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nu_correct: crashed while running nu_estimate_np_and_em (termination status=512)
by Durgerian, Sally 22 Jan '19

22 Jan '19

External Email - Use Caution Dear freesurfer team, I have been having a problem running freesurfer on one computer. The same commands and data work fine on other machines. The error message is: nu_correct: crashed while running nu_estimate_np_and_em (termination status=512) Looking through the message board, others have had a similar problem. I have tried many of the suggestions offered without success. Note that I have the problem using freesurfer-6.0.0 as well as freesurfer-5.3.3-HCP Information on the error messages, OS and some of the things I have tried are described below. I have seen a few inquiries of this type never resolved as far as I can tell: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-April/056844.ht… https://neurostars.org/t/fmriprep-crashing-during-freesurfer-nu-correct/2108 Anything you can suggest would be appreciated. Thanks, Sally ------------------------------------------------------------------------------------------------------------------------ I did make sure it is not a space problem:https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-Februar… ------------------------------------------------------------------------------------------------------------------------ I successfully tried the minc commands which used /opt/minc/1.9.16/bin - the files were created: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-February/050030… mri_convert.bin orig.mgz orig.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to orig.nii... <nifti_image.../> Using s-form transform: -1.0000, 0.0000, 0.0000, 127.0000, 0.0000, 0.0000, 1.0000, -145.1500, 0.0000, -1.0000, 0.0000, 147.0000, 0.0000, 0.0000, 0.0000, 1.0000, name | start | step | cosines yspace | -145.1500 | 1.0000 | 0.0000 1.0000 0.0000 zspace | 147.0000 | -1.0000 | -0.0000 -0.0000 1.0000 xspace | 127.0000 | -1.0000 | 1.0000 -0.0000 -0.0000 mri_convert.bin junk.mnc junk.mgh $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from junk.mnc... TR=0.00, 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 junk.mgh... ------------------------------------------------------------------------------------------------------------------------ Here's the OS info: CentOS Linux release 7.4.1708 (Core) ------------------------------------------------------------------------------------------------------------------------ Here's the contents of recon-all.error: ------------------------------ SUBJECT FS_TEST DATE Tue Jan 22 17:07:30 GMT 2019 USER me HOST mycomputer PROCESSOR x86_64 OS Linux Linux mycomputer 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ /usr/local/freesurfer-6.0.0/bin/recon-all PWD <path to data>/FS_TEST/mri CMD mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 ------------------------------------------------------------------------------------------------------------------------ Here's the contents of FS_TEST/mri/mri_nu_correct.mni.log ------------------------------ <path to data>/FS_TEST/mri /usr/local/freesurfer-6.0.0/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux mycomputer 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Tue Jan 22 17:07:26 GMT 2019 Program nu_correct, built from: N3 1.12.00 tmpdir is ./tmp.mri_nu_correct.mni.81524 <path to data>/FS_TEST/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.81524/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.81524/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.81524/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue Jan 22 17:07:29 GMT 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.81524/nu0.mnc ./tmp.mri_nu_correct.mni.81524/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.81524/0/ -iterations 1000 -distance 50 Cannot read input file: ./tmp.mri_nu_correct.mni.81524/nu0.mnc [me@mycomputer:<path to data>/FS_TEST/mri/] [2019-01-22 17:07:29] running: /opt/minc/1.9.16/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.81524/0/ ./tmp.mri_nu_correct.mni.81524/nu0.mnc ./tmp.mri_nu_correct.mni.81524/nu1.imp nu_correct: crashed while running nu_estimate_np_and_em (termination status=512) ERROR: nu_correct ------------------------------------------------------------------------------------------------------------------------ ## The file that nu_correct is looking for is there: ls FS_TEST/mri/tmp.mri_nu_correct.mni.81524/nu0.mnc FS_TEST/mri/tmp.mri_nu_correct.mni.81524/nu0.mnc ------------------------------------------------------------------------------------------------------------------------ Here's the contents of FS_TEST/scripts/recon-all.log -------------------------------------------------------- Tue Jan 22 17:07:02 GMT 2019 <path to data>/FS_TEST /usr/local/freesurfer-6.0.0/bin/recon-all -i T1w_acpc_dc_restore.nii.gz -subjid FS_TEST -all subjid FS_TEST setenv SUBJECTS_DIR <path to data> FREESURFER_HOME /usr/local/freesurfer-6.0.0 Actual FREESURFER_HOME /usr/local/freesurfer-6.0.0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux mycomputer 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 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 4096 maxlocks unlimited maxsignal 514889 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 131844476 1382916 504384 2483852 129957176 127079832 Swap: 4194300 226832 3967468 ######################################## 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: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 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: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: N3 1.12.00 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 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: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 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: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/01/22-17:07:02-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: me Machine: mycomputer Platform: Linux PlatformVersion: 3.10.0-693.17.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer-6.0.0/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 /usr/local/freesurfer-6.0.0/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### <path to data>/FS_TEST mri_convert <path to data>/T1w_acpc_dc_restore.nii.gz <path to data>/FS_TEST/mri/orig/001.mgz mri_convert.bin <path to data>/T1w_acpc_dc_restore.nii.gz <path to data>/FS_TEST/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from <path to data>/T1w_acpc_dc_restore.nii.gz... TR=2300.00, 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 <path to data>/FS_TEST/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Tue Jan 22 17:07:12 GMT 2019 Found 1 runs <path to data>/FS_TEST/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 <path to data>/FS_TEST/mri/orig/001.mgz <path to data>/FS_TEST/mri/rawavg.mgz <path to data>/FS_TEST mri_convert <path to data>/FS_TEST/mri/rawavg.mgz <path to data>/FS_TEST/mri/orig.mgz --conform mri_convert.bin <path to data>/FS_TEST/mri/rawavg.mgz <path to data>/FS_TEST/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from <path to data>/FS_TEST/mri/rawavg.mgz... TR=2300.00, 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) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to <path to data>/FS_TEST/mri/orig.mgz... mri_add_xform_to_header -c <path to data>/FS_TEST/mri/transforms/talairach.xfm <path to data>/FS_TEST/mri/orig.mgz <path to data>/FS_TEST/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Tue Jan 22 17:07:26 GMT 2019 <path to data>/FS_TEST/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 <path to data>/FS_TEST/mri /usr/local/freesurfer-6.0.0/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux mycomputer 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Tue Jan 22 17:07:26 GMT 2019 Program nu_correct, built from: N3 1.12.00 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.81524 <path to data>/FS_TEST/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.81524/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.81524/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.81524/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue Jan 22 17:07:29 GMT 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.81524/nu0.mnc ./tmp.mri_nu_correct.mni.81524/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.81524/0/ -iterations 1000 -distance 50 Cannot read input file: ./tmp.mri_nu_correct.mni.81524/nu0.mnc [me@mycomputer:<path to data>/FS_TEST/mri/] [2019-01-22 17:07:29] running: /opt/minc/1.9.16/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.81524/0/ ./tmp.mri_nu_correct.mni.81524/nu0.mnc ./tmp.mri_nu_correct.mni.81524/nu1.imp nu_correct: crashed while running nu_estimate_np_and_em (termination status=512) ERROR: nu_correct Linux mycomputer 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s FS_TEST exited with ERRORS at Tue Jan 22 17:07:30 GMT 2019 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ------------------------------------------------------------------------------------------------------------------------

1 0

LME MATHLAB tools
by Getaneh Bayu 22 Jan '19

22 Jan '19

1 0

test
by Tefera, Getaneh B 22 Jan '19

22 Jan '19

External Email - Use Caution This is a test

1 0

LME MATLAB tools
by Tefera, Getaneh B 22 Jan '19

22 Jan '19

External Email - Use Caution Dear Freesurfer Experts, I have a question about how to interpret cortical thickness difference between groups using LME MATLAB tools. I have three groups(g0, g1, and g2) and five time points(t= 0,0.5, 1,2,3). I am trying to use LME model with random effects y-int and time from the base line. Based on the LME tutorial and the questions and answers from Freesurfer support list: Y=B1+B2*t+B3*g1+B4*g1*t+B5*g2+B6*g2*t+ .... To see the difference between group g0 and group g1, I constructed the following contrast matrix using the tutorial provided in LME MATLAB tools C = [zeros(1,3) [1 0 0] zeros(1,4)]; CM.C=[zeros(1,3) [1 0 0] zeros(1,4)]; Based on the tutorial I run the following functions. rhstats = lme_mass_fit_Rgw(X,[1 2],rhY,ni,rhTh0,rhRgs,rhsphere); F_rhstats = lme_mass_F(rhstats,CM); fs_write_fstats(F_rhstats,rhmri,'/backup/cross/rh_AB_cross_sig.mgh','sig'); nv=length(rhstats); Beta2 = zeros(1,nv); for i=1:nv if ~isempty(rhstats(i).Bhat) Beta2(i) = rhstats(i).Bhat(2); end; end; rhmri1 = rhmri; rhmri1.volsz(4) = 1; fs_write_Y(Beta2,rhmri1,'rhBeta2.mgh'); [detvtx,sided_pval,pth] = lme_mass_FDR2(F_rhstats.pval,F_rhstats.sgn,rhcortex,0.05,0); fs_write_Y(sided_pval,rhmri1,'spval.mgh'); When I view sig.mgh using tksurfer I see regions with red and blue color. 1) Does the result shows the oveall change for all the five time points? 2) How do I know the difference between the two groups for each 5 time points? 3) Does red means thickness of group A is lgreater than thickness of group B? 4) what does rhBeta2.mgh and spval.mgh tell us? How can I extract the information from the file? With regards Getaneh Hi Kersten, I am sorry I did not make the question more specific. I have three groups. I want see the power analysis by checking the sample size calculation for the cortical thickness analysis . [sz1,sz2] = lme_plannedSampleSize(Zi,ZiCol,Dhat,phisqhat,effsz,... dr,pw,alpha,gr_pr) my question is how can I get Dhat ( Estimated random effects covariance matrix) and phisqhat (Estimated intra-subject variability) to calculate the sample size of the pairs . Based on your suggestion to get Dhat and phisqhat I have to run " lme_fit_FS(X,[1,2],y ,ni)" When I run lme_fit_FS(X,[1,2],y ,ni), where Y is obtained from the following [Y,mri] = fs_read_Y('lh.thickness_sm10.mgh'), I get error. Which function with what argument is good to use to find Dhat and phisqhat? Are these values the same for left and right cortical thickness data? I am sorry for the inconvenience . with regards Getaneh ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.ha "rvard.edu> on behalf of Diers, Kersten /DZNE <Kersten.Diers(a)dzne.de> Sent: Thursday, January 11, 2018 3:50 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] LME Hi, I am not entirely sure that I understand the goal of this particular analysis, so I don't have any suggestions at the moment. Maybe you could give some more detail, if this is still an issue. Best regards, Kersten -----Original Message----- From: "Tefera, Getaneh B" <Getaneh.B.Tefera(a)uth.tmc.edu> Reply-to: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] LME Date: Wed, 10 Jan 2018 17:58:58 +0100 Dear Kersten, Thank you so much. When I run the procedure with left and right cortical thickness data I get different phisqhat values Phisqhat:0.2530 for the left and Phisqhat:0.0903 for the right The Dhat matrix is also different. Is that Ok? If so , shall I consider two sample sizes for the left and right? With regards Getaneh -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces @nmr.mgh.harvard.edu] On Behalf Of Diers, Kersten /DZNE Sent: Wednesday, January 10, 2018 7:10 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] LME Hi Getaneh, the estimates for D and phisq for a given analysis are contained within the data structure that is returned by the lme_fit_FS procedure. I.e. for the tutorial data, the command was: total_hipp_vol_stats = lme_fit_FS(X,[1 2],Y(:,1)+Y(:,2),ni); Dhat and phisqhat are fields of the 'total_hipp_vol_stats' structure, and can be accessed by typing 'total_hipp_vol_stats.Dhat' and 'total_hipp_vol_stats.phisqhat', respectively. Best regards, Kersten -----Original Message----- From: "Tefera, Getaneh B" <Getaneh.B.Tefera(a)uth.tmc.edu> Reply-to: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] LME Date: Tue, 9 Jan 2018 23:02:08 +0100 Hi Kersten. Thank you very much . I am not planning a new design for sample size calculation. Can you please help me how to find those values? Thank you Getaneh ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mg h.harvard.edu> on behalf of Diers, Kersten /DZNE <Kersten.Diers(a)dzne.d e > > Sent: Tuesday, January 9, 2018 5:56 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] LME Hi Getaneh, please find my responses below. -----Original Message----- From: "Tefera, Getaneh B" <Getaneh.B.Tefera(a)uth.tmc.edu> Reply-to: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] LME Date: Mon, 8 Jan 2018 22:54:49 +0100 Dear Freesurfer experts, I have three groups g0, g1, and g2. I am trying to use LME model with random effects y-int and time from the base line. Based on the LME tutorial and the questions and answers from Freesurfer support list: Y=B1+B2*t+B3*g1+B4*g1*t+B5*g2+B6*g2*t+ ... The slope of g0 : 0 1 0 0 0 0 The slope of g1: 0 1 0 1 0 0 The slope of g2: 0 1 0 0 0 1 The slope difference between g0 and g1: 0 0 0 1 0 0 The slope difference between g0 and g2: 0 0 0 0 0 1 The slope difference between g1 and g2: 0 0 0 -1 0 1 1) Is this contrast matrix correct to observe pairwise slope difference? In the tutorial the contrast matrix C = [zeros(3,3) [1 0 0 0 0; -1 0 1 0 0; 0 0 -1 0 1] zeros(3,6)] This is a correct matrix, but only for the particular design given in the tutorial, i.e. 4 groups and several covariates. Also, it is not strictly speaking a pairwise test, but will indicate if there is *any* difference between the slopes of the groups (i.e. it will give only one F- and p-value). If you specifically want to test differences between particular pairs, use contrast matrices with just a single row. 2) Is it necessary to combine contrast matrix of the pair difference the same as the tutorial? If so, my contrast matrix can be C=[0 0 0 1 0 0; 0 0 0 -1 0 1] It makes sense to look at the overall effect prior to looking at pairwise differences. If you don't have any additional covariates, that matrix is OK for looking the overall effect. Otherwise, add as many columns of zeros as you have covariates, similar to the tutorial. 3) How can we interpret the result for this contrast matrix? This is an F-test to detect if there is any difference between the slopes of the groups. 4) How can I obtain B1, B2, ... ? Consider the following command from the tutorial: total_hipp_vol_stats = lme_fit_FS(X,[1 2],Y(:,1)+Y(:,2),ni); Then B1 and B2 will be the first two entries of total_hipp_vol_stats.Bhat [sz1,sz2] = lme_plannedSampleSize(Zi,ZiCol,Dhat,phisqhat,effsz,... dr,pw,alpha,gr _pr) 5) For sample size calculation how can I get Dhat ( Estimated random effects covariance matrix) and phisqhat (Estimated intra-subject variability)? If you are planning a new design, these estimates should be based on prior knowledge and can be derived e.g. from a pilot study or from the literature. Best regards, Kersten With regards Getaneh _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harva rd.edu_mailman_listinfo_freesurfer&d=DwIGaQ&c=6vgNTiRn9_pqCD9hKx9JgXN1V apJQ8JVoF8oWH1AgfQ&r=f2w_aQllkjZisjakf5SS_8h7m7gQVFtFYcFC7K0Nk8k&m=w3Go ND77ORaREflQR6B1sxt8pIPGPzd8Oh_hzfJ_rhk&s=7GFfEuDrrPYWE- NE_mVYzsQUEvfZizwe853OSP2n_Zo&e= The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://urldefense.proofpoint.com/v2/ur l?u=http-3A__www.partners.org_co mplianceline&d=DwIGaQ&c=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ&r=f 2w_aQllkjZisjakf5SS_8h7m7gQVFtFYcFC7K0Nk8k&m=w3GoND77ORaREflQR6B1sxt8pI PGPzd8Oh_hzfJ_rhk&s=_JumR_-uS8QiP3xZfqqQ73pib0Pi-_MI1tUhsm2z5bA&e= . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harva rd.edu_mailman_listinfo_freesurfer&d=DwIGaQ&c=6vgNTiRn9_pqCD9hKx9JgXN1V apJQ8JVoF8oWH1AgfQ&r=f2w_aQllkjZisjakf5SS_8h7m7gQVFtFYcFC7K0Nk8k&m=hFe7 jo1OaOiJPYJN1sciBovML-jRiS7s_7h32CzMnCY&s=1X6nJq9b-3c- 2R4AgFUDMpC2l7itlL1ORo6Ipf9ljLs&e= The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://urldefense.proofpoint.com/v2/ur l?u=http- 3A__www.partners.org_complianceline&d=DwIGaQ&c=6vgNTiRn9_pqCD9hKx9JgXN1 VapJQ8JVoF8oWH1AgfQ&r=f2w_aQllkjZisjakf5SS_8h7m7gQVFtFYcFC7K0Nk8k&m=hFe 7jo1OaOiJPYJN1sciBovML- jRiS7s_7h32CzMnCY&s=lcIqRosuNio5NrM5LeJnk6gIGAk_7570yXenCjzgEdk&e= . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e- mail. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harva rd.edu_mailman_listinfo_freesurfer&d=DwIGaQ&c=6vgNTiRn9_pqCD9hKx9JgXN1V apJQ8JVoF8oWH1AgfQ&r=f2w_aQllkjZisjakf5SS_8h7m7gQVFtFYcFC7K0Nk8k&m=hFe7 jo1OaOiJPYJN1sciBovML-jRiS7s_7h32CzMnCY&s=1X6nJq9b-3c- 2R4AgFUDMpC2l7itlL1ORo6Ipf9ljLs&e= _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e… The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli… . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e…

1 0

LME MATLAB tools
by Tefera, Getaneh B 22 Jan '19

22 Jan '19

1 0

mapping a volumetric statistical map to the cerebellum surface
by john Anderson 22 Jan '19

22 Jan '19

External Email - Use Caution Dear FS experts, I have a statistical map from the output of a surface based analysis in subcortical regions. This statistical map shows significant difference between the groups in the cerebellum cortex. I reconstructed the cerebellar surfaces using the command "mri_tessalte). Now, I would like to map the volumetric statistical map to the constructed cerebellum surfaces. How can I do that? I tried the command "mri_vol2surf" in many different wants but it didn't work! Thanks for any guidance! John

2 3

fsaverage, brainstem and cerebellum
by john Anderson 22 Jan '19

22 Jan '19

External Email - Use Caution Dear FS experts, For visualization purposes, is there any way to show the cerebellum and brain stem regions (similar to the attached figure), this figure was published used CONN toolbox but I am not sure how they were able to map functional data in brain surface and show the cerebellum and brain stem with fsaverage. I appreciate any suggestion Jon

3 9

Problems with GM segmentation
by Rosalia Dacosta Aguayo 22 Jan '19

22 Jan '19

External Email - Use Caution Dear Free Surfer team, I few days ago I sent you personally the dicom files as well as the mask of the lesion you asked me for as I am having problems with GM segmentation. I would greatly appreciate if you could help me with this issue and tell me how I could manage the problem so I can solve it as I have many participants with the same issue. Yours sincerely, Rosalia

1 0

problems with bbregister's output image
by Sam W. 22 Jan '19

22 Jan '19

External Email - Use Caution Hello, I have registered example_func.nii.gz to the anatomical image using bbregister and then I looked at the registered file with tkregister2. $ bbregister --bold --lta reg.lta --mov example_func.nii.gz --s sub001 --o f-in-anat.nii.gz $ tkregister2 --s sub001 --mov f-in-anat.nii.gz --reg reg.lta --surf However if I click "coronal" tkregister2 shows the coronal surface as expected, whereas it shows the horizontal volume. If I click "horizontal" it shows the horizontal surface, whereas it shows the coronal volume. When I click "sagittal" the sagittal surface and volume are loaded, but the orientations are different. When I use the example_func as the mov image in tkregister2 I don't get this issue. I don't understand why the registered image "f-in-anat.nii.gz" is not aligned with the anatomical image with the tkregister2 command, because "f-in-anat.nii.gz" is exactly the output image of the bbregister transformation from functional to anatomical space, isn't it? Could someone please help me understand this? Thanks Sam

2 1

Error using mri_convert and recon-all
by Isil Bilgin 22 Jan '19

22 Jan '19

External Email - Use Caution Dear All, I want to convert my .nii structural file to .mgz file. I tried using mri_convert however I got a permission denied message. Since I am not the administrator in the system, hence I cannot change the permissions at the moment, so I guess I will have to wait for IT to help me soon. Instead, I wanted to try recon-all -i STRUCT_FOLDER1/xxx.dcm -i STRUCT_FOLDER2/xxx.dcm -autorecon1 -subjid 10 [/bash] command. However, I am getting an "if: Expression Syntax" error. So I am not sure why might be the cause for that, though. So I might really appreciate your helps please. I am using 4.4.0-139-generic #165-Ubuntu SMP Wed Oct 24 10:58:50 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux and bash. I found a similar discussion from the archive ( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-September/02569…) but there was no agreed solution I guess. So I wonder if there is any other way of converting the structural nii file to .mgz until these problems are solved? Thank you very much for the help in advance Kind regards Isil

3 6

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