Dear all, I've been running the FreeSurferPipelineBatch code with some of the data that we have and the program exits out of this when calculating the Talairach coordinates using the recon-all script from the FreeSurfer directory. I've attached the log file I get when I run the script.
I also get the same error when running the FreeSurferPipelineBatch script with the example data from the HCP. Any suggestions on where I'm going wrong? Kind regards, Dinal Jayasekera PhD Student in Biomedical Engineering Washington University in St. Louis B.S. in Biomedical Engineering | Minor in Biophysics and Electrical Engineering The George Washington University _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Mon Jul 23 14:13:19 CDT 2018 /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9 /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/projects/freesurfer/bin/recon-all -i /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/T1w_acpc_dc_restore_1mm.nii.gz -subjid Control_9 -sd /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w -motioncor -talairach -nuintensitycor -normalization -openmp 8 subjid Control_9 setenv SUBJECTS_DIR /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w FREESURFER_HOME /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/projects/freesurfer Actual FREESURFER_HOME /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/projects/freesurfer build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v5.3.0-HCP Linux FSL-1 4.15.0-24-generic #26~16.04.1-Ubuntu SMP Fri Jun 15 14:35:08 UTC 2018 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 513899 maxlocks unlimited maxsignal 513899 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 131696752 3611252 1212216 1416632 126873284 125250072 Swap: 133881852 0 133881852 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:19-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: Feb 1 2014 03:28:19 CVS: $Id: mris_make_surfaces.c,v 1.147 2014/01/29 20:42:02 fischl Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2018/07/23-19:13:20-GMT BuildTimeStamp: May 13 2013 18:53:32 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: functionalspinelab Machine: FSL-1 Platform: Linux PlatformVersion: 4.15.0-24-generic CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/projects/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/projects/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9 mri_convert /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/T1w_acpc_dc_restore_1mm.nii.gz /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9/mri/orig/001.mgz mri_convert /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/T1w_acpc_dc_restore_1mm.nii.gz /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/T1w_acpc_dc_restore_1mm.nii.gz... TR=2500.00, 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) writing to /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Mon Jul 23 14:13:23 CDT 2018 Found 1 runs /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9/mri/orig/001.mgz /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9/mri/rawavg.mgz /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9 mri_convert /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9/mri/rawavg.mgz /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9/mri/orig.mgz --conform mri_convert /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9/mri/rawavg.mgz /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9/mri/rawavg.mgz... TR=2500.00, 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) Original Data has (1, 1, 1) mm size and (181, 217, 181) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9/mri/orig.mgz... mri_add_xform_to_header -c /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9/mri/transforms/talairach.xfm /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9/mri/orig.mgz /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Jul 23 14:13:31 CDT 2018 /mnt/md126p2/Ubuntu/home/functionalspinelab/Desktop/Dinal/mystudy/Control_9/T1w/Control_9/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux FSL-1 4.15.0-24-generic #26~16.04.1-Ubuntu SMP Fri Jun 15 14:35:08 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s Control_9 exited with ERRORS at Mon Jul 23 14:13:35 CDT 2018 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting