Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

FW: help install freesurfer
by Fleisher, Adam 23 Jul '06

23 Jul '06

I am trying to install Freesurfer on RedHat Linux EL3 x86_64. I am using a csh shell and the setup seems to work fine. But, when I test tkmedit, it gives me an error: "tkmedit: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory" I have seen threads that say I need to locate libglut and create a symbolic link from libglut.so.3 to my current version. Where is libglut located and how do I create a link? Anyone have this problem with explicit fix instructions? Thanks, Adam

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recon-all malloc error
by Rutvik Desai 21 Jul '06

21 Jul '06

recon-all exited with the following error. Running on a Powermac G5 with 1G ram. Any ideas? thanks, Rutvik --------------------------------------------- Fix Topology rh Thu Jul 20 13:29:52 CDT 2006 /usr/local/freesurfer/subjects/2628/scripts mris_fix_topology 2628 rh reading input surface /usr/local/freesurfer/subjects/2628/surf/rh.qsphere... before topology correction, eno=-510 (nv=191807, nf=384696, ne=577013, g=256) using quasi-homeomorphic spherical map to tessellate cortical surface... mris_fix_topology(124) malloc: *** vm_allocate(size=2075615232) failed (error code=3) mris_fix_topology(124) malloc: *** error: can't allocate region mris_fix_topology(124) malloc: *** set a breakpoint in szone_error to debug could not allocate 16108 edges for retessellation Cannot allocate memory reading T1 volume from T1... reading wm segmentation from wm... 136542 ambiguous faces found in tessellation 246 of 4410 overlapping edges discarded 1 of 299 overlapping edges discarded 175 of 1655 overlapping edges discarded retessellating defect 3 with 4269 vertices (convex hull=26247). 661414 of 8448632 overlapping edges discarded 7 of 59 overlapping edges discarded 0 of 45 overlapping edges discarded retessellating defect 6 with 16108 vertices (convex hull=7747). ERROR: mris_fix_topology exited with non-zero status

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label coordinates
by Doug Greve 21 Jul '06

21 Jul '06

Kevin has changed the way freesurfer writes labels. Previously, the coordinates were from the orig surface. From now on (in the development distribution) they will correspond to the white surface. As Kevin points out, the surface from which the coordinates were derived will be in the first line of the label file to help us keep track of the change. doug -------- Original Message -------- Subject: [Fsdev] tksurfer labels now written in white space Date: Fri, 21 Jul 2006 10:48:10 -0400 From: Kevin Teich <kteich(a)nmr.mgh.harvard.edu> To: fsdev(a)nmr.mgh.harvard.edu I changed label.c and label.h to add a text field. The LabelToXXX functions write a note to that field, "coords=XXX". LabelWrite now writes this field in the comment line of the label. I replaced all calls to LabelToOriginal in tksurfer with calls to LabelToWhite. -- Kevin Teich _______________________________________________ Fsdev mailing list Fsdev(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/fsdev -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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FLASH atlas
by Derin Cobia 21 Jul '06

21 Jul '06

Hello, I read in the archive that you were planning on releasing two new atlases (for MP-RAGE and FLASH) last year. Were those (or even newer ones) distributed? I have some FLASH sequences I want to run. Thanks! -Derin

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source of thickness information for mris_preproc
by Lars M. Rimol 21 Jul '06

21 Jul '06

Hi, When one runs mris_preproc with e.g. -meas thickness, does it get the thickness information from the files in the stats directory within each subject's directory - or from the ?h.thickness files under the surf directories? Thank you! -- yours, LMR

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freesurfer movies
by Thomas Stephan 20 Jul '06

20 Jul '06

Dear List, I used tksurfers 'make frame' button to save frames to a movie. What type of movie file is generated by this function, and which viewer or converter could I use to see or convert it? Best regards Thomas -- ====================================================================== Dr. Thomas Stephan Email: tstephan(a)nefo.med.uni-muenchen.de Klinikum Grosshadern Neurologisches Forschungshaus Marchioninistr. 23 Fon: +49 089 / 7095-4819 81377 Muenchen Fax: +49 089 / 7095-4801 ======================================================================

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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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