Wed Dec 9 11:37:57 GMT 2015 /UK_Biobank_MRI/FS_Output/1006924_20216_2_0 /UK_Biobank_MRI/freesurfer/bin/recon-all -i /UK_Biobank_MRI/WorkDir/1006924_20216_2_0/1.3.12.2.1107.5.2.19.45594.201507130826307583602667.dcm -s 1006924_20216_2_0 -sd /UK_Biobank_MRI/FS_Output -no-isrunning -all subjid 1006924_20216_2_0 setenv SUBJECTS_DIR /UK_Biobank_MRI/FS_Output FREESURFER_HOME /UK_Biobank_MRI/freesurfer Actual FREESURFER_HOME /UK_Biobank_MRI/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-dev-20151207 Linux CCACE-PROC01 3.16.7-24-desktop #1 SMP PREEMPT Mon Aug 3 14:37:06 UTC 2015 (ec183cc) 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 193285 maxlocks unlimited maxsignal 193285 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 49495560 43531452 5964108 119680 242188 41644952 -/+ buffers/cache: 1644312 47851248 Swap: 314567668 1376 314566292 ######################################## program versions used $Id: recon-all,v 1.555 2015/11/17 14:18:41 mreuter 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: $ TimeStamp: 2015/12/09-11:37:57-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: talairach_avi,v 1.11 2015/01/13 20:22:51 nicks Exp $ mri_convert --version dev build (use --all-info flag for full version info) ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: tkregister2.c,v 1.129 2014/02/26 21:31:58 greve Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mri_normalize.c,v 1.85 2015/08/05 19:24:14 fischl Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mri_watershed.cpp,v 1.101 2015/07/10 18:57:33 greve Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mri_segment.c,v 1.43 2015/02/05 23:34:40 zkaufman Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mri_label2label.c,v 1.47 2014/12/22 19:59:18 greve Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mri_em_register.c,v 1.103 2015/08/26 16:51:09 fischl Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mri_ca_normalize.c,v 1.65 2015/10/10 17:28:19 fischl Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mri_ca_register.c,v 1.94 2015/11/24 20:36:25 greve Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mri_ca_label.c,v 1.109 2015/08/26 16:46:38 fischl Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mri_tessellate.c,v 1.38 2014/03/22 00:41:04 greve Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mris_inflate.c,v 1.44 2012/01/05 18:36:17 greve Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mris_sphere.c,v 1.60 2015/11/24 20:36:25 greve Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mris_fix_topology.c,v 1.49 2015/11/24 20:36:25 greve Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mris_make_surfaces.c,v 1.161 2015/11/06 16:00:27 fischl Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mris_register.c,v 1.62 2015/11/24 20:36:25 greve Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mris_volmask.cpp,v 1.26 2014/11/06 03:40:22 nicks Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mris_anatomical_stats.c,v 1.78 2015/07/06 21:58:51 greve Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mris_calc.c,v 1.53 2015/06/04 20:50:50 nicks Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.76 2015/09/22 19:55:12 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mri_robust_register.cpp,v 1.76 2015/09/22 19:55:12 mreuter Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.51 2015/09/22 20:57:47 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mri_robust_template.cpp,v 1.51 2015/09/22 20:57:47 mreuter Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mri_segstats.c,v 1.119 2015/10/06 18:46:12 greve Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2015/12/09-11:37:58-GMT BuildTimeStamp: Dec 7 2015 21:02:52 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: root Machine: CCACE-PROC01 Platform: Linux PlatformVersion: 3.16.7-24-desktop CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /UK_Biobank_MRI/freesurfer/average GCA RB_all_2015-08-04.gca GCASkull RB_all_withskull_2014-08-21.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /UK_Biobank_MRI/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /UK_Biobank_MRI/FS_Output/1006924_20216_2_0 mri_convert /UK_Biobank_MRI/WorkDir/1006924_20216_2_0/1.3.12.2.1107.5.2.19.45594.201507130826307583602667.dcm /UK_Biobank_MRI/FS_Output/1006924_20216_2_0/mri/orig/001.mgz mri_convert /UK_Biobank_MRI/WorkDir/1006924_20216_2_0/1.3.12.2.1107.5.2.19.45594.201507130826307583602667.dcm /UK_Biobank_MRI/FS_Output/1006924_20216_2_0/mri/orig/001.mgz $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $ reading from /UK_Biobank_MRI/WorkDir/1006924_20216_2_0/1.3.12.2.1107.5.2.19.45594.201507130826307583602667.dcm... Getting Series No INFO: Found 419 files in /UK_Biobank_MRI/WorkDir/1006924_20216_2_0 INFO: Scanning for Series Number 6 Scanning Directory INFO: found 208 files in series INFO: loading series header info. RunNo = 5 INFO: sorting. INFO: (256 256 208), nframes = 1, ismosaic=0 sdfi->UseSliceScaleFactor 0 datatype = 4, short=4, float=3 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 0.99588 -0.00207 -0.09064 2.28818; -0.00197 0.99873 -0.04441 6.02739; 0.09067 0.04441 0.99461 -18.01645; 0.00000 0.00000 0.00000 1.00000; FileName /UK_Biobank_MRI/WorkDir/1006924_20216_2_0/1.3.12.2.1107.5.2.19.45594.2015071308262694923402218.dcm Identification NumarisVer syngo MR D13 ScannerModel Skyra PatientName 4Q SD BV 3A^Bio Date and time StudyDate 20150713 StudyTime 081353.040000 SeriesTime 082634.795000 AcqTime 082133.247500 Acquisition parameters PulseSeq *tfl3d1_16ns Protocol T1_p2_1mm_fov256_sag_TI_880 PhEncDir ROW EchoNo 1 FlipAngle 8 EchoTime 2.01 InversionTime 880 RepetitionTime 2000 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 5 SeriesNo 6 ImageNo 1 NImageRows 256 NImageCols 256 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 112.1262 127.3281 94.2596 VolRes 1.0000 1.0000 1.0000 VolDim 256 256 208 Vc 0.0021 -0.9990 0.0444 Vr -0.0907 -0.0444 -0.9949 Vs -0.9959 0.0020 0.0907 VolCenter -2.7861 -6.0264 -17.9711 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) IsDWI = 0 INFO: no Siemens slice order reversal detected (good!). TR=2000.00, TE=2.01, TI=880.00, flip angle=8.00 i_ras = (0.00206772, -0.999011, 0.0444174) j_ras = (-0.0906682, -0.0444219, -0.99489) k_ras = (-0.995879, 0.00197012, 0.0906704) writing to /UK_Biobank_MRI/FS_Output/1006924_20216_2_0/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Wed Dec 9 11:38:42 GMT 2015 Found 1 runs /UK_Biobank_MRI/FS_Output/1006924_20216_2_0/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 /UK_Biobank_MRI/FS_Output/1006924_20216_2_0/mri/orig/001.mgz /UK_Biobank_MRI/FS_Output/1006924_20216_2_0/mri/rawavg.mgz /UK_Biobank_MRI/FS_Output/1006924_20216_2_0 mri_convert /UK_Biobank_MRI/FS_Output/1006924_20216_2_0/mri/rawavg.mgz /UK_Biobank_MRI/FS_Output/1006924_20216_2_0/mri/orig.mgz --conform mri_convert /UK_Biobank_MRI/FS_Output/1006924_20216_2_0/mri/rawavg.mgz /UK_Biobank_MRI/FS_Output/1006924_20216_2_0/mri/orig.mgz --conform $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $ reading from /UK_Biobank_MRI/FS_Output/1006924_20216_2_0/mri/rawavg.mgz... TR=2000.00, TE=2.01, TI=880.00, flip angle=8.00 i_ras = (0.00206772, -0.999011, 0.0444174) j_ras = (-0.0906682, -0.0444219, -0.99489) k_ras = (-0.995879, 0.00197012, 0.0906704) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /UK_Biobank_MRI/FS_Output/1006924_20216_2_0/mri/orig.mgz... mri_add_xform_to_header -c /UK_Biobank_MRI/FS_Output/1006924_20216_2_0/mri/transforms/talairach.xfm /UK_Biobank_MRI/FS_Output/1006924_20216_2_0/mri/orig.mgz /UK_Biobank_MRI/FS_Output/1006924_20216_2_0/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Wed Dec 9 11:38:55 GMT 2015 /UK_Biobank_MRI/FS_Output/1006924_20216_2_0/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 200 --stop 1e-4 --shrink 4 /UK_Biobank_MRI/FS_Output/1006924_20216_2_0/mri /UK_Biobank_MRI/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 200 --stop 1e-4 --shrink 4 nIters 1 $Id: mri_nu_correct.mni,v 1.23 2015/06/18 00:21:28 nicks Exp $ Linux CCACE-PROC01 3.16.7-24-desktop #1 SMP PREEMPT Mon Aug 3 14:37:06 UTC 2015 (ec183cc) x86_64 x86_64 x86_64 GNU/Linux Wed Dec 9 11:38:55 GMT 2015 tmpdir is ./tmp.mri_nu_correct.mni.13570 /UK_Biobank_MRI/FS_Output/1006924_20216_2_0/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.13570/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.13570/nu0.mnc -odt float $Id: mri_convert.c,v 1.225 2015/10/19 18:48:26 fischl Exp $ reading from orig.mgz... TR=2000.00, TE=2.01, TI=880.00, flip angle=8.00 i_ras = (-1, 4.65661e-10, 0) j_ras = (0, -3.20142e-10, -1) k_ras = (0, 1, 1.67347e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.13570/nu0.mnc... -------------------------------------------------------- Iteration 1 Wed Dec 9 11:38:57 GMT 2015 nu_correct -clobber ./tmp.mri_nu_correct.mni.13570/nu0.mnc ./tmp.mri_nu_correct.mni.13570/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.13570/0/ -iterations 1000 -stop 1e-4 -distance 200 -shrink 4 ERROR: file ./tmp.mri_nu_correct.mni.13570/nu1.mnc does not exist! Linux CCACE-PROC01 3.16.7-24-desktop #1 SMP PREEMPT Mon Aug 3 14:37:06 UTC 2015 (ec183cc) x86_64 x86_64 x86_64 GNU/Linux recon-all -s 1006924_20216_2_0 exited with ERRORS at Wed Dec 9 11:38:57 GMT 2015 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting