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

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Re: [Freesurfer] Unexpected...

Daniel Davidson Callow

15 Feb 2019 15 Feb '19

9:22 a.m.

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!

Thanks, D*aniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park dcallow@umd.edu dcallow@gmail.com 443-254-6298

Attachments:

attachment.html (text/html — 7.8 KB)
dt_recon.log (application/octet-stream — 156.8 KB)

Show replies by date

Greve, Douglas N.,Ph.D.

15 Feb 15 Feb

11:17 a.m.

New subject: dt_recon error MatrixReadTxT: could not scan value [1][1]

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!

Thanks, Daniel Callow PhD Student, Neuroscience and Cognitive Science Exercise for Brain Health Lab University of Maryland, College Park dcallow@umd.edumailto:dcallow@gmail.com 443-254-6298

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Daniel Callow

1:29 p.m.

External Email - Use Caution

Thanks! *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 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!

Thanks, D*aniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park dcallow@umd.edu dcallow@gmail.com 443-254-6298

Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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

Daniel Callow

1:43 p.m.

External Email - Use Caution

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

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

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

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

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

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

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

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

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 *ddcc2442@gmail.com ddcc2442@gmail.com* 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!

Thanks, D*aniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park dcallow@umd.edu dcallow@gmail.com 443-254-6298

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participants (3)

Daniel Callow
Daniel Davidson Callow
Greve, Douglas N.,Ph.D.