Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

freesurfer 6 error: dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib
by Ritobrato Datta 14 Dec '15

14 Dec '15

Hello All, I installed freesurfer 6 on a mac running OS-X Yosemite 10.10.4. I am getting the following error when I run recon-all from freesurfer 6. Can you please suggest how to fix it ? Thank you, Ri ri@Magi [0] ~/ri/SampleDatasets$ export FREESURFER_HOME=/Applications/freesurfer6;export SUBJECTS_DIR=/Applications/freesurfer6/subjects;export PATH=/Applications/freesurfer6/bin:$PATH;/Applications/freesurfer6/bin/recon-all -s Dataset1-only-T1 -i Dataset1/MPRAGE.nii.gz -all Subject Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20151015 Current Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20151015 INFO: SUBJECTS_DIR is /Applications/freesurfer6/subjects Actual FREESURFER_HOME /Applications/freesurfer6 Darwin Magi.uphs.upenn.edu 14.4.0 Darwin Kernel Version 14.4.0: Thu May 28 11:35:04 PDT 2015; root:xnu-2782.30.5~1/RELEASE_X86_64 x86_64 dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mri_convert Reason: image not found dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mri_convert Reason: image not found dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mri_make_uchar Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mri_normalize Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mri_watershed Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mri_gcut Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mri_segment Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mri_label2label Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mri_em_register Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mri_ca_normalize Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mri_ca_register Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mri_ca_label Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mri_pretess Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mri_fill Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mri_tessellate Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mri_concatenate_lta Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mri_normalize_tp2 Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mris_smooth Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mris_inflate Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mris_curvature Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mris_sphere Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mris_fix_topology Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mris_topo_fixer Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mris_ca_label Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mris_euler_number Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mris_make_surfaces Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mris_register Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mris_volmask Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mris_anatomical_stats Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mrisp_paint Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mris_curvature_stats Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mris_calc Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mri_robust_register Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mri_robust_template Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mri_and Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mri_or Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mri_fuse_segmentations Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mri_segstats Reason: image not found Trace/BPT trap dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mri_relabel_hypointensities Reason: image not found Trace/BPT trap /Applications/freesurfer6/subjects/Dataset1-only-T1 \n mri_convert /Users/iron/ri/SampleDatasets/Dataset1/MPRAGE.nii.gz /Applications/freesurfer6/subjects/Dataset1-only-T1/mri/orig/001.mgz \n dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer6/bin/mri_convert Reason: image not found Trace/BPT trap Darwin Magi.uphs.upenn.edu 14.4.0 Darwin Kernel Version 14.4.0: Thu May 28 11:35:04 PDT 2015; root:xnu-2782.30.5~1/RELEASE_X86_64 x86_64 recon-all -s Dataset1-only-T1 exited with ERRORS at Sat Dec 12 00:54:32 EST 2015

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interhemispheric registration in native space
by Milde, Christopher 14 Dec '15

14 Dec '15

Dear Freesurfer experts, is there a way to perform an interhemispheric registration with rh, lh surfaces in native space? Preferentially, I would perform the registration with smoothwm surfaces. I only found the xhemi command which refers to fsaverage as a target Best wishes, Christopher

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MNI to Surf RAS problems
by Inês Violante 14 Dec '15

14 Dec '15

Hi, I am trying to convert MNI coordinates to a subject's anatomical space surf coordinates. While this MNI305RAS = TalXFM*Norig*inv(Torig)*[tkrR tkrA tkrS 1]' works fine from surf coordinates to MNI I don't know how to make it work correctly the other way around... i.e., knowing MNI305RAS and wanting to know [tkrR tkrA tkrS]. Could anyone help me with this? Thank you! Ines

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Freesurfer 6 exits with errors after recon edits on skullstrip
by Lauri Tuominen 14 Dec '15

14 Dec '15

Dear Freesurfer experts, So, I ran recon-all on launchpad using /usr/local/freesurfer/stable6/bin/recon-all. This command worked nicely, but part of the occipital cortex was missing and I therefore ran the following command ( both in freesurfer6 ): recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -s atib This took care of the brain mask problem that I had with the previous recon. So I then ran on launchpad: recon-all -s atib -autorecon2 -autorecon3 -hippocampal-subfields-T1' The last command exits with errors. Please find the log-files attached. Thank you for your help! Best, Lauri P.s. Hopefully the attachments got trough this time. Lauri Tuominen, Research Fellow A. A. Martinos Center for Biomedical Imaging Psychiatric Neuroimaging Division Massachusetts General Hospital 149 Thirteenth Street, Suite 2611, Charlestown, MA 02129

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macaque brain equivalent for .gca files
by Mahmoud 14 Dec '15

14 Dec '15

Dear All, Are these two .gca files applicable to macaque brain processing? 1- RB_all_2008-03-26.gca 2- RB_all_withskull_2008-03-26.gca if not, is there any procedure to make these two files for non-human primates ? I really appreciate any help or insight. Thank you, Mahmoud

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ERROR: Talairach QA check failed! and ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED***
by Matthieu Vanhoutte 14 Dec '15

14 Dec '15

Dear experts, I am confronted with some problem in the "recon-all" of a few subjects concerning Talairach space, but don't know how to manage these. Please find below the recon-all log with errors : #-------------------------------------------- #@# Talairach Failure Detection Fri Dec 4 15:29:38 CET 2015 /NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6911, pval=0.4932 >= threshold=0.0050) awk -f /home/global//freesurfer5.3//bin/extract_talairach_avi_QA.awk /NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri/transforms/talairach_avi.log tal_QC_AZS /NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri/transforms/talairach_avi.log TalAviQA: 0.93027 z-score: -10 ERROR: Talairach QA check failed! z-score = -10 <= -9 = threshold atlas xform error = 0 < -60 | > 24 Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach INFO: Attempting MINC mritotal to perform Talairach align #-------------------------------------------- #@# Talairach Fri Dec 4 15:29:39 CET 2015 /NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm /NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri /home/global//freesurfer5.3//bin/talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ Linux wutang 3.13.0-24-generic #47-Ubuntu SMP Fri May 2 23:30:00 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Fri Dec 4 15:31:35 CET 2015 tmpdir is transforms/tmp.talairach.13347 /NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri mri_convert orig_nu.mgz transforms/tmp.talairach.13347/src.mnc mri_convert orig_nu.mgz transforms/tmp.talairach.13347/src.mnc $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=9.90, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (7.45058e-09, 1, 0) writing to transforms/tmp.talairach.13347/src.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -modeldir /home/global//freesurfer5.3//mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.13347/src.mnc transforms/talairach.auto.xfm Fri Dec 4 15:31:58 CET 2015 talairach done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Fri Dec 4 15:31:59 CET 2015 /NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0039, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux wutang 3.13.0-24-generic #47-Ubuntu SMP Fri May 2 23:30:00 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s M0_2011-02-23 exited with ERRORS at Fri Dec 4 15:32:00 CET 2015 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Thanks in advance for helping ! Best regards, Matthieu

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Re: [Freesurfer] Individual regions of CorticalParcellation_Yeo2011
by Parker, Richard 14 Dec '15

14 Dec '15

Hi Prof, Thanks for the speedy reply, When you specify fsaverage5 as -srcsubject and your own subject as -trgsubject, the code executes but the resulting .annot file looks like a mess. Your proposed two-step call to mri_surf2surf seems more promising. If I run the following: mri_surf2surf --srcsubject fsaverage5 --trgsubject fsaverage --hemi lh --sval-annot fsaverage5/label/lh.Yeo2011_17Networks_N1000.split_components.annot --tval ./lh.YeoUpsample.annot I end up with a .annot file in the same space as fsaverage, but there seem to be large gaps between the labels. Here's a screenshot of what I mean: http://imgur.com/VvqYEWx Do you have any suggestions on how to account for this? Is there some unresolved mismatch between the number of vertices following upsampling, perhaps? Best wishes, Richard Hi Richard, Sorry. My original reply was rejected by the list. Resending. In the mri_surf2surf command, Instead of the srcsubject being fsaverage, can you try using the srcsubject as fsaverage5 instead? Alternatively, you can try running mri_surf2surf twice. Once to upsample the fsaverage5 annot to fsaverage and then run the mri_surf2surf command from your email. (This might actually work better). Thanks, Thomas On Fri, Dec 11, 2015 at 12:51 AM, Parker, Richard <richard.r.par...(a)kcl.ac.uk> wrote: > Hi Professor Yeo, > > > > Thanks for providing a link to your split region MNI space files. > > > > Could you please advise on how to get these labels into subject native > space? > > > > If using the standard version of the network labels that comes packaged with > Freesurfer 5.3.0, I can get the annotation file into native space quite > easily with the following command: > > > > > > mri_surf2surf --srcsubject fsaverage --trgsubject $SUBJECT_NAME --hemi lh > --sval-annot > $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_17Networks_N1000.annot > --tval $SUBJECT_NAME/label/lh.Yeo2011_17Networks_N1000.annot > > > > However, in the dropbox link you posted, it doesn't seem that there is a > .annot file compatible with fsaverage. The fsaverage5 version is present, > but if I try slotting the fsaverage5 .annot file into the above call to > mri_surf2surf, I get disastrous results. > > > > Do you perhaps have a .annot file for the upsampled (and split) network > labels? Or perhaps there's an easier way to achieve what I'm after. I notice > that you have provided a .nii file for the network ROIs that is in the same > space as fsaverage, perhaps this file can be warped to native space somehow? > > > > Best wishes, > > > > Richard Parker > > King's College London > > > > > > > > > > > > > > > > Hi Erica, > > > > You can try this link: > > https://dl.dropboxusercontent.com/u/5734119/Outgoing/Yeo_JNeurophysiol11_Sp… > > > > Regards, > > Thomas > > > > On Wed, Oct 7, 2015 at 2:45 AM, Yi-Chia Erica Kung <orange...(a)gmail.com> > wrote: > >> Dear Prof. Yeo, > >> > >> I would like to extract the brain regions of the functional canonical > >> network, such as DMN, SAL, or CEN, withFreesurfer. And I found that you >> have > >> provided the split regions of 7&17 Network in previous discussion string. > >> >> (https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg41288.html > >> ) > >> > >> However, the dropbox download link you offered has expired. > >> Would you mind uploading it again? > >> > >> Thank you very much. > >> > >> Erica

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Re: [Freesurfer] Individual regions of CorticalParcellation_Yeo2011
by Parker, Richard 14 Dec '15

14 Dec '15

Hi Professor Yeo, Thanks for providing a link to your split region MNI space files. Could you please advise on how to get these labels into subject native space? If using the standard version of the network labels that comes packaged with Freesurfer 5.3.0, I can get the annotation file into native space quite easily with the following command: mri_surf2surf --srcsubject fsaverage --trgsubject $SUBJECT_NAME --hemi lh --sval-annot $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_17Networks_N1000.annot --tval $SUBJECT_NAME/label/lh.Yeo2011_17Networks_N1000.annot However, in the dropbox link you posted, it doesn't seem that there is a .annot file compatible with fsaverage. The fsaverage5 version is present, but if I try slotting the fsaverage5 .annot file into the above call to mri_surf2surf, I get disastrous results. Do you perhaps have a .annot file for the upsampled (and split) network labels? Or perhaps there's an easier way to achieve what I'm after. I notice that you have provided a .nii file for the network ROIs that is in the same space as fsaverage, perhaps this file can be warped to native space somehow? Best wishes, Richard Parker King's College London Hi Erica, You can try this link: https://dl.dropboxusercontent.com/u/5734119/Outgoing/Yeo_JNeurophysiol11_Sp… Regards, Thomas On Wed, Oct 7, 2015 at 2:45 AM, Yi-Chia Erica Kung <orange...(a)gmail.com> wrote: > Dear Prof. Yeo, > > I would like to extract the brain regions of the functional canonical > network, such as DMN, SAL, or CEN, withFreesurfer. And I found that you have > provided the split regions of 7&17 Network in previous discussion string. > (https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg41288.html > ) > > However, the dropbox download link you offered has expired. > Would you mind uploading it again? > > Thank you very much. > > Erica

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T1 to FS
by Reza Farimani 13 Dec '15

13 Dec '15

Hi everybody, I am new to freesurfer so sorry for my naive questions. I am trying to export raw DICOM files to freesurfer. The CD I have apparently have all T1,T2, and other MR image types. How should I filter only T1 for freesurfer? Thanks Reza

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Re: [Freesurfer] configure overlay display in tksurfer by keyboard inputs
by Slater David 13 Dec '15

13 Dec '15

Hi, I have the same problem with tksurfer in Ubuntu. The keyboard entry doesn't work for the tksurfer input boxes - I can't set any values in the overlay configuration window, edit label info, configure phase encoded data display etc. All of the text / numeric entry boxes have this issue. Any suggestions on how to fix this? My freesurfer verion is freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015 but I had the same problem before updating to v6-beta. Thanks, David -----Message d'origine----- De : freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] De la part de Bruce Fischl Envoyé : 15 August 2015 21:12 À : Freesurfer support list Objet : Re: [Freesurfer] configure overlay display in tksurfer by keyboard inputs Hi Lars can you give more details? What prevents you from entering values? Do you get any errors when tksurfer loads? cheers Bruce On Sat, 15 Aug 2015, Lars M. Rimol wrote: > > Hi all, > > I have installed FS 5.3 on an Ubuntu 14.04 system and find that I am > unable to set threshold values in the edit boxes in the "configure > overlay" display in tksurfer. Does anybody know how to fix this (without specifying the threshold on the command line each time)? > > Thank you! > > > > > > yours, > Lars M. Rimol, PhD > Department of Medicine > John A. Burns School of Medicine > University of Hawai'i > 1356 Lusitana Street, University Tower Honolulu, HI 96813 > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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