Hi all, I’m trying to run TRACULA on a single subject’s data, but trac-all -prep is exiting with the output below. Most notably, I think, is the section of the output that says "R: Subscript out of range.” repeatedly and then the section afterwards that says “keeping frames 0 1 2 3 4 5 6 7 8 9 / ERROR: valid frame numbers are between 0 and 0”. Does anyone have thoughts on what might be going on here?
I’ve attached my bvecs and bvals too, in case there is trouble there too. Thanks very much for any help. Best, Anna
0.00000000000000 0.00000000000000 0.00000000000000 0.00000000000000 0.00000000000000 0.00000000000000 0.00000000000000 0.00000000000000 0.00000000000000 0.00000000000000 0.00000000000000 0.00000000000000 0.00000000000000 0.00000000000000 0.00000000000000 0.00000000000000 0.00000000000000 0.00000000000000 0.00000000000000 0.00000000000000 0.00000000000000 0.00000000000000 0.00000000000000 0.00000000000000 0.00000000000000 0.00000000000000 0.00000000000000 0.00000000000000 0.00000000000000 0.00000000000000 0.99649667739868 0.06475614756346 -0.05292384698987 0.60556709766388 0.42478442192078 0.67293894290924 0.86823248863220 0.03115228191018 -0.49517852067947 0.67013686895370 0.45375373959541 -0.58738726377487 -0.08319617807865 -0.97095906734467 0.22431358695030 0.19819127023220 -0.76370823383331 0.61438584327698 -0.38230711221695 0.40581783652306 0.83015239238739 0.21735191345215 -0.75227254629135 -0.62196791172028 0.02298471517861 0.97281080484390 -0.23045811057091 -0.07650605589151 0.04117560386658 0.99621850252151 -0.14655694365501 0.75338035821915 0.64104521274567 -0.57700997591019 -0.78357273340225 0.23037599027157 0.12379934638739 -0.96946108341217 -0.21170438826084 0.04432926326990 0.02168774046004 -0.99878138303757 0.26761892437935 -0.38499519228935 -0.88326603174210 -0.28756865859032 0.78847736120224 -0.54369783401489 0.38445866107941 0.07492686808109 0.92009633779526 -0.83095681667328 0.54706901311874 0.10112489014864 0.32437109947205 0.77897244691849 0.53664255142212 0.52829635143280 0.79588997364044 -0.29573988914490 -0.16789475083351 0.45606943964958 -0.87396329641342 -0.59607589244843 0.39722976088524 -0.69778358936310 -0.42442059516907 0.90444123744965 -0.04304528608918 0.37679037451744 -0.90613275766373 0.19222989678383 -0.62092286348343 -0.47927498817444 0.62028235197067 -0.07215544581413 0.96755516529083 0.24213692545891 -0.25669917464256 -0.76215481758118 0.59432780742645 -0.52350831031799 -0.05601207166910 0.85017740726471 0.18893271684647 0.76144242286682 -0.62008827924728 -0.93878203630447 -0.25041463971138 -0.23660232126713 0.92434495687485 -0.25977137684822 0.27947291731834 -0.85333710908890 -0.08729962259531 0.51399856805801 0.61280375719070 -0.55279505252838 0.56470263004303 -0.40714001655579 -0.01904341205955 -0.91316711902618 0.36646711826324 0.92621129751205 0.08851362764835 -0.77262413501740 -0.05901937559247 -0.63211452960968 -0.71511095762253 -0.66166228055954 -0.22543147206306 -0.17854259908199 -0.41829714179039 0.89058959484100 -0.88413268327713 -0.43072432279587 0.18106889724731 -0.24447374045849 -0.79100799560547 -0.56083726882935 -0.60315960645676 -0.48198029398918 -0.63552600145340 0.90175306797028 0.24873784184456 0.35351192951202 0.72955089807510 -0.10027404874563 0.67653554677963 -0.91682189702988 0.25997617840767 -0.30306729674339 -0.68014901876450 0.66064327955246 -0.31772288680077 0.86024975776672 0.48736852407455 -0.14980775117874 -0.19012457132339 -0.44323825836182 -0.87600934505463 -0.52820658683777 0.75576055049896 0.38707065582275 0.13211445510387 0.46795129776001 0.87382322549820 0.89498126506805 -0.39065974950790 -0.21539171040058 0.55196392536163 -0.00862982682884 -0.83382308483124 0.74213677644730 -0.65859544277191 0.12443807721138 -0.34717303514481 -0.92652040719986 -0.14502120018005 -0.75233423709869 0.36954036355019 0.54537409543991 0.28638312220573 -0.37944245338440 0.87977713346481 0.30121210217476 0.39795523881912 -0.86654651165009 0.71197289228439 0.66156578063965 0.23542550206184 -0.98868387937546 0.09445825219154 0.11654109507799 0.55790656805038 -0.78184622526169 -0.27831059694290 0.65419042110443 -0.44598758220673 -0.61084365844727
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000 700.000000
——————————————————
INFO: SUBJECTS_DIR is
/mindhive/nklab/u/amynick/Tracula/Tracula_trio/diffusion_recons
INFO: Diffusion root is
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial
Actual FREESURFER_HOME /cm/shared/openmind/freesurfer/6.0.0
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /cm/shared/openmind/freesurfer/6.0.0
Previous: /software/pkg/freesurfer/freesurfer-6.0.0
trac-preproc -c
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/scripts/dmrirc.local
-log
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/scripts/trac-all.log
-cmd
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/scripts/trac-all.cmd
#-------------------------------------
/cm/shared/openmind/freesurfer/6.0.0/bin/trac-preproc
#-------------------------------------
#@# Image corrections Thu Nov 30 13:40:35 EST 2017
mri_convert --bvec-voxel
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/orig/171000-1-1.dcm
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/orig/171000-1-1.dcm
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/orig/171000-1-1.dcm...
Getting Series No
INFO: Found 4505 files in
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/orig
INFO: Scanning for Series Number 1
Scanning Directory
INFO: found 128 files in series
INFO: loading series header info.
RunNo = 0
INFO: sorting.
sdfiSameSlicePos() eps = 0.000001
INFO: (160 160 128), nframes = 1, ismosaic=0
sdfi->UseSliceScaleFactor 0
datatype = 4, short=4, float=3
PE Dir ROW ROW
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
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/orig/171000-1-1.dcm
Identification
NumarisVer syngo MR B17
ScannerModel TrioTim
PatientName KanCon02
Date and time
StudyDate 20161216
StudyTime 163713.171000
SeriesTime 164740.250000
AcqTime 164708.722500
Acquisition parameters
PulseSeq *fl3d1_ns
Protocol AAHScout_32ch
PhEncDir ROW
EchoNo 1
FlipAngle 8
EchoTime 1.37
InversionTime -1
RepetitionTime 3.15
PhEncFOV 260
ReadoutFOV 260
Image information
RunNo 0
SeriesNo 1
ImageNo 1
NImageRows 160
NImageCols 160
NFrames 1
SliceArraylSize 1
IsMosaic 0
ImgPos 101.6000 130.0000 130.0000
VolRes 1.6250 1.6250 1.6000
VolDim 160 160 128
Vc -0.0000 -1.0000 0.0000
Vr -0.0000 -0.0000 -1.0000
Vs -1.0000 -0.0000 0.0000
VolCenter -0.8000 0.0000 0.0000
TransferSyntaxUID unknown
UseSliceScaleFactor 0 (slice 0: 1)
IsDWI = 0
INFO: no Siemens slice order reversal detected (good!).
TR=3.15, TE=1.37, TI=-1.00, flip angle=8.00
i_ras = (-0, -1, 0)
j_ras = (-0, -0, -1)
k_ras = (-1, -0, 0)
writing to
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.nii.gz...
mri_probedicom --i
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/orig/171000-1-1.dcm
>
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dcminfo.dat
cp
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/orig/gradients.txt
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.bvecs
cp
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/orig/bvalues.txt
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.bvals
mv -f
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/bvecs.tmp
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.bvecs
mv -f
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/bvals.tmp
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.bvals
orientLAS
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.nii.gz
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig_las.nii.gz
INFO: input image orientation is PIL
INFO: input image determinant is -4.225
mri_convert -oni 128 -onj 160 -onk 160 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1 -oc
-0.812503 1.625 1.6125 -rt nearest
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.nii.gz
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig_las.nii.gz
mri_convert.bin -oni 128 -onj 160 -onk 160 -oid -1 0 0 -ojd 0 1 0 -okd 0 0 1
-oc -0.812503 1.625 1.6125 -rt nearest
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.nii.gz
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig_las.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.nii.gz...
TR=3.15, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0, -1, 0)
j_ras = (-0, -0, -1)
k_ras = (-1, -0, 0)
Reslicing using nearest
writing to
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig_las.nii.gz...
INFO: found
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.bvals,
copying
INFO: found
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig.bvecs,
converting to LAS
mv -f
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig_las.bvecs
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/bvecs
mv -f
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig_las.bvals
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/bvals
eddy_correct
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_orig_las.nii.gz
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi.nii.gz
0
processing
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi_tmp0000
mv -f
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/bvecs
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/bvecs.norot
xfmrot
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi.ecclog
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/bvecs.norot
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/bvecs
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
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ln -sf
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi.nii.gz
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/data.nii.gz
mri_convert --frame 0 1 2 3 4 5 6 7 8 9
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi.nii.gz
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/lowb.nii.gz
mri_convert.bin --frame 0 1 2 3 4 5 6 7 8 9
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi.nii.gz
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/lowb.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from
/mindhive/nklab/u/amynick/Tracula/Tracula_trio//diffusion_tutorial/kancon02/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
keeping frames 0 1 2 3 4 5 6 7 8 9
ERROR: valid frame numbers are between 0 and 0
Linux node044 3.10.0-514.26.2.el7.x86_64 #1 SMP Tue Jul 4 15:04:05 UTC 2017
x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Thu Nov 30 13:44:15 EST 2017
smime.p7s
Description: S/MIME cryptographic signature
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
