Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30090 discussions

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

merge in a sigle label the results obetained in fs-fast
by stdp82＠virgilio.it 21 Sep '17

21 Sep '17

Hi list, I would to merge (separatelly pos and neg) in a sigle .label which contain all the clusters which represent the seed-cortical connectivity after fs-fast analysis.I aim to avoid to extraxt manually single label for cluster by tksurfer. Thanks, Stefano

2 1

Error in Qcache
by Emmanuel Nwosu 21 Sep '17

21 Sep '17

Hi All, I will want to know if this error on this link https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-April/051464.ht… was resolved. I am having a similar problem while sampling to the fsaverage. Thanks Kind regards Emmanuel

2 1

recon-all question
by STACEY M SCHAEFER 21 Sep '17

21 Sep '17

Hello, I want to run recon-all again on scans that have already been hand-edited, the appropriate recon-all flags ran, and resulting output checked and approved. The images look good, but when the hippocampal subfield routine was later run on the images, it crashed, leaving an error in the recon-all.log. We want to be anal, and make sure there is no error again after running recon-all. In other words, we want the last line in the recon-all.log to reflect that the images all completed successfully. Is there a recommended flag (or flags) at this point? In other words, there are no additional edits to incorporate in the recon-all job, but we also don't want the earlier edits, control points, etc. ignored in this last rerun of recon-all. Thank you for your help! Stacey Stacey M. Schaefer, Ph.D. Center for Healthy Minds University of Wisconsin-Madison 625 W Washington Ave Madison WI 53703 608-263-9321

2 1

Longitudinal increase in thickness/volume
by Huang, Caleb (NIH/NINDS) [F] 21 Sep '17

21 Sep '17

Hello, I'm tracking atrophy in the precentral region. I've run the subjects through the longitudinal stream. Because of time constraints, I've mostly focused on editing the precentral regions as well as any significant errors outside of the region. I've observed increases in thickness of up to 0.1mm in the precentral region. In some cases there's an increase in volume as well. Upon inspection though, the precentral wm/pial surfaces look fine. Is this a normal range of error? Thank you, -Caleb

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