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30064 discussions

recon-all error
by sbasho＠nmr.mgh.harvard.edu 20 Jul '06

20 Jul '06

Hello, I received an error when running recon-all. It seems to have run into a problem during the 'Remove Neck' and 'SkullLTA' steps. I have included the output below of the last two steps before the error occured. Thank you. -Surina #@# Remove Neck Wed Jul 19 15:26:17 EDT 2006 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /usr/local/freesurfer/stable/average/RB_all_2006-02-15.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/usr/local/freesurfer/stable/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... mghWrite(nu_noneck.mgz, -1): could not open file gcam->type = vox reading labels out of gcam file... removing structures at least 25 mm from brain... 11405488 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 23 minutes and 41 seconds. #-------------------------------------- #@# SkullLTA Wed Jul 19 15:50:02 EDT 2006 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /usr/local/freesurfer/stable/average/RB_all_withskull_2006-02-15.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/stable/average/RB_all_withskull_2006-02-15.gca'... setting gca type = Normal gca type average std = 23.5 using min determinant for regularization = 55.2 0 singular and 6473 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... zcat: /autofs/space/tango_003/users/recon_modygp/surina/mody096/mri/nu_noneck.mgz.gz: No such file or directory mghRead(/autofs/space/tango_003/users/recon_modygp/surina/mody096/mri/nu_noneck.mgz, -1): read error mri_em_register: could not open input volume nu_noneck.mgz. Linux whump 2.6.9-34.ELsmp #1 SMP Wed Mar 8 00:27:03 CST 2006 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Wed Jul 19 15:50:30 EDT 2006

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error nu_correct
by skloeppe＠uke.uni-hamburg.de 20 Jul '06

20 Jul '06

Hi freesurfers, the script crashed when running "recon-all -s bert -all" to test a newly installed CentOS 4 version (v3.0.3) on a Windows XP system with VMware and Fedora Core 4. The path for both nu_correct (and nu_estimate_np_and_em: see second error message) seem to be correct (/mnt/d/Freesurfer/freesurfer/mni/bin/nu_correct). Any suggestions greatly appriciated Thanks, Stefan The error is as follows: #@# Nu Intensity Correction Thu Jul 20 07:47:00 BST 2006 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 /mnt/d/Freesurfer/freesurfer/subjects/bert/mri /mnt/d/Freesurfer/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.3 2005/12/08 01:27:21 greve Exp $ Linux localhost.localdomain 2.6.15-1.1830_FC4 #1 Thu Feb 2 17:23:41 EST 2006 i686 athlon i386 GNU/Linux Thu Jul 20 07:47:00 BST 2006 Setuid/gid script is writable by world. tmpdir is ./tmp.mri_nu_correct.mni.10059 /mnt/d/Freesurfer/freesurfer/subjects/bert/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10059/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10059/nu0.mnc 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) writing to ./tmp.mri_nu_correct.mni.10059/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Jul 20 07:47:09 BST 2006 nu_correct -clobber ./tmp.mri_nu_correct.mni.10059/nu0.mnc /tmp.mri_nu_correct.mni.10059/nu1.mnc Setuid/gid script is writable by world. ERROR: nu_correct Linux localhost.localdomain 2.6.15-1.1830_FC4 #1 Thu Feb 2 17:23:41 EST 2006 i686 athlon i386 GNU/Linux recon-all exited with ERRORS at Thu Jul 20 07:47:09 BST 2006 ***********the error is slightly different with one of myt own subjctes: #-------------------------------------------- #@# Nu Intensity Correction Thu Jul 20 07:32:48 BST 2006 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 /mnt/d/Freesurfer/freesurfer/subjects/sMS04134/mri /mnt/d/Freesurfer/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.3 2005/12/08 01:27:21 greve Exp $ Linux localhost.localdomain 2.6.15-1.1830_FC4 #1 Thu Feb 2 17:23:41 EST 2006 i686 athlon i386 GNU/Linux Thu Jul 20 07:32:48 BST 2006 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 tmpdir is ./tmp.mri_nu_correct.mni.9466 /mnt/d/Freesurfer/freesurfer/subjects/sMS04134/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9466/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9466/nu0.mnc Can't find the talairach xform '/mnt/d/Freesurfer/freesurfer/subjects/sMS04134/mri/transforms/talairach.xfm' Transform is not loaded into mri reading from orig.mgz... Talairach transform /mnt/d/Freesurfer/freesurfer/subjects/sMS04134/mri/transforms/talairach.xfm does not exist ... Cannot load tal xfm file /mnt/d/Freesurfer/freesurfer/subjects/sMS04134/mri/transforms/talairach.xfm 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 ./tmp.mri_nu_correct.mni.9466/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Jul 20 07:32:57 BST 2006 nu_correct -clobber ./tmp.mri_nu_correct.mni.9466/nu0.mnc /tmp.mri_nu_correct.mni.9466/nu1.mnc Setuid/gid script is writable by world. nu_correct: crashed while running nu_estimate_np_and_em (termination status=6400) ERROR: nu_correct Linux localhost.localdomain 2.6.15-1.1830_FC4 #1 Thu Feb 2 17:23:41 EST 2006 i686 athlon i386 GNU/Linux

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eTIV on older recons
by David Ziegler 20 Jul '06

20 Jul '06

Hello All! I'm trying to calculate eTIV (ICV) based on the new Buckner method, but for reconstructions that were completed prior to the most recent stable release (in 2003-2004). Are there any extra steps or special files that I should be aware of to make this run properly? Is the procedure for estimating ICV on older recons documented anywhere? I tried running mri_label_volume using the only .lta file available in the subject/mri/transforms directory (talairach_with_skull_un5_tinit_noneck_both_uns3.lta) but the resulting eTIV outputs are much smaller than one would expect. Here's a sample command and output: [engram:emoaging] (nmr-std-env) mri_label_volume -eTIV $SUBJECTS_DIR/emot_118/mri/transforms/talairach_with_skull_un5_tinit_noneck_both_uns3.lta $SUBJECTS_DIR/emot_118/mri/aseg.mgz 17 53 using eTIV from atlas transform of 878 cm^3 processing label 17... 3730 voxels (3730.0 mm^3) in label 17, %0.424837 of eTIV volume (877983) processing label 53... 3738 voxels (3738.0 mm^3) in label 53, %0.425748 of eTIV volume (877983) Any advice? Thanks! David

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Group-Specific template
by Chacko Cherian 19 Jul '06

19 Jul '06

Hello everyone, I would like to run a group-specific template on Freesurfer and compare my results with the default template(which is MNI,I assume)? Is this possible?Can I do cortical thickness measurement also in the same way? Thanks in advance, Chacko. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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error running tkmedit
by Chacko Cherian 19 Jul '06

19 Jul '06

Hello everyone, I am using a Red Hat Enterprise Linux AS release 3(Taroon update 6) version.While running tkmedit for the bert data..this is what i get.. tkmedit: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory. I tried the CentOS(without x86_64) version and the rh9 versions of freesurfer but both gave me the same error message. Could someone pls clarify. Thanks in advance Chacko. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Error message
by Chacko Cherian 19 Jul '06

19 Jul '06

Hello everyone, I got this message while running bert on my Linux machine.Is it because the NVIDIA graphics driver is not updated?? GLUT: Fatal Error in tkmedit: OpenGL GLX extension not supported by display: :0.0 Thanks in advance Chacko. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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dylib error on fresh install v. 3.0.3 Tiger
by James Kyle 19 Jul '06

19 Jul '06

Getting errors on a fresh install of 3.0.3 Tiger release. Any suggestions appreciated. If any more info is needed/would help just let me know. Command: mri_convert <input> <output> Error: dyld: mri_convert Undefined symbols: mri_convert undefined reference to ___stderrp expected to be defined in /usr/lib/libSystem.B.dylib mri_convert undefined reference to ___stdoutp expected to be defined in /usr/lib/libSystem.B.dylib Trace/BPT trap (Error is reproducible using any Freesurfer utility as far as I can tell) Current working environment var $DYLD_LIBRARY_PATH : echo $DYLD_LIBRARY_PATH $FREESURFER_HOME/lib/misc/lib:$FREESURFER_HOME/lib/tcltktixblt/lib: $FREESURFER_HOME/lib/gsl/lib:$FREESURFER_HOME/freesurfer/lib/ (replaced absolute path with the $FREESURFER_HOME var.) GDB backtrace output: run subjects/bert/mri/T1.mgz test.img Starting program: $FREESURFER_HOME/bin/mri_convert subjects/bert/mri/ T1.mgz test.img Reading symbols for shared libraries ++.. done dyld: $FREESURFER_HOME/bin/mri_convert Undefined symbols: $FREESURFER_HOME/bin/mri_convert undefined reference to ___stderrp expected to be defined in /usr/lib/libSystem.B.dylib $FREESURFER_HOME/bin/mri_convert undefined reference to ___stdoutp expected to be defined in /usr/lib/libSystem.B.dylib Program received signal SIGTRAP, Trace/breakpoint trap. 0x8fe01400 in __dyld_halt () (gdb) backtrace full #0 0x8fe01400 in __dyld_halt () No symbol table info available. #1 0x8fe0a2b0 in __dyld_check_and_report_undefineds () No symbol table info available. #2 0x8fe113b0 in __dyld_link_in_need_modules () No symbol table info available. #3 0x8fe0166c in __dyld__dyld_init () No symbol table info available.

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Gray matter volumes
by Derin Cobia 19 Jul '06

19 Jul '06

Hi again, Two questions: 1). You said earlier that GM volumes from mris_anatomical_stats are more accurate than from the aseg files. Would you recommend using the surface-based GM volumes instead of the ones from the aseg.stats files? I ask because we have ~200 subjects processed for volume, but not surface, meaning no mris_anatomical_stats. If we could avoid the added processing time on these it would be helpful, but don't want to do it at the expense of accuracy. 2). What structures are calculated into "total white matter volume" under mris_anatomical_stats? Does it include corpus callosum and others? Thanks. -Derin

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label list for lh.aparc.annot
by R. Chen 19 Jul '06

19 Jul '06

Hi, I use freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.3 For a subject, in folder ${SUBJECTS_HOME}/label, I can find two annotation file lh.aparc.a2005s.annot lh.aparc.annot In freesufer home, I can find a file surface_labels.txt. It looks like 0 Unknown 0 0 0 0 1 G_cingularis 25 60 60 0 2 G_cuneus 180 20 20 0 3 G_frontalis_inf-pars_opercularis 220 20 100 0 4 G_frontalis_inf-pars_orbitalis 140 60 60 0 5 G_frontalis_inf-pars_triangularis 180 220 140 0 6 G_frontalis_medius 140 100 180 0 7 G_frontalis_sup-pars_lateralis 180 20 140 0 8 G_frontalis_sup-pars_medialis 180 140 100 0 9 G_frontomarginalis 140 20 140 0 10 G_hippocampi 25 180 20 0 My question is whether this file is for lh.aparc.a2005s.annot or lh.aparc.annot? If this contains structure name for lh.aparc.a2005s.annot, where is the corresponding label list file for lh.aparc.annot. Thank you Ron --------------------------------- How low will we go? Check out Yahoo! Messengers low PC-to-Phone call rates.

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recon-all: error in topology correction step
by Johannes Klein 19 Jul '06

19 Jul '06

Hi everyone, I'm using recon-all to flatten a number of scans from patients and controls. Most of them work fine, but there are 3 that do not reconstruct correctly. They all seem to share the same problem: Recon-all aborts during the automatic topology correction step, and there's a line in the log saying mrisDefectAnalysis : defect XXX overlap defect YYY. I've checked registration to talairach, skull strip and initial surfaces, the only thing I could see was that in some cases, bits of the superior sagittal sinus were wrongly included in the lh.orig.nofix, or small bits of dura, but nothing major. I'm attaching the relevant output from the topology fixer for two different cases. I would be grateful if someone could point me at other things to try. Is it possible to visualise the defects' locations, so I could find out which defect is actually causing the overlap message? Thanks for your help everyone, Johannes ---------- CASE 1 #@# Fix Topology lh Wed Jun 14 04:04:29 BST 2006 \n cp ../surf/lh.orig.nofix ../surf/lh.orig \n \n cp ../surf/lh.inflated.nofix ../surf/lh.inflated \n /Volumes/JalapenoSAN/Scratch/natalie/schizophrenia/fs/PAT_2280/scripts \n mris_fix_topology -mgz -sphere qsphere.nofix -ga PAT_2280 lh \n reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.41 2006/02/06 19:41:59 nicks Exp $ $Id: mrisurf.c,v 1.441.2.1 2006/03/06 21:12:31 greve Exp $ before topology correction, eno=-656 (nv=197397, nf=396220, ne=594273, g=329) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 30743 ambiguous faces found in tessellation segmenting defects... defect 6 : 7 vertices have been added to the surface [ ... ] defect 314 : 2 vertices have been added to the surface total of 95 vertices has been added to the surface analyzing defects... mrisDefectAnalysis : defect 277 overlap defect 272 reading input surface /Volumes/JalapenoSAN/Scratch/natalie/schizophrenia/fs/PAT_2280/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Darwin jalapeno6.fmrib.ox.ac.uk 8.6.0 Darwin Kernel Version 8.6.0: Tue Mar 7 16:58:48 PST 2006; root:xnu-792.6.70.obj~1/RELEASE_PPC Power Macintosh powerpc recon-all exited with ERRORS at Wed Jun 14 04:08:10 BST 2006 CASE 2 #@# Fix Topology rh Thu Jun 15 12:13:05 BST 2006 \n cp ../surf/rh.orig.nofix ../surf/rh.orig \n \n cp ../surf/rh.inflated.nofix ../surf/rh.inflated \n /Volumes/JalapenoSAN/Scratch/natalie/schizophrenia/fs/PAT_3509/scripts \n mris_fix_topology -mgz -sphere qsphere.nofix -ga PAT_3509 rh \n reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.41 2006/02/06 19:41:59 nicks Exp $ $Id: mrisurf.c,v 1.441.2.1 2006/03/06 21:12:31 greve Exp $ before topology correction, eno=-2025 (nv=252518, nf=509180, ne=763723, g=1013) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 13 iterations marking ambiguous vertices... 137391 ambiguous faces found in tessellation segmenting defects... defect 12 : 4 vertices have been added to the surface [ ... ] defect 440 : 4 vertices have been added to the surface total of 340 vertices has been added to the surface analyzing defects... mrisDefectAnalysis : defect 395 overlap defect 393 reading input surface /Volumes/JalapenoSAN/Scratch/natalie/schizophrenia/fs/PAT_3509/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Darwin jalapeno4.fmrib.ox.ac.uk 8.6.0 Darwin Kernel Version 8.6.0: Tue Mar 7 16:58:48 PST 2006; root:xnu-792.6.70.obj~1/RELEASE_PPC Power Macintosh powerpc recon-all exited with ERRORS at Thu Jun 15 12:19:26 BST 2006

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