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
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 *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 CautionHello,
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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