Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30064 discussions

Re: [Freesurfer] Error in segmentHA_T1
by Iglesias Gonzalez, Eugenio 25 Sep '17

25 Sep '17

Dear Tiril, Were you pointed to downloading a version of Java when you first tried to run the subfields? If so, did you follow the instructions? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Tiril Pedersen Gurholt <t.p.gurholt(a)medisin.uio.no> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, 22 September 2017 at 20:47 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Error in segmentHA_T1 Dear Experts, I recently installed Freesurfer development version (dated Sept. 16, 2017) on a Mac Sierra (10.12.6). When trying to run segmentHA_T1.sh I encounter a java problem: "JavaVM: Failed to load JVM: /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bundle/Libraries/libserver.dylib». See full error message below. The java.opts file in MCRv80/bin/maci64 is dated Nov. 5, 2014. There also appears to be a problem with a Matlab app (?), although matlab runtime has been installed. Any ideas as to how to fix these problems? Best regards, Tiril Error message: #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Fri Sep 22 20:17:14 CEST 2017 ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/MCRv80//runtime/maci64:/Applications/freesurfer/MCRv80//bin/maci64:/Applications/freesurfer/MCRv80//sys/os/maci64: Warning: application is running on a locale different from the original platform locale. JavaVM: Failed to load JVM: /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bundle/Libraries/libserver.dylib JavaVM FATAL: Failed to load the jvm library. 2017-09-22 20:17:16.597 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.599 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.599 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.600 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.600 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.601 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.601 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.602 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.602 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. JavaVM: Failed to load JVM: /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bundle/Libraries/libserver.dylib JavaVM FATAL: Failed to load the jvm library. Fatal Error on startup: Unable to start the JVM because of a bad Java option or unknown error. Please check your java.opts file. #-------------------------------------------- #@# Hippocampal Subfields processing (T1) right Fri Sep 22 20:17:16 CEST 2017 ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/MCRv80//runtime/maci64:/Applications/freesurfer/MCRv80//bin/maci64:/Applications/freesurfer/MCRv80//sys/os/maci64: Warning: application is running on a locale different from the original platform locale. JavaVM: Failed to load JVM: /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bundle/Libraries/libserver.dylib JavaVM FATAL: Failed to load the jvm library. 2017-09-22 20:17:18.151 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.151 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.152 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.152 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.153 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.153 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.153 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.154 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.154 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. JavaVM: Failed to load JVM: /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bundle/Libraries/libserver.dylib JavaVM FATAL: Failed to load the jvm library. Fatal Error on startup: Unable to start the JVM because of a bad Java option or unknown error. Please check your java.opts file.

1 0

Brain.finalsurfs.mgz output
by Fereshte 24 Sep '17

24 Sep '17

Dear Experts, What is "brain.finalsurfs.mgz" file? I mean it is the output of which stage in recon-all pipeline? I couldn't find any information about this output on the site. Thank you. Cheers

2 2

Hemisphere white surface
by Fereshte 24 Sep '17

24 Sep '17

Dear Experts, I have run the autorecon2 without errors but i can't see rh.white and rh.white outputs ( lh.white.K and lh.white.H instead). Could you please help? Thank you

2 2

bad midline cut
by Gabor Perlaki 23 Sep '17

23 Sep '17

I've a subject, where the midline cut is bad (see the attached pictures), therefore the segmented left lateral ventricle also includes considerable number of voxels from the right one. Is it possible to correct it somehow?

1 0

Error in segmentHA_T1
by Tiril Pedersen Gurholt 22 Sep '17

22 Sep '17

Dear Experts, I recently installed Freesurfer development version (dated Sept. 16, 2017) on a Mac Sierra (10.12.6). When trying to run segmentHA_T1.sh I encounter a java problem: "JavaVM: Failed to load JVM: /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bundle/Libraries/libserver.dylib». See full error message below. The java.opts file in MCRv80/bin/maci64 is dated Nov. 5, 2014. There also appears to be a problem with a Matlab app (?), although matlab runtime has been installed. Any ideas as to how to fix these problems? Best regards, Tiril Error message: #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Fri Sep 22 20:17:14 CEST 2017 ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/MCRv80//runtime/maci64:/Applications/freesurfer/MCRv80//bin/maci64:/Applications/freesurfer/MCRv80//sys/os/maci64: Warning: application is running on a locale different from the original platform locale. JavaVM: Failed to load JVM: /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bundle/Libraries/libserver.dylib JavaVM FATAL: Failed to load the jvm library. 2017-09-22 20:17:16.597 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.599 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.599 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.600 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.600 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.601 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.601 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.602 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:16.602 segmentSubjectT1_autoEstimateAlveusML[10313:171678] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. JavaVM: Failed to load JVM: /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bundle/Libraries/libserver.dylib JavaVM FATAL: Failed to load the jvm library. Fatal Error on startup: Unable to start the JVM because of a bad Java option or unknown error. Please check your java.opts file. #-------------------------------------------- #@# Hippocampal Subfields processing (T1) right Fri Sep 22 20:17:16 CEST 2017 ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/MCRv80//runtime/maci64:/Applications/freesurfer/MCRv80//bin/maci64:/Applications/freesurfer/MCRv80//sys/os/maci64: Warning: application is running on a locale different from the original platform locale. JavaVM: Failed to load JVM: /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bundle/Libraries/libserver.dylib JavaVM FATAL: Failed to load the jvm library. 2017-09-22 20:17:18.151 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.151 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.152 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.152 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.153 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.153 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.153 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.154 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. 2017-09-22 20:17:18.154 segmentSubjectT1_autoEstimateAlveusML[10355:171872] This process is attempting to exclude an item from Time Machine by path without administrator privileges. This is not supported. JavaVM: Failed to load JVM: /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bundle/Libraries/libserver.dylib JavaVM FATAL: Failed to load the jvm library. Fatal Error on startup: Unable to start the JVM because of a bad Java option or unknown error. Please check your java.opts file.

1 0

Re: [Freesurfer] lobes volume (WM and GM)
by Gonzalo Rojas Costa 22 Sep '17

22 Sep '17

Hi Douglas: Why you specified 5mm as the default value for the --wmparc-dmax option in mri_aparc2aseg command? Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl http://www.aribrain.info https://scholar.google.com/citations?user=LO7LZ3oAAAAJ https://www.researchgate.net/profile/Gonzalo_Rojas2 https://cl.linkedin.com/in/gonzalorojascosta

2 5

curvature
by Jacobs H (NP) 22 Sep '17

22 Sep '17

Dear FreeSurfer, In the stats files (e.g aparc) there are also statistics for the "integrated rectified mean curvature", "integrated rectified gaussian curvature", "folding index" and "intrinsic curvature index". To what kind of properties do these measures refer and which one is advised to be used? Many thanks! Heidi

2 1

nu_correct failure
by miracle ozzoude 22 Sep '17

22 Sep '17

Hello expert, I ran several subjects on FS v6 and they failed on the same stage (mri_nu_correct.mni and nu_correct). How can I solve this problem? I have attache the recon-all.log file for 2 subjects. Best, Paul

1 1

Research Engineer position in Neuroimaging (Madrid, Spain)
by Susanna Carmona Cañabate 22 Sep '17

22 Sep '17

*Research Engineer position in Neuroimaging at the *“Biomedical Imaging and Instrumentation Group (BiiG) <https://image.hggm.es/en/laboratory>”, Madrid. The BiiG is a research organization located in Madrid (Spain) and affiliated with the “Instituto de Investigación Sanitaria Gregorio Marañón” and the “Universidad Carlos III”. The group is markedly multidisciplinary and has a broad research interest, from the development of new imaging techniques to processing methodologies and their application in practice. The candidate will support the *neuroimaging subdivision* of the group and will be involved in the development, maintenance and optimization of a *neuroimaging platform* that manages the storage and processing of multimodal brain MRI data using *cloud resources*. Most of his/her work will be integrated into a project that studies the *neural basis of human pregnancy*. *Qualifications:* · *Biomedical Engineering,* *Computational Neuroscience* *or related field* *with a strong computational background.* · *Proficiency in* *oral and written English.* · *Experience with* *Matlab and other* *programming languages (C, C++, bash* *and Python, Java)* · *Interest* *in* *neuroimaging* *research.* · *Ability to effectively interact with a multi-disciplinary team of investigators and staff.* · *Ability to work independently and as part of a team.* *Preferences:* *· **Experience with neuroimaging processing softwares* *(*FreeSurfer*, FSL, SPM, AFNI, ANTs and* *BrainVisa) will be very relevant for the selection of the applicant.* · *Familiarity with stimuli presentation softwares such as Eprime, Presentation or Psychtoolbox is preferred. * · *Methods and statistical background is preferred.* *Salary** based on experience and qualifications. * *Interested applicants should submit a cover letter and resume to* *scarmona(a)hggm.es <scarmona(a)hggm.es>. * *Deadline**: 1st of November 2017*

1 0

Adjusted or unadjusted CT values and interpretation of volume values in ocn.dat from group analysis
by Elizabeth Bartlett 21 Sep '17

21 Sep '17

Hello Freesurfer experts, I have performed a group level analysis of volume and cortical thickness using mri_glmfit and performed multiple comparisons correction with mri_glmfit-sim. I used the contrast matrix 0 1 0 to analyze 1 group with 2 covariates, along the 1st covariate (education) with the 2nd covariate being age. I get 2 significant clusters (after mult. comp. corr.) for CT and 2 for volume. When I look at the values in ./cache.th30.abs.y.ocn.dat, the average CT values within my sample are 2.57 and 2.50 for the 2 regions. *My first question is: *are the CT values outputted to ocn.dat adjusted for my 2nd covariate (age) or are they unadjusted CT values within the sig. cluster? The volume values contained within the ocn.dat files are also in the same range as the CT values, with averages of 2.50 and 1.87 for left superior frontal and right inferior parietal volume, respectively. *My second question is:* What is the metric for volume reported in ocn.dat? These values seem too low to be total cluster volume for each subject expressed as mm^2. The volumes reported in ./cache.th30.abs.sig.cluster.summary are more like what we I expect for volume (283.24 mm^2). Could these values be the average volume surrounding each vertex in the inflated mesh (volume contained within the surrounding vertices)? Thank you, Elizabeth

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer