Freesurfer December 2015

freesurfer@nmr.mgh.harvard.edu

115 participants
187 discussions

Re: [Freesurfer] mri_label2vol --fill-ribbon argument
by Arnaud Boré 14 Dec '15

14 Dec '15

Dear Freesurfer's experts, I wanted to add this picture so you can understand better what I mean by "The ribbon is not well filled". Is there a way to fill the ribbon completely ? [image: Images intégrées 1] Thank you in advance for your help. PS: If needed here is a link to the picture https://www.dropbox.com/s/wmeez9ajfuvni9r/label2vol_ribbon_not_filled_corre… Arnaud

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Freesurfer 6 - matlab crash
by Scott Quadrelli 14 Dec '15

14 Dec '15

Hi, I’m running freesurfer 6 on a cluster. I am having issues with the matlab crashing during the hippocampal segmentation. I am allocating 10gb for each job, however that hasn’t fixed the problem. Sometime the segmentation works fine, however many segmentations fail due to matlab crash. I have attached two example crash reports one with ‘segmentation violation’ the other common one is ‘Abort signal detection’. What else should we be looking at to fix the problem ? Cheers, Scott

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Graph theory analysis in R
by Watson, Christopher 14 Dec '15

14 Dec '15

Dear Freesurfer users, (apologies for cross-post) I am pleased to announce the release of an R package I created, called "brainGraph", for performing graph theory analyses of brain MRI data. You can use it for cortical thickness, volume, surface area, or LGI. It can also be used for tractography data (I have code that works with the outputs of FSL's "probtrackx2"), and it should work for resting-state fMRI as well. It is very heavily dependent on the fantastic R package "igraph" (see http://igraph.org/redirect.html) I created a GUI for quick and easy data exploration, but it isn't quite as polished as others out there (e.g., BrainNet Viewer). For usage, please see the User Guide I put together (direct PDF link: https://www.dropbox.com/s/j831n3q9muyz1go/brainGraph_UserGuide.pdf?dl=0 ). You will find some code for getting your data into R, and I have documented many analysis steps and include multiple figures. I hope this is intuitive for both veteran and novice R users. Additionally, there are System Requirements, Installation instructions, and links for help learning R. Some features that should be of interest include: * bootstrapping & permutation testing * random graph generation, small-worldness, and global/local/nodal efficiency * rich-club calculations * robustness ("targeted attack" or "random failure") & vulnerability: PDF of figure (PNG: https://www.dropbox.com/s/k14gdg1lomhh4l2/failPlot-1.pdf?dl=0) * Plotting GUI - full GUI (PNG): https://www.dropbox.com/s/e0hdng7flrxsgd2/brainGraph_GUI.png?dl=0 * Plotting GUI - union of vertex neighborhoods (PNG): https://www.dropbox.com/s/aag5cn1p1z9xzxr/brainGraph_GUI_neighborhoods.png?… * Plotting GUI - community (module) plots (PNG): https://www.dropbox.com/s/8zzpd5j268qstmg/brainGraph_GUI_communities.png?dl… You can install it directly in R by typing: install.packages('brainGraph') My Github page for the package (https://github.com/cwatson/brainGraph) contains the development version, and you can install that by typing: devtools::install_github('cwatson/brainGraph') Please see the NEWS.md file (https://github.com/cwatson/brainGraph/blob/master/NEWS.md) for updates made since the CRAN submission. To work properly on Windows, you may need to install the devel version. This is still a work-in-progress, so I am very happy to receive bug reports, feature requests, general coding help questions, (constructive) criticism, etc. Please join the Google Group that I set up for those purposes: https://groups.google.com/forum/?hl=en#!forum/brainGraph-help Chris Watson

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excessive topological defect
by Elisabetta del Re 14 Dec '15

14 Dec '15

Dear FreeSurfer team, we are running FreeSurfer on 1.5T cases. For a few of them we get error messages that I am attaching. Mostly the message error relates to excessive topological defect. Any suggestions you can give to us? Thank you, regards, Elisabetta -- Elisabetta C. del Re, Ph.D. Instructor, Department of Psychiatry Harvard Medical School phone 617 9675569 mail elisabetta_delre(a)hms.harvard.edu

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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

1 0

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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Freesurfer December 2015