search

CVNRneuroimaging / infrastructure

Issue tracking, system documentation and configs for operations side of the neuroimaging core @ Atlanta VA CVNR / Emory University
3 stars 2 forks source link

Freesurfer License #143

Closed simonero closed 9 years ago

simonero commented 9 years ago

I can't use freesurfer on qball3 because the license file is missing. It needs to be in $FREESURFER_HOME. I can't do it myself because of permissions restrictions.

I also can't use it on qball4 because I don't have permissions to "subjects".

I put a copy of my license file on the server in this location:

/data/birc/Atlanta/simoneTracts/00.Supporting_Files/license.txt

The name of the file needs to stay the same. I set it to full permissions (777) so other people could use the license as well.

Thanks!!

kmcgregor123456 commented 9 years ago

I will fix.

Keith McGregor, PhD VA RR&D Atlanta CoE Emory University 352.359.8084 www.varrd.emory.edu

From: simonero [notifications@github.com] Sent: Sunday, August 23, 2015 5:50 PM To: CVNRneuroimaging/infrastructure Subject: [infrastructure] Freesurfer License (#143)

I can't use freesurfer on qball3 because the license file is missing. It needs to be in $FREESURFER_HOME. I can't do it myself because of permissions restrictions.

I also can't use it on qball4 because I don't have permissions to "subjects".

I put a copy of my license file on the server in this location:

/data/birc/Atlanta/simoneTracts/00.Supporting_Files/license.txt

The name of the file needs to stay the same. I set it to full permissions (777) so other people could use the license as well.

Thanks!!

— Reply to this email directly or view it on GitHubhttps://github.com/CVNRneuroimaging/infrastructure/issues/143.

This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited.

If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

kmcgregor123456 commented 9 years ago

added the necessary license files and changed the permissions. try now

kmcgregor123456 commented 9 years ago

close after testing

simonero commented 9 years ago

Thank you Keith!! Thumbs up for qball3. Will close this as soon as I've tested qball4.

simonero commented 9 years ago

qball4 freesurfer test failed quickly at "-autorecon1" phase.

This issue is not mirrored by qball3 for the same subject.

Here is the log text:

|---------------------------------------------------------------

New invocation of recon-all

Fri Aug 28 09:24:22 EDT 2015 /usr/local/freesurfer/subjects/s210 /usr/local/freesurfer/bin/recon-all -s s210 -autorecon1 subjid s210 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux qball4.birc.emory.edu 3.13.0-39-generic #66-Ubuntu SMP Tue Oct 28 13:30:27 UTC 2014 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 192649 maxlocks unlimited maxsignal 192649 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited

         total       used       free     shared    buffers     cached

Mem: 24680696 20705160 3975536 58724 237408 18409332 -/+ buffers/cache: 2058420 22622276 Swap: 25154556 108568 25045988

######################################## 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: 2015/08/28-13:24:22-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 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: 2015/08/28-13:24:23-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/28-13:24:23-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/28-13:24:23-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/28-13:24:23-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/28-13:24:23-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/28-13:24:23-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/28-13:24:23-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400

======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/28-13:24:24-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/28-13:24:24-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/28-13:24:24-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/28-13:24:24-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/28-13:24:24-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/28-13:24:24-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/28-13:24:25-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/28-13:24:25-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/28-13:24:25-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/28-13:24:25-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/28-13:24:25-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/28-13:24:25-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/28-13:24:25-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/28-13:24:25-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/28-13:24:26-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/28-13:24:26-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/28-13:24:26-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/28-13:24:26-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/28-13:24:26-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/28-13:24:26-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/28-13:24:26-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/28-13:24:26-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/28-13:24:26-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/28-13:24:27-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 $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: 2015/08/28-13:24:27-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 $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: 2015/08/28-13:24:27-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/28-13:24:27-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/28-13:24:27-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/28-13:24:27-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/28-13:24:27-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: simoneroberts Machine: qball4.birc.emory.edu Platform: Linux PlatformVersion: 3.13.0-39-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs #######################################

--------------------------------------------

@# MotionCor Fri Aug 28 09:24:27 EDT 2015

Found 1 runs /usr/local/freesurfer/subjects/s210/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 /usr/local/freesurfer/subjects/s210/mri/orig/001.mgz /usr/local/freesurfer/subjects/s210/mri/rawavg.mgz

/usr/local/freesurfer/subjects/s210

mri_convert /usr/local/freesurfer/subjects/s210/mri/rawavg.mgz /usr/local/freesurfer/subjects/s210/mri/orig.mgz --conform

mri_convert /usr/local/freesurfer/subjects/s210/mri/rawavg.mgz /usr/local/freesurfer/subjects/s210/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/s210/mri/rawavg.mgz... 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) Original Data has (1, 1, 1) mm size and (176, 256, 256) 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 /usr/local/freesurfer/subjects/s210/mri/orig.mgz...

mri_add_xform_to_header -c /usr/local/freesurfer/subjects/s210/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/s210/mri/orig.mgz /usr/local/freesurfer/subjects/s210/mri/orig.mgz

INFO: extension is mgz

--------------------------------------------

@# Talairach Fri Aug 28 09:24:41 EDT 2015

/usr/local/freesurfer/subjects/s210/mri

mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz

Linux qball4.birc.emory.edu 3.13.0-39-generic #66-Ubuntu SMP Tue Oct 28 13:30:27 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s s210 exited with ERRORS at Fri Aug 28 09:24:44 EDT 2015

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

rrmm commented 9 years ago

i can reproduce on qball1 and 4 at least.

note: you probably don't want to put data (even test data) under /usr/local/freesurfer/ (which should probably not be user writable?). move the data under a user directory and point the SUBJECTS_DIR variable to match.

one of the subprograms is crashing during run, but doesn't provide terribly good diagnostics. I'll look into it some more.

simonero commented 9 years ago

Reproduce the error or reproduce the expected data?

Which program? There's a regular issue that occurs on both OS X and Linux during -autorecon2. Running -cortribbon and then -segstats after -autorecon2, before -autorecon3, solves that issue. (It's a little annoying but at least it's a consistent fix.) Is that what you are talking about, or something else??

I'm going to move all of the data I generated into my subject folders on /data/birc/ as soon as I'm done.

rrmm commented 9 years ago

reproduce a good run of 'recon-all -autorecon1 -subjid s210' on qball3, and a failure on qball1/4 of the same.

simonero commented 9 years ago

Are you running recon-all right now? I got an error when trying to run -autorecon2 for s210 about another instance already running. If not and it's an error I can kill it.

rrmm commented 9 years ago

i'm running in my user dir

rrmm commented 9 years ago

I was able to get a successful run on qball4 (only took 14 hours!).

This issue is most likely due to having to query for user info via ldap when doing filesystem ops. The auth server (or the links in-between) can't keep up.

Installation of nscd on affected hosts seems to cure it for me.

please confirm on qball4, and close if fixed.

kmcgregor123456 commented 9 years ago

close if corrected