Thu Apr 1 11:15:48 IST 2021 /home/amar/Testing/subj06 /home/amar/freesurfer/bin/recon-all -s subj06 -i 1.dcm -all subjid subj06 setenv SUBJECTS_DIR /home/amar/Testing FREESURFER_HOME /home/amar/freesurfer Actual FREESURFER_HOME /home/amar/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux amar-GV62VR-7RF 5.8.0-48-generic #54~20.04.1-Ubuntu SMP Sat Mar 20 13:40:25 UTC 2021 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 65536 kbytes maxproc 63356 maxlocks unlimited maxsignal 63356 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 16278272 3598148 9733640 261716 2946484 12076276 Swap: 2097148 0 2097148 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/04/01-05:45:49-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: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/04/01-05:45:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: amar Machine: amar-GV62VR-7RF Platform: Linux PlatformVersion: 5.8.0-48-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /home/amar/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /home/amar/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /home/amar/Testing/subj06 mri_convert /home/amar/Testing/1.dcm /home/amar/Testing/subj06/mri/orig/001.mgz mri_convert.bin /home/amar/Testing/1.dcm /home/amar/Testing/subj06/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/amar/Testing/1.dcm... Getting Series No INFO: Found 8 files in /home/amar/Testing INFO: Scanning for Series Number 5 Scanning Directory INFO: found 2 files in series INFO: loading series header info. RunNo = 4 INFO: sorting. sdfiSameSlicePos() eps = 0.000001 WARNING: file /home/amar/Testing/2.dcm does not contain a Siemens ASCII header has this file been anonymized? Proceeding as best as I can ... INFO: (400 400 2), nframes = 1, ismosaic=0 sdfi->UseSliceScaleFactor 0 datatype = 4, short=4, float=3 PE Dir unknown UNKNOWN FileName /home/amar/Testing/2.dcm Identification NumarisVer syngo MI.PET/CT 2012A ScannerModel SOMATOM Definition AS_mCT PatientName 130_S_4405 Date and time StudyDate 20140131 StudyTime 084142.406000 SeriesTime 085302.000000 AcqTime 090802.000001 Acquisition parameters PulseSeq unknown Protocol unknown PhEncDir unknown EchoNo 390 FlipAngle 0 EchoTime 0 InversionTime -1 RepetitionTime 0 PhEncFOV 0 ReadoutFOV 0 Image information RunNo 4 SeriesNo 5 ImageNo 390 NImageRows 400 NImageCols 400 NFrames 1 SliceArraylSize 0 IsMosaic 0 ImgPos 206.2890 390.5760 655.0470 VolRes 1.0182 1.0182 2.0270 VolDim 400 400 2 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs 0.0000 0.0000 -1.0000 VolCenter 2.6470 186.9340 653.0200 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) IsDWI = 0 INFO: no Siemens slice order reversal detected (good!). TR=0.00, TE=0.00, TI=-1.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (0, 0, -1) writing to /home/amar/Testing/subj06/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Thu Apr 1 11:15:49 IST 2021 Found 1 runs /home/amar/Testing/subj06/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 /home/amar/Testing/subj06/mri/orig/001.mgz /home/amar/Testing/subj06/mri/rawavg.mgz /home/amar/Testing/subj06 mri_convert /home/amar/Testing/subj06/mri/rawavg.mgz /home/amar/Testing/subj06/mri/orig.mgz --conform mri_convert.bin /home/amar/Testing/subj06/mri/rawavg.mgz /home/amar/Testing/subj06/mri/orig.mgz --conform WARNING ==================++++++++++++++++++++++++======================================= The physical sizes are (407.28 mm, 407.28 mm, 4.05 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 408 slices. If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu). ==================================================++++++++++++++++++++++++=============== $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/amar/Testing/subj06/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=-1.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (0, 0, -1) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/amar/Testing/subj06/mri/orig.mgz... **************************************** ERROR! FOV=408.000 > 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. **************************************** Linux amar-GV62VR-7RF 5.8.0-48-generic #54~20.04.1-Ubuntu SMP Sat Mar 20 13:40:25 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s subj06 exited with ERRORS at Thu Apr 1 11:15:57 IST 2021 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting