Thu Feb 13 17:25:56 CET 2014 /home/opbg /usr/local/freesurfer/bin/trac-all -prep -c /media/opbg/dati/Baldacchini/Beal00/Beal/dmrirc.tutorial Subject Beal SUBJECTS_DIR /media/opbg/dati/Baldacchini/Beal00 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 opbg opbg Linux opbg 3.11.0-17-generic #31-Ubuntu SMP Mon Feb 3 21:52:43 UTC 2014 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 62584 maxlocks unlimited maxsignal 62584 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 8061960 1515888 6546072 0 242836 768620 -/+ buffers/cache: 504432 7557528 Swap: 976892 0 976892 ######################################## Program versions: $Id: trac-all,v 1.53 2013/12/04 16:36:01 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:25:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_motion ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2014/02/13-16:25:56-GMT BuildTimeStamp: Dec 6 2013 21:04:41 CVS: User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:25:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:25:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:25:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:25:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_group ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2014/02/13-16:25:56-GMT BuildTimeStamp: Dec 6 2013 21:04:41 CVS: User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc opbg opbg Linux opbg 3.11.0-17-generic #31-Ubuntu SMP Mon Feb 3 21:52:43 UTC 2014 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 62584 maxlocks unlimited maxsignal 62584 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 8061960 1516888 6545072 0 242896 768564 -/+ buffers/cache: 505428 7556532 Swap: 976892 0 976892 #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Thu Feb 13 17:25:56 CET 2014 mri_convert /media/opbg/dati/Baldacchini/Beal00/Beal//DTI.nii /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig.nii.gz mri_convert /media/opbg/dati/Baldacchini/Beal00/Beal//DTI.nii /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig.nii.gz INFO: using NIfTI-1 qform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/opbg/dati/Baldacchini/Beal00/Beal//DTI.nii... TR=7900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999848, -0.00501785, 0.0166881) j_ras = (1.76101e-05, 0.957354, 0.288916) k_ras = (0.0174262, -0.288873, 0.957209) writing to /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig.nii.gz... cp /media/opbg/dati/Baldacchini/Beal00/Beal/bvecs /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig.mghdti.bvecs cp /media/opbg/dati/Baldacchini/Beal00/Beal/bvals /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig.mghdti.bvals mv -f /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/bvecs.tmp /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig.mghdti.bvecs mv -f /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/bvals.tmp /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig.mghdti.bvals flip4fsl /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig.nii.gz /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -8.79909 fslswapdim /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig.nii.gz x y z /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig_flip.nii.gz INFO: found /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig_flip.mghdti.bvecs /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/bvecs mv -f /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig_flip.mghdti.bvals /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/bvals eddy_correct /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig_flip.nii.gz /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi.nii.gz 0 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0000 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0001 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0002 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0003 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0004 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0005 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0006 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0007 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0008 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0009 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0010 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0011 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0012 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0013 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0014 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0015 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0016 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0017 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0018 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0019 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0020 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0021 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0022 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0023 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0024 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0025 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0026 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0027 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0028 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0029 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0030 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0031 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0032 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0033 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0034 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0035 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0036 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0037 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0038 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0039 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0040 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0041 mv -f /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/bvecs /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/bvecs.norot xfmrot /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi.ecclog /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/bvecs.norot /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/bvecs ln -sf /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi.nii.gz /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/data.nii.gz fslroi /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi.nii.gz /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/lowb.nii.gz 0 1 fslmaths /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/lowb.nii.gz -Tmean /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/lowb.nii.gz bet /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/lowb.nii.gz /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/lowb_brain.nii.gz -m -f 0.3 mv -f /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/lowb_brain_mask.nii.gz /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/diff #------------------------------------- #@# Image quality assessment Thu Feb 13 17:33:04 CET 2014 /usr/local/freesurfer/bin/dmri_motion --dwi /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig.nii.gz --mat /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi.ecclog --bval /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/bvals --out /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_motion.txt cwd /home/opbg cmdline /usr/local/freesurfer/bin/dmri_motion --dwi /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig.nii.gz --mat /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi.ecclog --bval /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/bvals --out /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_motion.txt sysname Linux hostname opbg machine x86_64 user opbg Output motion measure file: /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_motion.txt Input transform file: /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi.ecclog Input DWI file: /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig.nii.gz Input b-value table: /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/bvals Low-b image intensity threshold: 100 Nominal diffusivity: 0.001 Loading volume-to-baseline affine transformations Computing between-volume head motion measures INFO: Processed transforms for 42 volumes Loading DWI volume series from /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig.nii.gz Loading b-value table from /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/bvals Computing within-volume head motion measures Done in 1.836 sec. dmri_motion done #------------------------------------- #@# Inter-subject registration Thu Feb 13 17:33:06 CET 2014 flirt -in /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/lowb_brain.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/lowb_brain_mni.nii.gz -omat /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/xfms/diff2mni.mat -cost corratio convert_xfm -omat /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/xfms/mni2diff.mat -inverse /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/xfms/diff2mni.mat #------------------------------------- #@# Masks Thu Feb 13 17:33:22 CET 2014 ln -sf /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/diff/lowb_brain_mask.nii.gz /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/nodif_brain_mask.nii.gz #------------------------------------- #@# Tensor fit Thu Feb 13 17:33:22 CET 2014 dtifit -k /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi.nii.gz -m /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/diff/lowb_brain_mask.nii.gz -r /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/bvecs -b /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/bvals -o /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dtifit 0 128 0 128 0 50 0 slices processed 1 slices processed 2 slices processed 3 slices processed 4 slices processed 5 slices processed 6 slices processed 7 slices processed 8 slices processed 9 slices processed 10 slices processed 11 slices processed 12 slices processed 13 slices processed 14 slices processed 15 slices processed 16 slices processed 17 slices processed 18 slices processed 19 slices processed 20 slices processed 21 slices processed 22 slices processed 23 slices processed 24 slices processed 25 slices processed 26 slices processed 27 slices processed 28 slices processed 29 slices processed 30 slices processed 31 slices processed 32 slices processed 33 slices processed 34 slices processed 35 slices processed 36 slices processed 37 slices processed 38 slices processed 39 slices processed 40 slices processed 41 slices processed 42 slices processed 43 slices processed 44 slices processed 45 slices processed 46 slices processed 47 slices processed 48 slices processed 49 slices processed #------------------------------------- #@# Priors Thu Feb 13 17:33:25 CET 2014 /usr/local/freesurfer/bin/dmri_train --outdir /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.Beal.2838.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/mni/lowb_brain_mask.bbr.nii.gz --fa /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dtifit_FA.nii.gz --cptdir /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/diff --reg /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/xfms/mni2diff.bbr.mat --ncpts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc ERROR: fio_pushd: /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/mni cwd /home/opbg cmdline /usr/local/freesurfer/bin/dmri_train --outdir /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.Beal.2838.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/mni/lowb_brain_mask.bbr.nii.gz --fa /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dtifit_FA.nii.gz --cptdir /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/diff --reg /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/xfms/mni2diff.bbr.mat --ncpts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc sysname Linux hostname opbg machine x86_64 user opbg Output directory: /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/mni Output directory in test subject's space: /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/diff Output base: lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr Training subject directory list: /tmp/subj33.Beal.2838.txt Location of streamline files relative to base: dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk Location of start ROI files relative to base: dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz Location of end ROI files relative to base: dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz Location of cortex masks relative to base: dlabel/mni/cortex+2mm.nii.gz Label ID's from aparc+aseg to add to cortex mask: 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz Brain mask for output subject: Linux opbg 3.11.0-17-generic #31-Ubuntu SMP Mon Feb 3 21:52:43 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Thu Feb 13 17:33:25 CET 2014 New invocation of trac-all Fri Feb 14 14:50:12 CET 2014 /home/opbg /usr/local/freesurfer/bin/trac-all -prep -c /media/opbg/dati/Baldacchini/Beal00/Beal/dmrirc.tutorial Subject Beal SUBJECTS_DIR /media/opbg/dati/Baldacchini/Beal00 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 opbg opbg Linux opbg 3.11.0-17-generic #31-Ubuntu SMP Mon Feb 3 21:52:43 UTC 2014 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 62584 maxlocks unlimited maxsignal 62584 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 8061960 5614996 2446964 0 1268252 1474888 -/+ buffers/cache: 2871856 5190104 Swap: 976892 0 976892 ######################################## Program versions: $Id: trac-all,v 1.53 2013/12/04 16:36:01 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/14-13:50:12-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_motion ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2014/02/14-13:50:13-GMT BuildTimeStamp: Dec 6 2013 21:04:41 CVS: User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/14-13:50:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/14-13:50:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/14-13:50:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/14-13:50:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_group ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2014/02/14-13:50:13-GMT BuildTimeStamp: Dec 6 2013 21:04:41 CVS: User: opbg Machine: opbg Platform: Linux PlatformVersion: 3.11.0-17-generic CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc opbg opbg Linux opbg 3.11.0-17-generic #31-Ubuntu SMP Mon Feb 3 21:52:43 UTC 2014 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 62584 maxlocks unlimited maxsignal 62584 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 8061960 5645840 2416120 0 1268676 1504052 -/+ buffers/cache: 2873112 5188848 Swap: 976892 0 976892 #------------------------------------- /usr/local/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Fri Feb 14 14:50:13 CET 2014 mri_convert /media/opbg/dati/Baldacchini/Beal00/Beal//DTI.nii /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig.nii.gz mri_convert /media/opbg/dati/Baldacchini/Beal00/Beal//DTI.nii /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig.nii.gz INFO: using NIfTI-1 qform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/opbg/dati/Baldacchini/Beal00/Beal//DTI.nii... TR=7900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999848, -0.00501785, 0.0166881) j_ras = (1.76101e-05, 0.957354, 0.288916) k_ras = (0.0174262, -0.288873, 0.957209) writing to /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig.nii.gz... cp /media/opbg/dati/Baldacchini/Beal00/Beal/bvecs /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig.mghdti.bvecs cp /media/opbg/dati/Baldacchini/Beal00/Beal/bvals /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig.mghdti.bvals mv -f /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/bvecs.tmp /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig.mghdti.bvecs mv -f /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/bvals.tmp /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig.mghdti.bvals flip4fsl /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig.nii.gz /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -8.79909 fslswapdim /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig.nii.gz x y z /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig_flip.nii.gz INFO: found /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig_flip.mghdti.bvecs /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/bvecs mv -f /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig_flip.mghdti.bvals /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/bvals eddy_correct /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig_flip.nii.gz /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi.nii.gz 0 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0000 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0001 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0002 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0003 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0004 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0005 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0006 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0007 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0008 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0009 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0010 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0011 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0012 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0013 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0014 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0015 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0016 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0017 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0018 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0019 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0020 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0021 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0022 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0023 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0024 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0025 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0026 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0027 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0028 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0029 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0030 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0031 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0032 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0033 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0034 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0035 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0036 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0037 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0038 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0039 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0040 processing /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_tmp0041 mv -f /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/bvecs /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/bvecs.norot xfmrot /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi.ecclog /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/bvecs.norot /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/bvecs ln -sf /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi.nii.gz /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/data.nii.gz fslroi /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi.nii.gz /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/lowb.nii.gz 0 1 fslmaths /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/lowb.nii.gz -Tmean /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/lowb.nii.gz bet /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/lowb.nii.gz /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/lowb_brain.nii.gz -m -f 0.3 mv -f /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/lowb_brain_mask.nii.gz /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/diff #------------------------------------- #@# Image quality assessment Fri Feb 14 14:57:24 CET 2014 /usr/local/freesurfer/bin/dmri_motion --dwi /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig.nii.gz --mat /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi.ecclog --bval /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/bvals --out /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_motion.txt cwd /home/opbg cmdline /usr/local/freesurfer/bin/dmri_motion --dwi /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig.nii.gz --mat /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi.ecclog --bval /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/bvals --out /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_motion.txt sysname Linux hostname opbg machine x86_64 user opbg Output motion measure file: /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_motion.txt Input transform file: /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi.ecclog Input DWI file: /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig.nii.gz Input b-value table: /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/bvals Low-b image intensity threshold: 100 Nominal diffusivity: 0.001 Loading volume-to-baseline affine transformations Computing between-volume head motion measures INFO: Processed transforms for 42 volumes Loading DWI volume series from /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi_orig.nii.gz Loading b-value table from /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/bvals Computing within-volume head motion measures Done in 2.17 sec. dmri_motion done #------------------------------------- #@# Inter-subject registration Fri Feb 14 14:57:26 CET 2014 flirt -in /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/lowb_brain.nii.gz -ref /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz -out /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/lowb_brain_mni.nii.gz -omat /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/xfms/diff2mni.mat -cost corratio convert_xfm -omat /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/xfms/mni2diff.mat -inverse /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/xfms/diff2mni.mat #------------------------------------- #@# Masks Fri Feb 14 14:57:42 CET 2014 ln -sf /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/diff/lowb_brain_mask.nii.gz /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/nodif_brain_mask.nii.gz #------------------------------------- #@# Tensor fit Fri Feb 14 14:57:42 CET 2014 dtifit -k /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dwi.nii.gz -m /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/diff/lowb_brain_mask.nii.gz -r /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/bvecs -b /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/bvals -o /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dtifit 0 128 0 128 0 50 0 slices processed 1 slices processed 2 slices processed 3 slices processed 4 slices processed 5 slices processed 6 slices processed 7 slices processed 8 slices processed 9 slices processed 10 slices processed 11 slices processed 12 slices processed 13 slices processed 14 slices processed 15 slices processed 16 slices processed 17 slices processed 18 slices processed 19 slices processed 20 slices processed 21 slices processed 22 slices processed 23 slices processed 24 slices processed 25 slices processed 26 slices processed 27 slices processed 28 slices processed 29 slices processed 30 slices processed 31 slices processed 32 slices processed 33 slices processed 34 slices processed 35 slices processed 36 slices processed 37 slices processed 38 slices processed 39 slices processed 40 slices processed 41 slices processed 42 slices processed 43 slices processed 44 slices processed 45 slices processed 46 slices processed 47 slices processed 48 slices processed 49 slices processed #------------------------------------- #@# Priors Fri Feb 14 14:57:45 CET 2014 /usr/local/freesurfer/bin/dmri_train --outdir /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.Beal.4052.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/mni/lowb_brain_mask.bbr.nii.gz --fa /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dtifit_FA.nii.gz --cptdir /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/diff --reg /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/xfms/mni2diff.bbr.mat --ncpts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc ERROR: fio_pushd: /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/mni cwd /home/opbg cmdline /usr/local/freesurfer/bin/dmri_train --outdir /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.Beal.4052.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/mni/lowb_brain_mask.bbr.nii.gz --fa /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/dtifit_FA.nii.gz --cptdir /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/diff --reg /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dmri/xfms/mni2diff.bbr.mat --ncpts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc sysname Linux hostname opbg machine x86_64 user opbg Output directory: /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/mni Output directory in test subject's space: /media/opbg/dati/Baldacchini/Beal00/Beal/Beal/dlabel/diff Output base: lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr Training subject directory list: /tmp/subj33.Beal.4052.txt Location of streamline files relative to base: dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk Location of start ROI files relative to base: dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz Location of end ROI files relative to base: dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz Location of cortex masks relative to base: dlabel/mni/cortex+2mm.nii.gz Label ID's from aparc+aseg to add to cortex mask: 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz Brain mask for output subject: Linux opbg 3.11.0-17-generic #31-Ubuntu SMP Mon Feb 3 21:52:43 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Fri Feb 14 14:57:45 CET 2014