Dear TRACULA users, I'm trying to preprocess a DTI subject in TRACULA which has an already reconed-all error-free T1. I followed the tutorial, but trac-all -prep exited with errors very fast.
Please find attached the log and error files, and the dmrirc. Also bvals and bvecs (were obtained from dcm2nii). The raw dti.nii.gz has 16 volumes, the first being b0 and then 15 directions. Any ideas on what could be happening would be much appreciated, Thanks a lot in advance, Fred-
dmrirc.tutorial
Description: Binary data
dtipd1467690.bval
Description: Binary data
dtipd1467690.bvec
Description: Binary data
trac-all.error
Description: Binary data
jue sep 21 11:49:35 CEST 2017
/media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial
/usr/local/freesurfer/bin/trac-all
-prep -c dmrirc.tutorial
Subject t1pd1467690
SUBJECTS_DIR /media/freds/LinuxData/TRACULA_HSP/diffusion_recons
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
freds
utm
Linux utm 4.4.0-96-generic #119-Ubuntu SMP Tue Sep 12 14:59:54 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8192 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 64 kbytes
maxproc 127247
maxlocks unlimited
maxsignal 127247
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 32622380 8817588 12764464 14068 11040328 23313740
Swap: 3998716 0 3998716
########################################
Program versions:
$Id: trac-all,v 1.60.2.1 2016/12/20 17:04:05 zkaufman Exp $
mri_convert.bin --all-info
ProgramName: mri_convert.bin ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/21-09:49:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: freds Machine: utm Platform: Linux PlatformVersion: 4.4.0-96-generic CompilerName: GCC CompilerVersion: 40400
FLIRT version 6.0
$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
$Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $
ProgramName: dmri_motion ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/21-09:49:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: freds Machine: utm Platform: Linux PlatformVersion: 4.4.0-96-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/21-09:49:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: freds Machine: utm Platform: Linux PlatformVersion: 4.4.0-96-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/21-09:49:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: freds Machine: utm Platform: Linux PlatformVersion: 4.4.0-96-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/21-09:49:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: freds Machine: utm Platform: Linux PlatformVersion: 4.4.0-96-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/21-09:49:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: freds Machine: utm Platform: Linux PlatformVersion: 4.4.0-96-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: dmri_group ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/21-09:49:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: freds Machine: utm Platform: Linux PlatformVersion: 4.4.0-96-generic CompilerName: GCC CompilerVersion: 40400
New invocation of trac-preproc
freds
utm
Linux utm 4.4.0-96-generic #119-Ubuntu SMP Tue Sep 12 14:59:54 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8192 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 64 kbytes
maxproc 127247
maxlocks unlimited
maxsignal 127247
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 32622380 8821488 12760508 14068 11040384 23309868
Swap: 3998716 0 3998716
#-------------------------------------
/usr/local/freesurfer/bin/trac-preproc
#-------------------------------------
#@# Image corrections jue sep 21 11:49:35 CEST 2017
mri_convert --bvec-voxel /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dtipd1467690.nii.gz /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_orig.nii.gz
mri_convert.bin --bvec-voxel /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dtipd1467690.nii.gz /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dtipd1467690.nii.gz...
TR=10180.98, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999986, -0.000540319, -0.00517901)
j_ras = (-0.00192893, 0.96228, 0.272053)
k_ras = (-0.00483666, -0.27206, 0.962268)
writing to /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_orig.nii.gz...
cp /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dtipd1467690.bvec /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_orig.bvecs
cp /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dtipd1467690.bval /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_orig.bvals
mv -f /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/bvecs.tmp /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_orig.bvecs
mv -f /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/bvals.tmp /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_orig.bvals
orientLAS /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_orig.nii.gz /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_orig_las.nii.gz
INFO: input image orientation is LAS
INFO: input image determinant is -4.46445
mri_convert -oni 144 -onj 144 -onk 80 -oid -0.999986 -0.000540319 -0.00517901 -ojd -0.00192893 0.96228 0.272053 -okd -0.00483666 -0.27206 0.962268 -oc 1.24112 16.1441 -9.59488 -rt nearest /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_orig.nii.gz /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_orig_las.nii.gz
mri_convert.bin -oni 144 -onj 144 -onk 80 -oid -0.999986 -0.000540319 -0.00517901 -ojd -0.00192893 0.96228 0.272053 -okd -0.00483666 -0.27206 0.962268 -oc 1.24112 16.1441 -9.59488 -rt nearest /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_orig.nii.gz /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_orig_las.nii.gz
normalizing out_i_direction: (-0.999986, -0.000540319, -0.00517901) -> (-0.999986, -0.000540319, -0.00517901)
normalizing out_j_direction: (-0.00192893, 0.96228, 0.272053) -> (-0.00192893, 0.96228, 0.272053)
normalizing out_k_direction: (-0.00483666, -0.27206, 0.962268) -> (-0.00483666, -0.27206, 0.962268)
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_orig.nii.gz...
TR=10180.98, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999986, -0.000540319, -0.00517901)
j_ras = (-0.00192893, 0.96228, 0.272053)
k_ras = (-0.00483666, -0.27206, 0.962268)
Reslicing using nearest
writing to /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_orig_las.nii.gz...
INFO: found /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_orig.bvals, copying
INFO: found /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_orig.bvecs, converting to LAS
mv -f /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_orig_las.bvecs /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/bvecs
mv -f /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_orig_las.bvals /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/bvals
eddy_correct /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_orig_las.nii.gz /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi.nii.gz 0
processing /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_tmp0000
processing /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_tmp0001
processing /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_tmp0002
processing /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_tmp0003
processing /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_tmp0004
processing /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_tmp0005
processing /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_tmp0006
processing /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_tmp0007
processing /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_tmp0008
processing /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_tmp0009
processing /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_tmp0010
processing /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_tmp0011
processing /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_tmp0012
processing /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_tmp0013
processing /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_tmp0014
processing /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi_tmp0015
mv -f /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/bvecs /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/bvecs.norot
xfmrot /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi.ecclog /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/bvecs.norot /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/bvecs
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.
printf: ‘0,0000000’: value not completely converted
printf: ‘0,0000000’: value not completely converted
printf: ‘0,0000000’: value not completely converted
printf: ‘0,4965249’: value not completely converted
printf: ‘-0,2872737’: value not completely converted
printf: ‘0,8191076’: value not completely converted
printf: ‘0,5022092’: value not completely converted
printf: ‘-0,6739593’: value not completely converted
printf: ‘-0,5418161’: value not completely converted
printf: ‘-0,7047899’: value not completely converted
printf: ‘-0,6833624’: value not completely converted
printf: ‘0,1904911’: value not completely converted
printf: ‘0,1071990’: value not completely converted
printf: ‘-0,4893399’: value not completely converted
printf: ‘0,8654805’: value not completely converted
printf: ‘-0,2918404’: value not completely converted
printf: ‘-0,4962466’: value not completely converted
printf: ‘0,8176598’: value not completely converted
printf: ‘-0,6296802’: value not completely converted
printf: ‘-0,1246230’: value not completely converted
printf: ‘0,7667931’: value not completely converted
printf: ‘-0,6607441’: value not completely converted
printf: ‘-0,0726702’: value not completely converted
printf: ‘0,7470859’: value not completely converted
printf: ‘0,6696415’: value not completely converted
printf: ‘-0,3853905’: value not completely converted
printf: ‘0,6348655’: value not completely converted
printf: ‘-0,7049923’: value not completely converted
printf: ‘-0,6106495’: value not completely converted
printf: ‘-0,3606861’: value not completely converted
printf: ‘0,6933248’: value not completely converted
printf: ‘-0,4278974’: value not completely converted
printf: ‘-0,5798311’: value not completely converted
printf: ‘0,7045444’: value not completely converted
printf: ‘-0,6899188’: value not completely converted
printf: ‘0,1662213’: value not completely converted
printf: ‘0,2784206’: value not completely converted
printf: ‘-0,8581491’: value not completely converted
printf: ‘-0,4313477’: value not completely converted
printf: ‘-0,2873936’: value not completely converted
printf: ‘-0,8514335’: value not completely converted
printf: ‘-0,4387083’: value not completely converted
printf: ‘-0,7072122’: value not completely converted
printf: ‘-0,6933477’: value not completely converted
printf: ‘0,1382744’: value not completely converted
printf: ‘-0,7023523’: value not completely converted
printf: ‘-0,3799939’: value not completely converted
printf: ‘-0,6019188’: value not completely converted
printf: ‘0,0000000’: value not completely converted
printf: ‘0,0000000’: value not completely converted
printf: ‘0,0000000’: value not completely converted
ln -sf /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi.nii.gz /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/data.nii.gz
mri_convert --frame 16 /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi.nii.gz /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/lowb.nii.gz
mri_convert.bin --frame 16 /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi.nii.gz /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/lowb.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial/t1pd1467690/dmri/dwi.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.999986, -0.000540319, -0.00517901)
j_ras = (-0.00192893, 0.96228, 0.272053)
k_ras = (-0.00483666, -0.27206, 0.962268)
keeping frame 16
ERROR: valid frame numbers are between 0 and 15
Linux utm 4.4.0-96-generic #119-Ubuntu SMP Tue Sep 12 14:59:54 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at jue sep 21 11:55:15 CEST 2017
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