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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