Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

Re: [Freesurfer] Freeview on Mac not starting due PETSC error {Disarmed}
by fsbuild 14 Jun '20

14 Jun '20

External Email - Use Caution Hello Alex, Please make sure you have the latest version of Xquartz (2.7.11) installed on the Mac from, https://www.xquartz.org.  You can right click and select “Get Info” on the XQuartz.app under Applications -> Utilities in order to check the version.   Launch XQuartz, wait for it to open an X window, and in that window run xeyes or xgc to see if it displays basic graphics. If you set FREESURFER_HOME in your shell init file(s), I would check it is set to the 7.1.0 release so that you are source’ing the SetUpFreeSurfer{.sh,csh} script from 7.1.0 (and not from previous releases) .  I would also unset or comment out setting LD_LIBRARY_PATH before you source the SetUpFreeSurfer{.sh,csh} script in any shell init files or in your environment. - R. On Jun 14, 2020, at 00:07, Alex White <alexander.l.white(a)gmail.com> wrote:        External Email - Use Caution        Hello freesurfer team! I can’t get Freeview to start up on my Mac (Catalina v 10.15.15). It worked intermittently earlier this year, then stopped working. I updated Freeview, and then all of freesurfer, and still have the same problem. So now I have this version of freesurfer:  freesurfer-darwin-macOS-7.1.0-20200511-813297bTyping “freeview” into the terminal generates the following error: [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/troubleshootin…: 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 16, Tue Sep 23 10:02:49 CDT 2008 HG revision: 31306062cd1a6f6a2496fccb4878f485c9b91760[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 darwin15. named gse7359200.local by alexlw Sat Jun 13 20:58:43 2020[0]PETSC ERROR: Libraries linked from /autofs/cluster/pubsw/arch/MacOS10.11/packages/petsc/2.3.3/src/petsc/lib/darwin15.6.0-c-opt[0]PETSC ERROR: Configure run at Mon Apr 22 13:14:02 2019[0]PETSC ERROR: Configure options --with-debugging=no --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 0I searched through the log of previous emails and found several others with “PETSC errors” but could not discern a common solution. Help? Thank you, Alex White PS: I also can’t get Freeview to launch on a linux machine, and will send a report on that in a separate email. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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ver 7.1: recon-all executes out of order?
by Roman Fleysher 12 Jun '20

12 Jun '20

External Email - Use Caution Dear FreeSurfer Develovers, FreeSurfer 7.1 was recently installed on our cluster. I am testing it and stumbled on the error. It is difficult for me to debug it myself (perhaps if https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV7<https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0>.1 existed it would help me). I hope you can help. The symptom is that I run: recon-all -s FOLDER_1 -hemi lh -white -smooth2 -inflate2 -sphere -surfreg -cortparc -pial -sd FOLDER_2 Notice strange combination: -s FOLDER_1 -sd FOLDER_2 . Data is actually in FOLDER_2 where specific subject is set up in the environmental variable. The error message in recon-all.log is: mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 error: No such file or directory error: MRISread(../surf/lh.white.preaparc): could not open file error: No such file or directory error: mris_smooth: could not read surface file ../surf/lh.white.preaparc Indeed, file ../surf/lh.white.preaparc does not exist. It seems to indicate that -white was not actually executed before -smooth2. This command worked on version 6.0. Is this a bug in recon-all script version 7.1? Is this expected? Previous successful command on the same data was: recon-all -s FOLDER_1 -hemi lh -fix -sd FOLDER_2 General info: 1) FreeSurfer version: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b 2) Platform: likely CentOS, not sure how to tell 3) uname -a: Linux loginnode4 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: not attached because folder structure contains sensitive information that is hard to remove. Thank you, Roman

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Re: [Freesurfer] lGI permutation and monte-carlo
by Avi Gharehgazlou 12 Jun '20

12 Jun '20

External Email - Use Caution Thank you so much for your input, it was very helpful and I really appreciate it. Regarding your question with relation to my 4th question, when I run the below command line to visualize my results after correcting for multiple comparisons using monte-carlo at 1.3 significance level in this example, I assumed the clusters that appear on freeview are only my significant clusters (clusters that survived monte carlo correction) since I put " cache.th13.abs.sig.cluster.mgh" and then as overlay " cache.th13.abs.sig.ocn.annot " in my command line. If not, will you please tell me how I can see only clusters that are significant after correction for multiple comparisons (at 1.3 sig level in this case)? Also, in my command line, I can put either lh.pial or lh.inflated to see the results//clusters on the pial or inflated surface, respectively. Correct? vglrun freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.pial:overlay=lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir/group.diff/cache.th13.abs.sig.cluster.mgh:overlay_threshold=1.3,5:annot=lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir/group.diff/cache.th13.abs.sig.ocn.annot -viewport 3d Thank you so much, Avi

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Matlab runtime installation error for Freesurfer v7.1.0
by Yann Quidé 11 Jun '20

11 Jun '20

External Email - Use Caution Hi team, I am trying to install fs_install_mcr R2014b, but encounter an error just at the end of it: mv: rename /var/folders/1f/4_zl7p9n795c2yq1dgb3hvt40000gq/T/tmp.Xvv7Ku4d/install-target/v84 to /Applications/freesurfer/7.1.0/MCRv84: Permission denied Any idea how I can fix this to finalise the installation? I should have the admin rights on the machine. Thanks, Yann

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Re: [Freesurfer] Regarding installation in CentOS7
by fsbuild 11 Jun '20

11 Jun '20

External Email - Use Caution Hello Rahul, Did you try following the instructions on the wiki pages about how to do an install with the tar archive or RPM ?  Please see links to Linux and/or Mac install and setup, https://surfer.nmr..mgh.harvard.edu/fswiki/rel7downloads -R. On Jun 11, 2020, at 16:25, Rahul Sharma <sharmarahul.26dec(a)gmail.com> wrote:        External Email - Use Caution        Unable to perform installation. Please help me out regarding the same.Regards:Rahul SharmaResearch ScholarNIT Silchar (Assam)9827834360_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Regarding installation in CentOS7
by Rahul Sharma 11 Jun '20

11 Jun '20

External Email - Use Caution Unable to perform installation. Please help me out regarding the same. Regards: Rahul Sharma Research Scholar NIT Silchar (Assam) 9827834360

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Final result of monkey make_averge_subject
by Pam Garcia 11 Jun '20

11 Jun '20

External Email - Use Caution Hi FS developers, I have some questions related to make_average_subject I followed the steps describe here https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates to 1. build a monkey curvature pattern 2. build FS monkey average using 40 subjects I've finished the surface and volume average, but the anatomy of the prefrontal lobe looks rounded and the size of the brain was adjusted to the human MNI. I suppose that this is due to the affine registration. My questions are the follows: 1. Is there some way to avoid the affine registration or only use 3 DOF for registration when the average is built? All the images were previously registered to MNI monkey space 2. In the case that the affine registration can´t be avoided is it correct to use a surface gotten from the template image and next use this as average in mris_preproc?

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Postdoc position available in PET/MRI at Martinos Center, MGH/HMS
by Wey, Hsiao-Ying 10 Jun '20

10 Jun '20

Research Fellow in Simultaneous PET/MR Neuroimaging Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School We are seeking two postdoctoral fellows to join our team to pursue research in simultaneous PET/MR imaging in neuroscience applications. Our research focuses on developing and applying novel PET/MRI methods to investigate the neurochemical underpinnings of psychiatric and neurological disorders. We have projects and training opportunities in the following area: (1) Quantify neuroreceptor dynamics and functional with pharmacological challenges in animal models and human subjects, with applications in pain, addiction, and psychiatric disorders; and (2) Assess the impacts of neurovascular coupling/function on PET radiotracer kinetics, with applications in neurodegenerative disorders. Our research programs are highly translational spanning from animal models, first-in-human studies, to clinical applications. The appointment as a Massachusetts General Hospital, Harvard Medical School research fellow will be for 1 year with possibility for extension based on performance and the availability of funding. The positions are available immediately. The successful candidate will be a highly motivated researcher with a desire to begin an independent career related to or involving neuroimaging. The position requires a Ph.D. degree in Medical Physics, Biomedical Engineering, Computer Science, Neuroscience or a related field. However, we will consider candidates of any scientific background. This position requires experience in analysis of medical imaging data. Experience with MRI or PET is a plus. Extremely strong candidates with minimal imaging experience are still encouraged to apply. Strong written and oral English communication skills are required. [cid:clip_image001.png]Additional Skills/Abilities/Competencies The job requires a candidate who is mature, responsible and flexible with excellent organizational and people skills. S/He must be able to work with in a fast-paced environment and should be able to problem-solve/troubleshoot, juggle and prioritize multiple tasks and seek assistance when appropriate. Application Interested applicants should send a cover letter describing research interests and experience, an updated CV, and names and contact information of three references to: Hsiao-Ying (Monica) Wey, Ph.D. (E-mail: hsiaoying.wey(a)mgh.harvard.edu) Please contain “Research Fellow Application: Your Name” in the e-mail subject line. The Massachusetts General Hospital and Harvard Medical School are equal opportunity and affirmative action employers. Best, Hsiao-Ying (Monica) ------ Hsiao-Ying (Monica) Wey, Ph.D. Assistant Professor of Radiology, Harvard Medical School Director of Translational Imaging, Chemical Neuroscience Program A. A. Martinos Center for Biomedical Imaging Institute for Innovation in Imaging (i3) Massachusetts General Hospital 149 Thirteenth Street, Room 10.110 Charlestown, MA 02129 Phone: (617) 724-1384 Email: hsiaoying.wey(a)mgh.harvard.edu

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Fwd: Postdoc position available - computational modeling of fMRI/MEG data, and real-time fMRI neurofeedback of language
by Douglas N. Greve 10 Jun '20

10 Jun '20

-------- Forwarded Message -------- Subject: Postdoc position available - computational modeling of fMRI/MEG data, and real-time fMRI neurofeedback of language Date: Wed, 10 Jun 2020 10:54:03 +0000 From: Narly Golestani <Narly.Golestani(a)unige.ch> To: Narly Golestani <Narly.Golestani(a)unige.ch> External Email - Use Caution Dear Colleagues, I would be grateful if you could please circulate the below job advertisement to anyone who may be interested. Many thanks in advance and best wishes, Narly. ****************************************** With the launch of a new ‘NCCR Evolving Language’ (http://www.snf.ch/SiteCollectionDocuments/nfs/Faktenblatt_NCCR_evolvinglang…) which involves nearly 40 different research groups from a large variety of disciplines across Switzerland, we seek to fill a *Postdoc position for a four-year project* starting in September 2020, or at the selected candidate’s earliest convenience. Our goal is to make progress in understanding *the importance of prosody in language processing*. To this end, we plan to carry out a set of studies involving both *computational modeling of fMRI *and/or of*MEG data *and*real-time fMRI neurofeedback *to understand the *mechanisms whereby prosody and rhythm support linguistic processing per se*. The computational modeling work will be an extension of our recent work on the neural encoding of acoustic information in speech sounds (https://www.ncbi.nlm.nih.gov/pubmed/31285622) The research will be done in the group of Narly *Golestani*in Geneva (www.brainandlanguagelab.org <http://www.brainandlanguagelab.org>), in collaboration with researchers in Switzerland and abroad (Elia *Formisano*in Maastricht, and Frank *Scharnowski*in Vienna). Applicants should hold a degree in *Cognitive Neuroscience*, *Biomedical Engineering, Computational Neuroscience, or a related field*, and should have solid experience in *human brain imaging *and*programming*, and ideally also *in computational modelling (i.e. encoding / decoding) of fMRI *and/or of*MEG data, real-time fMRI based neurofeedback, machine learning and statistics*. Knowledge of French would be an asset. The NCCR places great emphasis on gender diversity and we particularly encourage women to apply. To apply, please send a cover letter, CV, names and contact information of 2-3 references as well as any other relevant documents to Narly.Golestani(a)unige.ch <mailto:Narly.Golestani@unige.ch>. Feel free to contact me should you have any questions. *Deadline for application: June 30^th 2020.* *-----------------------------------------------------------------------------------------------------------------------------------------------------------------* *Brain and Language Lab* **Prof. Narly GOLESTANI* * Department of Psychology Campus Biotech *9 Chemin des Mines, * *1202 Genève* *+41 22 379 53 52* <https://outlook.unige.ch/owa/redir.aspx?SURL=5WTo-p-J-W9FrDydU-0WU4PdMytUGs…>http://www.brainandlanguagelab.org https://twitter.com/brain_lang_lab *-----------------------------------------------------------------------------------------------------------------------------------------------------------------* <https://outlook.unige.ch/owa/redir.aspx?SURL=5WTo-p-J-W9FrDydU-0WU4PdMytUGs…>

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Unmatched error
by COLLEEN PLETCHER 09 Jun '20

09 Jun '20

External Email - Use Caution Hello, I am currently attempting to run a brain through the longitudinal stream after performing edits on the longitudinal brain, using the command recon-all -long timepoint1 base -autorecon2-wm -autorecon3. I am getting an error that says Unmatched ". All of the data for both timepoint 1 and the base is there and readable. I am using version 6.0. Any advice on how to fix this problem? Thank you!

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