glamor-virtual-machine:/mnt/hgfs/proj__Brain/Data_FS# recon-all -all -s subj001Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 INFO: SUBJECTS_DIR is /mnt/hgfs/proj__Brain/Data_FS Actual FREESURFER_HOME /usr/local/freesurfer Linux glamor-virtual-machine 2.6.35-22-generic #33-Ubuntu SMP Sun Sep 19 20:32:27 UTC 2010 x86_64 GNU/Linux #-------------------------------------------- #@# MotionCor Sun Feb 20 00:51:20 EST 2011 Found 1 runs /mnt/hgfs/proj__Brain/Data_FS/subj001/mri/orig/001.mgz 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 /mnt/hgfs/proj__Brain/Data_FS/subj001/mri/orig/001.mgz /mnt/hgfs/proj__Brain/Data_FS/subj001/mri/rawavg.mgz /mnt/hgfs/proj__Brain/Data_FS/subj001 mri_convert /mnt/hgfs/proj__Brain/Data_FS/subj001/mri/rawavg.mgz /mnt/hgfs/proj__Brain/Data_FS/subj001/mri/orig.mgz --conform mri_convert /mnt/hgfs/proj__Brain/Data_FS/subj001/mri/rawavg.mgz /mnt/hgfs/proj__Brain/Data_FS/subj001/mri/orig.mgz --conform $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /mnt/hgfs/proj__Brain/Data_FS/subj001/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 (0.7, 0.7, 1.5) mm size and (256, 256, 124) voxels. Data is conformed to 1 mm size and 256 voxels for all directions Reslicing using trilinear interpolation writing to /mnt/hgfs/proj__Brain/Data_FS/subj001/mri/orig.mgz... mri_add_xform_to_header -c /mnt/hgfs/proj__Brain/Data_FS/subj001/mri/transforms/talairach.xfm /mnt/hgfs/proj__Brain/Data_FS/subj001/mri/orig.mgz /mnt/hgfs/proj__Brain/Data_FS/subj001/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Nu Intensity Correction Sun Feb 20 00:51:32 EST 2011 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 /mnt/hgfs/proj__Brain/Data_FS/subj001/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.12 2009/12/16 20:15:41 greve Exp $ Linux glamor-virtual-machine 2.6.35-22-generic #33-Ubuntu SMP Sun Sep 19 20:32:27 UTC 2010 x86_64 GNU/Linux Sun Feb 20 00:51:32 EST 2011 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 tmpdir is ./tmp.mri_nu_correct.mni.4982 /mnt/hgfs/proj__Brain/Data_FS/subj001/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.4982/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.4982/nu0.mnc -odt float $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from orig.mgz... TR=0.00, 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.4982/nu0.mnc... -------------------------------------------------------- Iteration 1 Sun Feb 20 00:51:37 EST 2011 nu_correct -clobber ./tmp.mri_nu_correct.mni.4982/nu0.mnc ./tmp.mri_nu_correct.mni.4982/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.4982/0/ [root@glamor-virtual-machine:/mnt/hgfs/proj__Brain/Data_FS/subj001/mri/] [2011-02-20 00:51:37] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.4982/0/ ./tmp.mri_nu_correct.mni.4982/nu0.mnc ./tmp.mri_nu_correct.mni.4982/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 22 CV of field change: 0.000991636 [root@glamor-virtual-machine:/mnt/hgfs/proj__Brain/Data_FS/subj001/mri/] [2011-02-20 00:52:06] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.4982/nu0.mnc ./tmp.mri_nu_correct.mni.4982/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Sun Feb 20 00:52:20 EST 2011 nu_correct -clobber ./tmp.mri_nu_correct.mni.4982/nu1.mnc ./tmp.mri_nu_correct.mni.4982/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.4982/1/ [root@glamor-virtual-machine:/mnt/hgfs/proj__Brain/Data_FS/subj001/mri/] [2011-02-20 00:52:21] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.4982/1/ ./tmp.mri_nu_correct.mni.4982/nu1.mnc ./tmp.mri_nu_correct.mni.4982/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 16 CV of field change: 0.00094021 [root@glamor-virtual-machine:/mnt/hgfs/proj__Brain/Data_FS/subj001/mri/] [2011-02-20 00:52:44] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.4982/nu1.mnc ./tmp.mri_nu_correct.mni.4982/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.4982/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.4982/ones.mgz $Id: mri_binarize.c,v 1.23.2.1 2010/07/28 20:07:29 greve Exp $ cwd /mnt/hgfs/proj__Brain/Data_FS/subj001/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.4982/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.4982/ones.mgz sysname Linux hostname glamor-virtual-machine machine x86_64 user root input ./tmp.mri_nu_correct.mni.4982/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.4982/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 Found 16777216 values in range Counting number of voxels Found 16777216 voxels in final mask mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.4982/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.4982/sum.junk --avgwf ./tmp.mri_nu_correct.mni.4982/input.mean.dat $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.4982/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.4982/sum.junk --avgwf ./tmp.mri_nu_correct.mni.4982/input.mean.dat sysname Linux hostname glamor-virtual-machine machine x86_64 user root Loading ./tmp.mri_nu_correct.mni.4982/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.4982/input.mean.dat mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.4982/ones.mgz --i ./tmp.mri_nu_correct.mni.4982/nu2.mnc --sum ./tmp.mri_nu_correct.mni.4982/sum.junk --avgwf ./tmp.mri_nu_correct.mni.4982/output.mean.dat $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.4982/ones.mgz --i ./tmp.mri_nu_correct.mni.4982/nu2.mnc --sum ./tmp.mri_nu_correct.mni.4982/sum.junk --avgwf ./tmp.mri_nu_correct.mni.4982/output.mean.dat sysname Linux hostname glamor-virtual-machine machine x86_64 user root Loading ./tmp.mri_nu_correct.mni.4982/ones.mgz Loading ./tmp.mri_nu_correct.mni.4982/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.4982/output.mean.dat mris_calc -o ./tmp.mri_nu_correct.mni.4982/nu2.mnc ./tmp.mri_nu_correct.mni.4982/nu2.mnc mul .92568628037958714125 Saving result to './tmp.mri_nu_correct.mni.4982/nu2.mnc' (type=3) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.4982/nu2.mnc nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.4982/nu2.mnc nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from ./tmp.mri_nu_correct.mni.4982/nu2.mnc... TR=0.00, 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) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to nu.mgz... Sun Feb 20 00:53:52 EST 2011 mri_nu_correct.mni done #-------------------------------------------- #@# Talairach Sun Feb 20 00:53:52 EST 2011 /mnt/hgfs/proj__Brain/Data_FS/subj001/mri talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Sun Feb 20 00:55:00 EST 2011 /mnt/hgfs/proj__Brain/Data_FS/subj001/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) INFO: Attempting MINC mritotal to perform Talairach align #-------------------------------------------- #@# Talairach Sun Feb 20 00:55:00 EST 2011 /mnt/hgfs/proj__Brain/Data_FS/subj001/mri talairach --i nu.mgz --xfm transforms/talairach.auto.xfm /mnt/hgfs/proj__Brain/Data_FS/subj001/mri /usr/local/freesurfer/bin/talairach --i nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.6 2007/03/15 23:23:11 greve Exp $ Linux glamor-virtual-machine 2.6.35-22-generic #33-Ubuntu SMP Sun Sep 19 20:32:27 UTC 2010 x86_64 GNU/Linux Sun Feb 20 00:55:00 EST 2011 tmpdir is transforms/tmp.talairach.5742 /mnt/hgfs/proj__Brain/Data_FS/subj001/mri mri_convert nu.mgz transforms/tmp.talairach.5742/src.mnc mri_convert nu.mgz transforms/tmp.talairach.5742/src.mnc $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from nu.mgz... TR=0.00, 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 transforms/tmp.talairach.5742/src.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.5742/src.mnc transforms/talairach.auto.xfm Sun Feb 20 00:55:23 EST 2011 talairach done INFO: transforms/talairach.xfm already exists! The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm This is done to retain any edits made to transforms/talairach.xfm Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Sun Feb 20 00:55:23 EST 2011 /mnt/hgfs/proj__Brain/Data_FS/subj001/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Linux glamor-virtual-machine 2.6.35-22-generic #33-Ubuntu SMP Sun Sep 19 20:32:27 UTC 2010 x86_64 GNU/Linux recon-all -s subj001 exited with ERRORS at Sun Feb 20 00:55:23 EST 2011