Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30081 discussions

Error opening Freeview
by Zeng,Victor (BIDMC - Psychiatry) 01 Jul '19

01 Jul '19

?Hi all, I'm having issues opening Freeview (The most recent version): it loads .mgz and labels correctly, but then after 5 seconds it shuts off, giving off this error: qt_xcb_createCursorXRender: query_pict_formats failed [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Si… ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Signal received! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Unknown Name on a linux-gnu named beta by nick Mon Jul 1 16:25:24 2019 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 Segmentation fault ? I was wondering if there's anything I can do to debug, or whether it's just a lack of computer capacity on our end. Best, Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab ph: 617 754 1237 -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

2 1

LME - Monte Carlo
by tom parker 01 Jul '19

01 Jul '19

External Email - Use Caution Dear FreeSurfers, I was reading the wiki documents about how to run LME analyses in FreeSurfer. I found that one of the disadvantages is that, at the moment, it only allows FDR corrections to be applied for multiple comparisons. I have 2 patient groups that show cortical thinning compared to controls at baseline when I correct with Monte Carlo but nothing survives with FDR. Now, I would like to see if these cortical thinning patterns change over time so I thought I should keep things consistent and use Monte Carlo for the longitudinal analysis as well. Is there any way of using Monte Carlo for LME? I read some suggestions in emails that were sent 2 years ago but I was wondering if there are any updates or if there is a guide with recommended steps? Thank you so much!

1 0

Citing the development version for use of hippocampal/amygdala sub-field segmentation
by Daniel Callow 01 Jul '19

01 Jul '19

External Email - Use Caution Hello, I used the longitudinal HippocampalSubfieldsAndNucleiOfAmygdala <https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm…> pipeline to create subject-specific hippocampal ROI's for a paper I am preparing for submission. I would like to know what the best way to cite this technique is. This is what I currently have in my methods section. Subjects T1-weighted anatomical images were processed with the FreeSurfer image analysis suite (http://surfer.nmr.mgh.harvard.edu/, version 6.0) and Automated hippocampal subfield segmentation was performed for each subjects T1 weighted image using the Freesurfer longitudinal hippocampal subfield segmentation program(Iglesias et al., 2015, 2016). Do I need to cite my use of the development version? And if so how is the best way to go about doing this? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

1 0

Surfaces with different numbers of vertices.
by Nillo, Ryan Michael R 01 Jul '19

01 Jul '19

Hello Freesurfer users/developers, I have surface with ~73,400 vertices generated from the Freesurfer version 6 fsaverage brain, left hemisphere. I have a surface map that was created by mapping a volume to the fsaverage white surface. Is there a way to map the surface map to the new surface with less vertices? Is there a way to map values from the 73,000 vertices-map to the standard fsaverage pal surface? Thanks in advance, Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging External Email - Use Caution

3 8

Re: [Freesurfer] Question about OptSeq
by Greve, Douglas N.,Ph.D. 01 Jul '19

01 Jul '19

No, there is not. optseq assumes you will be doing an FIR analysis (=finite impulse response = not assuming a shape to the hemodynamic response). In this analysis, this must be the relationship. If you assume a shape, then this relationship is not necessary. In your case, you can set the dPSD=1. On 7/1/2019 7:19 AM, Davide Nardo wrote: External Email - Use Caution Dear Prof Greve, I hope you don’t mind if I ask you a question about OptSeq. It looks like a constraint in using OptSeq is that any event duration must be an integer multiple of the dPSD, which in turn needs to be an integer multiple of the TR, and seemingly there is no exception to this rule. I am in a situation in which my TR = 2 sec, and my event duration = 3 sec, therefore I get an error message when running OptSeq. However, I am puzzled by this, as in my experience with fMRI an event duration does not necessarily need to be a multiple of the TR… Is there any way I can circumvent this requirement in OptSeq? Best. Davide Nardo -- Davide Nardo, PhD MRC Cognition and Brain Sciences Unit University of Cambridge 15 Chaucer Road Cambridge, CB2 7EF Davide.Nardo(a)mrc-cbu.cam.ac.uk<mailto:Davide.Nardo@mrc-cbu.cam.ac.uk>

1 0

[DEADLINE EXTENSION]: The 2nd International Workshop on Machine Learning in Clinical Neuroimaging (MLCN 2019): ENTERING THE ERA OF BIG DATA VIA TRANSFER LEARNING AND DATA HARMONIZATION
by MLCN Workshop 30 Jun '19

30 Jun '19

External Email - Use Caution Dear Colleagues,The submission deadline for MLCN 2019 workshop as a satellite event of the MICCAI 2019 conference has been extended to 14/07/2019. For more information, please visit https://mlcnws.com/call-for-papers/ . Call for Papers Recent advances in neuroimaging and machine learning provide an exceptional opportunity for investigators and physicians to discover complex relationships between brain, behaviors, and mental and neurological disorders. The MLCN 2019 workshop (https://mlcnws.com) as a satellite event of MICCAI 2019 (https://www.miccai2019.org) aims to bring together researchers in both theory and application from various fields in domains such as *e.g.* machine learning, neuroimaging, predictive clinical neuroscience, *etc.* Topics of interests include, but are not limited to: - Transfer learning in clinical neuroimaging - Model stability in transfer learning - Data prerequisites for successful transfer learning - Domain adaptation in neuroimaging - Data harmonization across sites - Data pooling – practical issues - Cross-domain learning in neuroimaging - Interpretability for transfer learning - Unsupervised methods for domain adaptation - Multi-site data analysis, from preprocessing to modeling - Big data in clinical neuroimaging - Scalable machine learning methods - Benefits, problems, and solutions of working with very large datasets SUBMISSION PROCESS: The workshop seeks high quality, original, and unpublished work on algorithms, theory, and applications of machine learning in clinical neuroimaging related to big data, transfer learning, and data harmonization. Papers should be submitted electronically in Springer Lecture Notes in Computer Science (LCNS) style ( https://www.springer.com/gp/computer-science/lncs/conference-proceedings-gu…) with up to 8-pages and using the CMT system at https://cmt3.research.microsoft.com/MLCN2019. The MLCN workshop uses a double-blind review process in the evaluation phase, thus authors must ensure anonymous submissions. Accepted papers will be published in a joint proceeding with the MICCAI 2019 conference. IMPORTANT DATES: - Paper submission deadline: July 14, 2019 (23:59 PST) - Notification of Acceptance: August 5, 2019 - Camera-ready Submission: August 12, 2019 - Workshop Date: October 13, 2019 Best regards, MLCN 2019 Organizing Committee <https://mlcnws.com/organization/>, Email: mlcnworkshop(a)gmail.com Website: https://mlcnws.com/ twitter: @MLCNworkshop <https://twitter.com/MLCNworkshop>

1 0

Re: [Freesurfer] Longitudinal Masking and FDR
by Hua, Jessica 29 Jun '19

29 Jun '19

External Email - Use Caution Hi Kersten, I used this code to calculate the threshold: P = [ F_lhstats1.pval(lhcortex) F_rhstats1.pval(rhcortex) ]; G = [ F_lhstats1.sgn(lhcortex) F_rhstats1.sgn(rhcortex) ]; [detvtx,sided_pval,pth] = lme_mass_FDR2(P,G,[],0.05,0); pcor = -log10(pth) I substituted 0.1, 0.2, 0.5, 0.8, and 1 where the 0.05 is, and I kept getting the same pcor value of 4.8943. Jessica Hua

1 0

mis-registartion question
by Nasiriavanaki, Zahra 28 Jun '19

28 Jun '19

Dear Freesurfers Hi I checked the functional to anatomical data registration using tkregister-sess -s $subj -fsd bold -per-run -bbr-sum. (The functional data is only collected from parietal and occipital lobes in 7T scanner). The values obtained from tkregister-sess are too high (0.95) for 7 out of 8 runs. When I looked at the snapshots obtained from QA_tools, they looked ok (top row images). But, when I looked at the volumes of the individual runs using tkregister2 command, the registration doesn't look good (bottom row images). tkregister2 --s $subj --mov /$subj/bold/011/template.nii.gz --surf --reg new.dat --regheader . I'm wondering if I need to do manual edits, and I appreciate any advice on that. Thanks Mona [cid:91ee52eb-c146-4bee-8cc8-19bf01ef7547][cid:487a26fa-1c27-4ed5-bd48-26a587d477d7] [cid:479ab0d3-00f7-406c-886c-4d83c945708e][cid:332d78df-9a82-4c35-a603-aa7a1734ba0f] Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

2 4

total cortical area
by Barletta, Valeria 28 Jun '19

28 Jun '19

Dear Freesurfers, Where in the /mri/stats folder can I find the total cortical surface in mm2? Is it in the ?h.aparc.stats or in the ?h.curv.stats? Thank you, Valeria

1 0

How to account for gender in a contrast matrix
by Basavaraju, Rakshathi 28 Jun '19

28 Jun '19

External Email - Use Caution Dear all FS users, I wanted to know the way of accounting for gender in a simple regression analysis of cortical thickness against 2 continuous variables. Th example of contrast matrix given in the downloaded tutorial data for cortical thickness with age without accounting for gender is, 0 0 0.5 0.5 . However if we want to factor in gender how do we do it? Is it 0.5 0.5 0.5 0.5? or something else? Answers regarding same will be very much appreciated. Thanks, Dr. Rakshathi Basavaraju (MD Psychiatry) Postdoctoral Research Scientist Taub Institute Columbia University Irving Medical Centre 622 West, 168th Street, New York - 10032 E-Mail: rb3419(a)cumc.columbia.edu<mailto:rb3419@cumc.columbia.edu> http://www.wellcomedbt.org/fellowsprofile/dr-rakshathi-basavaraju-288

1 0

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