfer//bin/dt_recon --sd /Volumes/DANIEL/tutorial_data/diffusion_recons/ --i /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm --s AES101.Ex --b dwi.bvals dwi.voxel_space.bvecs --o /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex.

hlhp-105.umd.edu

administrator

/usr/local/fsl/bin/eddy_correct

ECRefTP 0

#@#-------------------------------

Converting input

Mon Feb 18 10:19:18 EST 2019

cd /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex

mri_convert /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii

mri_convert.bin /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii 

$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $

reading from /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm...

Getting Series No 

INFO: Found 71 files in /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex

INFO: Scanning for Series Number 171

Scanning Directory 

INFO: found 65 files in series

INFO: loading series header info.

RunNo = 170

WARNING: Run 1 appears to be truncated

  Files Found: 65, Files Expected (lRep+1): 1

FileName /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm

Identification

NumarisVer        syngo MR B17

ScannerModel      TrioTim 

PatientName       AES101

Date and time

StudyDate         20170409

StudyTime         105710.343000 

SeriesTime        120657.984000 

AcqTime           120650.230000 

Acquisition parameters

PulseSeq          *ep_b0

Protocol          ep2d_diff_mddw_D64

PhEncDir          COL

EchoNo            1

FlipAngle         90

EchoTime          106

InversionTime     -1

RepetitionTime    6300

PhEncFOV          210

ReadoutFOV        210

Image information

RunNo             170

SeriesNo          171

ImageNo           1

NImageRows        768

NImageCols        768

NFrames           65

SliceArraylSize   35

IsMosaic          1

ImgPos            630.8714 646.6747 -31.8394 

VolRes              1.6406   1.6406   3.6000 

VolDim            128      128       35 

Vc                 -1.0000  -0.0000   0.0000 

Vr                 -0.0000  -1.0000   0.0000 

Vs                 -0.0000  -0.0000   1.0000 

VolCenter           0.0000   0.0000   0.0000 

TransferSyntaxUID 1.2.840.10008.1.2.1

INFO: sorting.

INFO: (128 128  35), nframes = 65, ismosaic=1

sdfi->UseSliceScaleFactor 0

datatype = 4, short=4, float=3

Could not parse NUMARIS version string syngo MR B17

found in dicom tag 18,1020 (len = 3 != 6)

Repetition Time = 6300, TR = 6300 ms

PE Dir COL COL

AutoAlign matrix detected 

AutoAlign Matrix --------------------- 

 1.00000   0.00000   0.00000   0.00000;

 0.00000   1.00000   0.00000   0.00000;

 0.00000   0.00000   1.00000   0.00000;

 0.00000   0.00000   0.00000   1.00000;

FileName /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm

Identification

NumarisVer        syngo MR B17

ScannerModel      TrioTim 

PatientName       AES101

Date and time

StudyDate         20170409

StudyTime         105710.343000 

SeriesTime        120657.984000 

AcqTime           120650.230000 

Acquisition parameters

PulseSeq          *ep_b0

Protocol          ep2d_diff_mddw_D64

PhEncDir          COL

EchoNo            1

FlipAngle         90

EchoTime          106

InversionTime     -1

RepetitionTime    6300

PhEncFOV          210

ReadoutFOV        210

Image information

RunNo             170

SeriesNo          171

ImageNo           1

NImageRows        768

NImageCols        768

NFrames           65

SliceArraylSize   35

IsMosaic          1

ImgPos            105.8714 121.6747 -31.8394 

VolRes              1.6406   1.6406   3.6000 

VolDim            128      128       35 

Vc                 -1.0000  -0.0000   0.0000 

Vr                 -0.0000  -1.0000   0.0000 

Vs                 -0.0000  -0.0000   1.0000 

VolCenter           0.8714  16.6747  31.1606 

TransferSyntaxUID 1.2.840.10008.1.2.1

UseSliceScaleFactor 0 (slice 0: 1)

IsDWI = 1

sagrev = 0, correv =0, trarev = 0

Vs = -0 -0 1

INFO: no Siemens slice order reversal detected (good!). 

TR=6300.00, TE=106.00, TI=-1.00, flip angle=90.00

i_ras = (-1, -0, 0)

j_ras = (-0, -1, 0)

k_ras = (-0, -0, 1)

writing to /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii...

Saving bvals and bvecs

#@#-------------------------------

Eddy/Motion Correct

Mon Feb 18 10:19:30 EST 2019

cd /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./ectmp

eddy_correct /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii 0

Image Exception : #61 :: Multiple possible filenames detected for basename: /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi

Multiple possible filenames detected for basename: /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi

Image Exception : #61 :: Multiple possible filenames detected for basename: /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi

libc++abi.dylib: terminating with uncaught exception of type armawrap::AWException: Multiple possible filenames detected for basename: /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi

/usr/local/fsl/bin/eddy_correct: line 94: 64175 Abort trap: 6           fslsplit $input ${output}_tmp

Usage: fslmerge <-x/y/z/t/a/tr> <output> <file1 file2 .......> [tr value in seconds]

     -t : concatenate images in time

     -x : concatenate images in the x direction

     -y : concatenate images in the y direction

     -z : concatenate images in the z direction

     -a : auto-choose: single slices -> volume, volumes -> 4D (time series)

     -tr : concatenate images in time and set the output image tr to the final option value

rm: /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp????.*: No such file or directory

rm: /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_ref*: No such file or directory

Any help you could provide for trouble shooting the issue would be greatly appreciated!

Best,