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Hello, 

When I run 

dt_recon --debug --i /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/image000001.dcm --s ${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon/${subj}.${cond}.

It does produce a -dwi.bvals -dwi.voxel_space.bvecs file and I get this output in the error log (also attached). For reference the bvals and bvecs files were correct.


MatrixReadTxT: could not scan value [1][1]


could not allocate 1684305759 x 1144402954 matrix


could not allocate 1684305759 x 1144402954 matrix


unsupported matlab format 540094003 (unknown)


And this is what I get in the command line while it is running. It does create a NIFTI file and it seems like it is trying to eddy current correct. 



setenv FSLOUTPUTTYPE NIFTI

setenv FSLOUTPUTTYPE NIFTI



echo "#@#-------------------------------" | tee -a $LF

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log

echo #@#-------------------------------

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

echo "Converting input" | tee -a $LF

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log

echo Converting input

Converting input

date | tee -a $LF

date

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log

Fri Feb 15 13:24:19 EST 2019

set f = $OutDir/dwi.nii

set f = /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii

set cmd = ( mri_convert $InputVol $f ) ;

set cmd = ( mri_convert /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii )

echo "cd `pwd`" | tee -a $LF

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log

echo cd `pwd`

pwd

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

echo $cmd | tee -a $LF

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log

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

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

$cmd | & tee -a $LF

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

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log

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

if ( $status ) exit 1 ;

if ( 0 ) exit 1

echo "" | tee -a $LF

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log

echo 


echo "" | tee -a $LF

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log

echo 



if ( $#bvals == 0 ) then

if ( 0 == 0 ) then

if ( $#infodump == 0 ) then

if ( 0 == 0 ) then


set infodump = $OutDir/dwi-infodump.dat

set infodump = /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-infodump.dat

set cmd = ( mri_probedicom --i $InputVol ) ;

set cmd = ( mri_probedicom --i /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm )

echo "cd `pwd`" | tee -a $LF

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log

echo cd `pwd`

pwd

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

echo $cmd | tee -a $LF

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log

echo mri_probedicom --i /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm

mri_probedicom --i /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm

$cmd | & tee -a $LF > $infodump

mri_probedicom --i /Volumes/DANIEL/tutorial_data/diffusion_recons/AES101.Ex/image000001.dcm

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log

if ( $status ) exit 1 ;

if ( 0 ) exit 1

echo "" | tee -a $LF

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log

echo 


echo "" | tee -a $LF

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log

echo 


endif

endif

endif

endif



set fec = $OutDir/dwi-ec.nii

set fec = /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii

if ( $DoEddyCorrect ) then

if ( 1 ) then

echo "#@#-------------------------------" | tee -a $LF

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log

echo #@#-------------------------------

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

echo "Eddy/Motion Correct" | tee -a $LF

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log

echo Eddy/Motion Correct

Eddy/Motion Correct

date | tee -a $LF

date

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log

Fri Feb 15 13:24:31 EST 2019

set ectmp = $OutDir/ectmp

set ectmp = /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./ectmp

mkdir -p $ectmp

mkdir -p /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./ectmp

pushd $ectmp > /dev/null

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

set cmd = ( eddy_correct $f $fec $ECRefTP )

set cmd = ( eddy_correct /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii 0 )




echo "cd `pwd`" | tee -a $LF

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log

echo cd `pwd`

pwd

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

echo $cmd | tee -a $LF

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log

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

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

$cmd | & tee -a $LF

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

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0000

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0001

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0002

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0003

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0004

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0005

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0006

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0007

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0008

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0009

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0010

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0011

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0012

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0013

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0014

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0015

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0016

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0017

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0018

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0019

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0020

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0021

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0022

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0023

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0024

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0025

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0026

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0027

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0028

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0029

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0030

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0031

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0032

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0033

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0034

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0035

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0036

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0037

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0038

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0039

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0040

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0041

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0042

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0043

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0044

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0045

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0046

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0047

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0048

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0049

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0050

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0051

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0052

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0053

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0054

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0055

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0056

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0057

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0058

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0059

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0060

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0061

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0062

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0063

processing /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec_tmp0064

if ( $status ) exit 1 ;

if ( 0 ) exit 1

if ( ! -e $fec ) then

if ( ! -e /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii ) then

popd > /dev/null

popd

rm -r $ectmp

rm -r /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./ectmp

echo "" | tee -a $LF

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log

echo 


echo "" | tee -a $LF

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log

echo 


else

else



echo "#@#-------------------------------" | tee -a $LF

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log

echo #@#-------------------------------

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

echo "Fitting Tensors" | tee -a $LF

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log

echo Fitting Tensors

Fitting Tensors

date | tee -a $LF

date

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log

Fri Feb 15 13:33:13 EST 2019



set cmd = ( gzip $f )

set cmd = ( gzip /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii )

echo $cmd | tee -a $LF

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log

echo gzip /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii

gzip /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii

$cmd | & tee -a $LF

gzip /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi.nii

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log

if ( $status ) exit 1 ;

if ( 0 ) exit 1

echo "" | tee -a $LF

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log

echo 


echo "" | tee -a $LF

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log

echo 


set cmd = ( gzip $fec )

set cmd = ( gzip /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii )

echo $cmd | tee -a $LF

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log

echo gzip /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii

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

$cmd | & tee -a $LF

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

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log

if ( $status ) exit 1 ;

if ( 0 ) exit 1

echo "" | tee -a $LF

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log

echo 


echo "" | tee -a $LF

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log

echo 



set cmd = ( mri_glmfit --y $fec.gz --glmdir $OutDir ) ;

set cmd = ( mri_glmfit --y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz --glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. )

if ( $#bvals == 0 ) then

if ( 0 == 0 ) then

set cmd = ( $cmd --dti $infodump )

set cmd = ( mri_glmfit --y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz --glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. --dti /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-infodump.dat )

else

else

if ( $SaveERes ) set cmd = ( $cmd --eres-save )

if ( 0 ) set cmd = ( mri_glmfit --y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz --glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. --dti /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-infodump.dat --eres-save )

if ( $EResPCA ) set cmd = ( $cmd --pca )

if ( 0 ) set cmd = ( mri_glmfit --y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz --glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. --dti /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-infodump.dat --pca )

if ( $#PruneThr ) set cmd = ( $cmd --prune_thr $PruneThr )

if ( 0 ) set cmd = ( mri_glmfit --y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz --glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. --dti /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-infodump.dat --prune_thr )

if ( $#mask ) set cmd = ( $cmd --mask $mask ) ;

if ( 0 ) set cmd = ( mri_glmfit --y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz --glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. --dti /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-infodump.dat --mask )


echo "cd `pwd`" | tee -a $LF

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log

echo cd `pwd`

pwd

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

echo $cmd | tee -a $LF

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log

echo mri_glmfit --y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz --glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. --dti /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-infodump.dat

mri_glmfit --y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz --glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. --dti /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-infodump.dat

$cmd | & tee -a $LF

mri_glmfit --y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz --glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. --dti /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-infodump.dat

tee -a /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dt_recon.log


$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $

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

cmdline mri_glmfit.bin --y /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz --glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex. --dti /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-infodump.dat 

sysname  Darwin

hostname hlhp-105.umd.edu

machine  x86_64

user     administrator

FixVertexAreaFlag = 1

UseMaskWithSmoothing     1

OneSampleGroupMean 0

y    /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz

logyflag 1

X    /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-infodump.dat

usedti  2

glmdir /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex.

IllCondOK 0

ReScaleX 1

DoFFx 0

Creating output directory /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex.

Loading y from /Volumes/DANIEL/tutorial_data/dtrecon/AES101.Ex./dwi-ec.nii.gz

   ... done reading.

MatrixReadTxT: could not scan value [1][1]



When creating the NIFTI file with mri_convert I still get a similar error because the code seems to ignore the NIFTI file input and just looks at the DICOMS


I have attached the script I use below.


Daniel Callow

PhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
443-254-6298


On Fri, Feb 15, 2019 at 11:18 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> wrote:
Can you do this in two steps? First, convert the dicom to a volume format (eg, mgz or nii.gz) with 
mri_convert image0000001.dcm dwi.nii.gz
This may or may not create bvals and bvecs. If not, then you will have to supply them. If they are created, look at them and make sure they are right.
Next run dt_recon specifying the input and the bvals/bvecs

On 2/15/19 9:22 AM, Daniel Davidson Callow wrote:

        External Email - Use Caution        

Hello,

I tried to run dt_recon, however, I received the following error message. Attached is the error log.

dt_recon --debug --i /Volumes/DANIEL/tutorial_data/diffusion_recons/${subj}.${cond}/image000001.dcm --s ${subj}.${cond} --o /Volumes/DANIEL/tutorial_data/dtrecon/

MatrixReadTxT: could not scan value [1][1]


No such file or directory

WARNING: matlab elment type is 1852050003, which is not a matrix.

mri_glmfit.bin(51624,0x7fffaff913c0) malloc: *** mach_vm_map(size=9155227648) failed (error code=3)

*** error: can't allocate region

*** set a breakpoint in malloc_error_break to debug

could not allocate 1684305759 x 1144402954 matrix


Cannot allocate memory

mri_glmfit.bin(51624,0x7fffaff913c0) malloc: *** mach_vm_map(size=13474447360) failed (error code=3)

*** error: can't allocate region

*** set a breakpoint in malloc_error_break to debug

could not allocate 1684305759 x 1144402954 matrix


Cannot allocate memory

unsupported matlab format 540094003 (unknown)


Cannot allocate memory

It also seems when dt_Recon is trying to process different subjects in parallel they are being processed in the same folder? does this create an issue?

Any help you can provide in debugging the issue would be greatly appreciated!


Daniel Callow

PhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
443-254-6298