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ERROR: recon-all -subcortseg
by Akio Yamamoto 23 May '13

23 May '13

Hi Freesurfer experts, After installing v5.3.0 (CentOS 6 64bit), the command "recon-all -s test -i sample-001.mgz -i sample-002.mgz -autorecon1" finished without error. Then, when I ran "recon-all -s test -subcortseg", I got the following error: ========== $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --ctab /usr/local/freesurfer/5.3.0/dist/ASegStatsLUT.txt --subject test sysname Linux hostname dhcp006 machine x86_64 user yamamoto UseRobust 0 atlas_icv (eTIV) = 1629767 mm^3 (det: 1.195328 ) MRISread(/home/yamamoto/freesurfer/5.3.0/dist/subjects/test/surf/lh.white): could not open file ========== I encountered this error in v5.2.0, and am still having the same error in v5.3.0. Is this a known issue? I attached the recon-all.log file. Any help is greatly appreciated. Best, Akio

3 4

recon-all failed with errors
by Cat Chong 23 May '13

23 May '13

Dear Experts, I am able to to initiate recon-all but it fails at various stages during the recon-all process even though I should have plenty memory available to run the process. This is the error message I am getting and below is the log file. I am using the freesurfer-Darwin-lion-stable-pub-v5.3.0 on a Mac OSX Lion 10.7.5 INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu May 23 14:05:55 MST 2013 /home/m117348/Documents/Schwedt_MRI/1004_out/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n Darwin r5007111.mayo.edu 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 recon-all -s 1004_out exited with ERRORS at Thu May 23 14:06:26 MST 2013 ------------------------------------- FREESURFER_HOME /Applications/freesurfer/ Actual FREESURFER_HOME /Applications/freesurfer build-stamp.txt: freesurfer-Darwin-lion-stable-pub-v5.3.0 Darwin r5007111.mayo.edu 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 256 memorylocked unlimited maxproc 709 PhysMem: 1987M wired, 5293M active, 2487M inactive, 9767M used, 22G free. ######################################## 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: 2013/05/23-21:05:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 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: 2013/05/23-21:05:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks(a)aspasia.local (i686-apple-darwin10.2.0) on 2010-02-26 at 14:19:30 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:12-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 $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: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 $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: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-21:05:13-GMT BuildTimeStamp: May 14 2013 09:12:01 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: m117348 Machine: r5007111.mayo.edu Platform: Darwin PlatformVersion: 11.4.2 CompilerName: GCC CompilerVersion: 40200 ####################################### GCADIR /Applications/freesurfer//average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /Applications/freesurfer//average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /home/m117348/Documents/Schwedt_MRI/1004_out \n mri_convert /home/m117348/Documents/Schwedt_MRI/1004.mgz /home/m117348/Documents/Schwedt_MRI/1004_out/mri/orig/001.mgz \n mri_convert /home/m117348/Documents/Schwedt_MRI/1004.mgz /home/m117348/Documents/Schwedt_MRI/1004_out/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/m117348/Documents/Schwedt_MRI/1004.mgz... TR=2400.00, TE=3.16, TI=1000.00, flip angle=8.00 i_ras = (0.0109648, -0.99885, 0.0466696) j_ras = (-0.0118836, -0.0467993, -0.998834) k_ras = (-0.999869, -0.0103974, 0.0123829) writing to /home/m117348/Documents/Schwedt_MRI/1004_out/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Thu May 23 14:05:27 MST 2013 Found 1 runs /home/m117348/Documents/Schwedt_MRI/1004_out/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. \n cp /home/m117348/Documents/Schwedt_MRI/1004_out/mri/orig/001.mgz /home/m117348/Documents/Schwedt_MRI/1004_out/mri/rawavg.mgz \n /home/m117348/Documents/Schwedt_MRI/1004_out \n mri_convert /home/m117348/Documents/Schwedt_MRI/1004_out/mri/rawavg.mgz /home/m117348/Documents/Schwedt_MRI/1004_out/mri/orig.mgz --conform \n mri_convert /home/m117348/Documents/Schwedt_MRI/1004_out/mri/rawavg.mgz /home/m117348/Documents/Schwedt_MRI/1004_out/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/m117348/Documents/Schwedt_MRI/1004_out/mri/rawavg.mgz... TR=2400.00, TE=3.16, TI=1000.00, flip angle=8.00 i_ras = (0.0109648, -0.99885, 0.0466696) j_ras = (-0.0118836, -0.0467993, -0.998834) k_ras = (-0.999869, -0.0103974, 0.0123829) Original Data has (1, 1, 1) mm size and (256, 256, 176) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/m117348/Documents/Schwedt_MRI/1004_out/mri/orig.mgz... \n mri_add_xform_to_header -c /home/m117348/Documents/Schwedt_MRI/1004_out/mri/transforms/talairach.xfm /home/m117348/Documents/Schwedt_MRI/1004_out/mri/orig.mgz /home/m117348/Documents/Schwedt_MRI/1004_out/mri/orig.mgz \n INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu May 23 14:05:55 MST 2013 /home/m117348/Documents/Schwedt_MRI/1004_out/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n Darwin r5007111.mayo.edu 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 recon-all -s 1004_out exited with ERRORS at Thu May 23 14:06:26 MST 2013 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Re: [Freesurfer] Siemens dicom error on mri_convert
by Douglas N Greve 23 May '13

23 May '13

Is it straight off the scanner? It does not have the siemens ascii header which usually means that it has been manipulated in some way. You can try using mri_convert with --it dicom doug On 05/23/2013 12:57 PM, Cat Chong wrote: > no it has not. > > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* freesurfer(a)nmr.mgh.harvard.edu > *Sent:* Thursday, May 23, 2013 9:43 AM > *Subject:* Re: [Freesurfer] Siemens dicom error on mri_convert > > has this file been anonymized? > On 05/23/2013 12:39 PM, Cat Chong wrote: > > Hello Experts, > > I am trying to run the mri_convert command prior to the recon-all > > command on Siemens T1 dicoms (as suggested in the archives). I am > > using freesurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0, > > Mac OS X Lion 10.7.5 > > I am using the command below: > > mri_convert -it siemens_dicom -ot mgz 1002/IM-0001-0001.dcm 2001.mgz > > Below is the command line error I receive, it is a similar error I > > receive when I try to use the command recon-all on the Siemens dicoms. > > I have used freesurfer before on GE dicoms and never had a problem > > running recon-all. Is this error message particular to the Siemens > > dicoms, and would you be able to tell me how to proceed? > > Thank you very much for you help, > > Cat > > reading from 1002/IM-0001-0001.dcm... > > Getting Series No > > Scanning Directory > > INFO: Found 130 files in 1002 > > INFO: Scanning for Series Number 2 > > INFO: found 128 files in series > > INFO: loading series header info. > > INFO: sorting. > > RunNo = 1 > > WARNING: Run 1 appears to be truncated > > Files Found: 128, Files Expected (lRep+1): 1 > > FileName 1002/IM-0001-0001.dcm > > Identification > > NumarisVer syngo MR D11 > > ScannerModel Skyra > > PatientName RS-FMRI^RS-FMRI > > Date and time > > StudyDate 20130222 > > StudyTime 082109.140000 > > SeriesTime 082812.906000 > > AcqTime 082237.315000 > > Acquisition parameters > > PulseSeq *tfl3d1_16ns > > Protocol SAG MP Rage > > PhEncDir ROW > > EchoNo 1 > > FlipAngle 8 > > EchoTime 3.03 > > InversionTime 1000 > > RepetitionTime 2400 > > PhEncFOV 0 > > ReadoutFOV 0 > > Image information > > RunNo 1 > > SeriesNo 2 > > ImageNo 1 > > NImageRows 256 > > NImageCols 256 > > NFrames 128 > > SliceArraylSize 0 > > IsMosaic 1 > > ImgPos -78.6002 128.0000 93.1332 > > VolRes 1.0000 1.0000 1.2500 > > VolDim 0 0 0 > > Vc -0.0000 -1.0000 0.0000 > > Vr -0.0000 -0.0000 -1.0000 > > Vs 0.0000 0.0000 0.0000 > > VolCenter 0.0000 0.0000 0.0000 > > TransferSyntaxUID 1.2.840.10008.1.2.1 > > WARNING: file 1002/IM-0001-0001.dcm does not contain a Siemens ASCII > > header > > has this file been anonymized? > > ERROR: cannot unpack mosiacs without ASCII header > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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 > http://www.partners.org/complianceline > <http://www.partners.org/complianceline>. 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. > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Contrast vector & link with folder name and QDEC-generated sentence
by Tudor Popescu 23 May '13

23 May '13

Hello, I was wondering whether someone could please explain exactly how values are assigned to each column of the design matrix, when a C.dat contrast vector (e.g. [0, 0, 1, -1]) is created, in the "correlation" as opposed to in the "intercept" types of contrasts ... I am asking this because I have a hard time understanding how does a contrast's automatically-created namesake folder (which includes the keywords 'Avg'/'Diff'/'X' and 'Intercept'/'Cor'), such as "lh-Diff-group1-group2-Cor-thickness-behaviouralMeasure", as well as its phrasing in QDEC ("Does the thickness-age correlation differ between group1 and group2?"), exactly correspond to that C.dat vector. Many thanks! Tudor

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Re: [Freesurfer] Still confused by group analysis..
by Douglas N Greve 23 May '13

23 May '13

Sorry, that read gender and age. The contrast takes age into account, it is just a problem with the code that generates the sentence. Have not had a chance to answer the others, I thought I'd try to get one wrapped up. It looks like you added a few more questions at the end. Unless they are closely related to the previous questions, can you send them separately, it is hard to keep track with all the replies to replies. doug On 05/23/2013 02:51 PM, Tudor Popescu wrote: > Thanks Doug, however my question was why does QDEC not also display a > contrast to the effect of "Does the avg thickness, accounting for > *gender and age*, differ between group1 and group2?", instead it only > displays "Does the avg thickness, accounting for *gender*, differ > between group1 and group2?" > > Also, I was wondering whether you got a chance to see my other > questions from the same email.. > > Many thanks! > Tudor > > On 23 May 2013 17:49, Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > when I run qdec using your table and my data, I get a full > complement of contrasts, see attached. > doug > > > > > On 05/22/2013 01:43 PM, Tudor Popescu wrote: > > > > 1) In a design with group and gender as discrete > factors and age > > as a continuous factor, why is it that QDEC only > displays the > > contrast "Does the avg thickness, accounting for > gender, differ > > between group1 and group2?" and not also > "..acounting for gender > > and age,.."? > > > I thought that it would have. Are you coding age > as a nuisance > variable? > Also, are you coding gender as a continuous > variable? That is > something > you should not do. > > > I was not coding age as a nuisance variable but as a > continuous variable (co-variate). Gender was a > discrete/fixed > factor but I'm not sure whether this means > 'continuous' in the > sense discussed in your exchange with Arman. Anyway, > in this > configuration, it seems gender and age are not accounted > (controlled) for at the same time. > > It should be. Can you send your qdec table? > > See attached > > > > > 3) From the group tutorial, I see that > mris_preproc > has to be > > called with flag "--cache-in > ess.fwhm10thickn.fsaverage". > However, > > after running recon-all (including with the > –qcache > option) > on all > > my subjects, none of their folders contains > a file named > > ?h.thickness.fwhm10.fsaverage.mgh > > > Where does it say to use ess.fwhm10thickn.fsaverage? > > Sorry, typo. The flag is actually "--cache-in > thickness.fwhm10.fsaverage", I file that I do not have > after > having run recon-all (including with the --qcache option) > > Try running recon-all again with just the --qcache flag. > > This is what I had done previously; the command was: > recon-all -s C${i} -qcache > where the ${i} was a counter in a script, to run the command > on all my subjects > > > > > 5) What is the difference between running > make_average_subject and > > running mris_preproc with --target fsaverage? > > > make average subject makes the average subject. > mris_preproc > samples the > data into a common space defined by the registration > surface and > concatenates the input subjects into a single stack. > > But should the registration surface used by > mris_preproc (i.e. > its "--target" flag) come from the 'average' subject > or from > 'fsaverage'? In other words, which one of these > becomes the > study-specific template? > > You have to tell mris_preproc both the target and the surface > registration to use if you want to use a different > average subject. > > The command I used is: > > mris_preproc --fsgd group_gender__age.fsgd --target average > --hemi rh --meas thickness --out rh.thickness.mgh > > So if I understand correctly, the fact that I didn't indicate > a surface registration means that the surface from the > "average" subject will be used, rather than the one from > "fsaverage"? I still don't understand the difference between > those two, and which, if any, can be referred to as the > study-specific template. > > B) All concatenated volumes from mris_preproc's output > files > (?h.thickness.mgh) appear blank in freeview, even > though the > individual structurals all look fine. Also, > lh.thickness.mgh > and rh.thickness.mgh have, surprisingly, *exactly* the > same > file size, which is also a bit small (~25MB) to be able to > contain 38 registered structurals, which suggests > something > went wrong... > > These are surface overlay files, not volumes. You can't load > surfaces as volumes in freeview. > > So assuming I don't visually inspect the surface overlays, can > I assume that mris_preproc ran fine if lh.thickness.mgh and > rh.thickness.mgh have exactly the same file size? > > C) When running mri_surf2surf, I get an error saying > that file > /surf/lh.white cannot be opened. The 'average' folder > produced > after I ran make_average_subject does not contain a > /surf/lh.white file, only a /surf/lh.white_avg file! I > didn’t > find a log file from make_average_subject so i don’t > know if > it gave any errors.. > > It's extremely helpful to have command lines ... > > > Sorry, my commands were: > make_average_subject --subjects C01 C02 C03 C04 C05 C06 C07 > C08 C09 C10 C11 C12 C13 C14 C15 C16 C17 C18 C19 M01 M02 M03 > M04 M05 M06 M07 M08 M09 M10 M11 M12 M13 M14 M15 M16 M17 M18 M19 > mri_surf2surf --hemi lh --s average --sval lh.thickness.mgh > --fwhm 10 --tval lh.thickness.10.mgh > _________________________ > > Could someone please explain how the following descriptions of > a contrast are exactly linked: > i) a contrast's namesake folder (including keywords > 'Avg'/'Diff'/'X' and 'Intercept'/'Cor'; e.g. > "lh-Diff-group1-group2-Cor-thickness-behaviouralMeasure"), > ii) its phrasing in QDEC ("Does the thickness-age correlation > differ between group1 and group2?"), > iii) the assignment of values to each column of the design > matrix, in the C.dat contrast vector (e.g. [0, 0, 1, -1]) > > _________________________ > (this is actually a bug report) After setting a different FDR > threshold and pressing the "Set Using FDR" button, more often > than not the results image doesn’t change accordingly. I > noticed that the button only has an effect after moving around > the QDEC window and/or waiting a minute or so > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > 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 > http://www.partners.org/complianceline . 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. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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warning after running mris_fwhm
by Glen Lee 23 May '13

23 May '13

Hello FreeSurfer experts, I just ran smoothing on a single 2D EPI image with a binary mask (that excludes NaN vertices), but it didn't seem work out well as the output image (e.g., test.mgh) contains zero values throughout vertices. Also, I've got two warning messages (see below): while one of which seems harmless (5311 NaNs), the other (ar=0 <=0) may be critical. If anyone has any idea/ suggestions, please help. -Glen mris_fwhm --hemi lh --s fsaverage_sym --mask mask.mgh --fwhm 4 --i rabold4_0065_sym_L.mgh --o test.mgh fsaverage_sym lh white Number of vertices 163842 Number of faces 327680 Total area 61972.710938 GroupSurface 85910.812500 AvgVtxArea 0.378247 AvgVtxDist 0.693419 StdVtxDist 0.190498 WARNING: 5311 NaNs found in volume rabold4_0065_sym_L.mgh... Loading mask mask.mgh Found 158531 voxels in mask Polynomial detrending, order = 0 Smoothing input by fwhm=4.000000, gstd=1.698644, niters=11 Computing spatial AR1 ar1mn = 0, ar1std = 0, ar1max = 0 avg vertex dist 0.693419 WARNING: ar1 = 0 <= 0. Setting fwhm to 0. avg vertex dist 0.693419 fwhm = 0.000000

2 2

command not found
by clelia pellicano 23 May '13

23 May '13

Hi, I have run recon-all -s bert -all to try my installation and it worked. Now, when I try to use other command (and also again recon-all -s bert -all) I always get this: dyn1097-8:subjects cpellica$ tkmedit bert orig.mgz -bash: tkmedit: command not found dyn1097-8:subjects cpellica$ tkmedit -s bert orig.mgz -bash: tkmedit: command not found dyn1097-8:subjects cpellica$ tksurfer -s bert rh pial -bash: tksurfer: command not found dyn1097-8:subjects cpellica$ qdec -bash: qdec: command not found dyn1097-8:subjects cpellica$ recon-all help -bash: recon-all: command not found dyn1097-8:subjects cpellica$ recon-all -s bert -all -bash: recon-all: command not found I don't know how to do. Please, could you help me? Thanks Clelia

2 1

qdec for .stats file
by stdp82＠virgilio.it 23 May '13

23 May '13

Hi list, how can I use qdec to investigate the difference among groups regarding the measures contained in .stats file (for example thalamic volume)? Thanks, Stefano

2 1

Siemens dicom error on mri_convert
by Cat Chong 23 May '13

23 May '13

Hello Experts, I am trying to run the mri_convert command prior to the recon-all command on Siemens T1 dicoms (as suggested in the archives). I am using freesurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0, Mac OS X Lion 10.7.5 I am using the command below: mri_convert -it siemens_dicom -ot mgz 1002/IM-0001-0001.dcm 2001.mgz Below is the command line error I receive, it is a similar error I receive when I try to use the command recon-all on the Siemens dicoms. I have used freesurfer before on GE dicoms and never had a problem running recon-all. Is this error message particular to the Siemens dicoms, and would you be able to tell me how to proceed? Thank you very much for you help, Cat reading from 1002/IM-0001-0001.dcm... Getting Series No Scanning Directory INFO: Found 130 files in 1002 INFO: Scanning for Series Number 2 INFO: found 128 files in series INFO: loading series header info. INFO: sorting. RunNo = 1 WARNING: Run 1 appears to be truncated Files Found: 128, Files Expected (lRep+1): 1 FileName 1002/IM-0001-0001.dcm Identification NumarisVer syngo MR D11 ScannerModel Skyra PatientName RS-FMRI^RS-FMRI Date and time StudyDate 20130222 StudyTime 082109.140000 SeriesTime 082812.906000 AcqTime 082237.315000 Acquisition parameters PulseSeq *tfl3d1_16ns Protocol SAG MP Rage PhEncDir ROW EchoNo 1 FlipAngle 8 EchoTime 3.03 InversionTime 1000 RepetitionTime 2400 PhEncFOV 0 ReadoutFOV 0 Image information RunNo 1 SeriesNo 2 ImageNo 1 NImageRows 256 NImageCols 256 NFrames 128 SliceArraylSize 0 IsMosaic 1 ImgPos -78.6002 128.0000 93.1332 VolRes 1.0000 1.0000 1.2500 VolDim 0 0 0 Vc -0.0000 -1.0000 0.0000 Vr -0.0000 -0.0000 -1.0000 Vs 0.0000 0.0000 0.0000 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 WARNING: file 1002/IM-0001-0001.dcm does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header

2 1

3 recon-all errors: v5.0.0
by Sudhin A. Shah 23 May '13

23 May '13

1) BEST FITNESS (M) is 984.24263 mri =0.000 curv = 4.318 unmri = -1001.515 ( f=0.00 , v=0.00 , c=4.32 , q= 8.64 ) ( f=0.00 , v=0.00 , c=4.32 , q= 8.64 ) 63 patches have been generated - 38 self-intersected max face = 36973(40653) - loop = 46 (73) - ntries = [27,14799] ERROR: _FindFacePath: could not find path! Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s xtyzW exited with ERRORS at Tue May 21 05:48:38 EDT 2013 =============== 2)*************************WATERSHED************************** Sorting... mri_watershed Error: Problem in the COG calculation: T1.mgz may not contain properly normalized white-matter. Confirm that T1.mgz has enough white-matter voxels of value 110. If white-matter contains few if any voxels of value 110, try adding wm control-points to nu.mgz, and re-run recon-all. Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s cbvfB exited with ERRORS at Fri May 17 17:45:23 EDT 2013 ============== 3)CORRECTING DEFECT 2 (vertices=30163, convex hull=6211) error in the retessellation normal vector of length zero at vertex 88778 with 0 faces vertex 88778 has 0 face No such file or directory Linux sudhin-Precision-WorkStation-690 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux recon-all -s ghjG exited with ERRORS at Thu May 16 05:11:49 EDT 2013

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