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