Hi all, I'm trying to run recon-all on some data using one of the hpc clusters at my institution using FreeSurfer v. 5.3.0. I've used 4.5.0 without a problem but I'm trying to rerun the data with the new version.
I keep getting this error (FreeSurfer's log file is attached here) regarding the mni/bin folder. Could this be an error on their end? Not sure if maybe 5.3 wasn't installed correctly on the hpc machines. Any help is really appreciated! Thanks, Natalie -- Natalie V. Garcia Graduate Fellow, Cognitive Neuroscience Department of Psychology The Pennsylvania State University 423 Moore Building University Park, PA 16802 nvg...@psu.edu
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /gpfs/group/s/sleic/kss23/ldn/Freesurfer/5.3.0/sex_diff_5.3.0/strucdata_5.3.0 Actual FREESURFER_HOME /gpfs/apps/x86_64-rhel6/freesurfer/5.3.0/freesurfer -rw-rw----+ 1 nvg109 nvg109 19843 May 12 13:06 /gpfs/group/s/sleic/kss23/ldn/Freesurfer/5.3.0/sex_diff_5.3.0/strucdata_5.3.0/8118/scripts/recon-all.log Linux cyberstar208.hpc.rcc.psu.edu 2.6.32-431.3.1.el6.x86_64 #1 SMP Fri Dec 13 06:58:20 EST 2013 x86_64 x86_64 x86_64 GNU/Linux Can't locate MNI/Startup.pm in @INC (@INC contains: /usr/lib64/perl5/5.10.0/x86_64-linux-thread-multi/CORE/ /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /usr/global/freesurfer/5.3.0/freesurfer/mni/bin/nu_correct line 37. BEGIN failed--compilation aborted at /usr/global/freesurfer/5.3.0/freesurfer/mni/bin/nu_correct line 37. #-------------------------------------------- #@# MotionCor Mon May 12 13:12:41 EDT 2014 Found 1 runs /gpfs/group/s/sleic/kss23/ldn/Freesurfer/5.3.0/sex_diff_5.3.0/strucdata_5.3.0/8118/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 /gpfs/group/s/sleic/kss23/ldn/Freesurfer/5.3.0/sex_diff_5.3.0/strucdata_5.3.0/8118/mri/orig/001.mgz /gpfs/group/s/sleic/kss23/ldn/Freesurfer/5.3.0/sex_diff_5.3.0/strucdata_5.3.0/8118/mri/rawavg.mgz /gpfs/group/s/sleic/kss23/ldn/Freesurfer/5.3.0/sex_diff_5.3.0/strucdata_5.3.0/8118 mri_convert /gpfs/group/s/sleic/kss23/ldn/Freesurfer/5.3.0/sex_diff_5.3.0/strucdata_5.3.0/8118/mri/rawavg.mgz /gpfs/group/s/sleic/kss23/ldn/Freesurfer/5.3.0/sex_diff_5.3.0/strucdata_5.3.0/8118/mri/orig.mgz --conform mri_convert /gpfs/group/s/sleic/kss23/ldn/Freesurfer/5.3.0/sex_diff_5.3.0/strucdata_5.3.0/8118/mri/rawavg.mgz /gpfs/group/s/sleic/kss23/ldn/Freesurfer/5.3.0/sex_diff_5.3.0/strucdata_5.3.0/8118/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /gpfs/group/s/sleic/kss23/ldn/Freesurfer/5.3.0/sex_diff_5.3.0/strucdata_5.3.0/8118/mri/rawavg.mgz... TR=1700.00, TE=1.78, TI=850.00, flip angle=9.00 i_ras = (0.0196223, -0.999733, 0.0122095) j_ras = (-0.0346559, -0.0128847, -0.999316) k_ras = (-0.999207, -0.0191857, 0.0348995) 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 /gpfs/group/s/sleic/kss23/ldn/Freesurfer/5.3.0/sex_diff_5.3.0/strucdata_5.3.0/8118/mri/orig.mgz... mri_add_xform_to_header -c /gpfs/group/s/sleic/kss23/ldn/Freesurfer/5.3.0/sex_diff_5.3.0/strucdata_5.3.0/8118/mri/transforms/talairach.xfm /gpfs/group/s/sleic/kss23/ldn/Freesurfer/5.3.0/sex_diff_5.3.0/strucdata_5.3.0/8118/mri/orig.mgz /gpfs/group/s/sleic/kss23/ldn/Freesurfer/5.3.0/sex_diff_5.3.0/strucdata_5.3.0/8118/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon May 12 13:12:59 EDT 2014 /gpfs/group/s/sleic/kss23/ldn/Freesurfer/5.3.0/sex_diff_5.3.0/strucdata_5.3.0/8118/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux cyberstar208.hpc.rcc.psu.edu 2.6.32-431.3.1.el6.x86_64 #1 SMP Fri Dec 13 06:58:20 EST 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 8118 exited with ERRORS at Mon May 12 13:13:05 EDT 2014 For more details, see the log file /gpfs/group/s/sleic/kss23/ldn/Freesurfer/5.3.0/sex_diff_5.3.0/strucdata_5.3.0/8118/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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