[Freesurfer] Freeview error
External Email - Use Caution
Hi, I'm trying to open freeview in a linux node in my institution's
computing cluster and an error is coming up consistently - see below. Can
you please advise? Thank you.
agc01:~ moana004$ module list
> No Modulefiles Currently Loaded.
> agc01:~ moana004$ module load freesurfer/6.0.0
> agc01:~ moana004$
> study_sharedfolder=/home/moanae/shared/project_K99_ChrTMDHCP_qunex02; \
> > subjID_list="20005 10015 11012"; \
> > for subjID in ${subjID_list}; do freeview
> ${study_sharedfolder}/sessions/${subjID}/hcp/${subjID}/T1w/${subjID}/mri/brainmask.gcuts.mgz:colormap=heat
> ${study_sharedfolder}/sessions/${subjID}/hcp/${subjID}/T1w/${subjID}/mri/T1.mgz:opacity=0.5;
> done
> libGL error: unable to load driver: swrast_dri.so
> libGL error: failed to load driver: swrast
> [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://secure-web.cisco.com/1Bgfp-85Thmw5Xhnu5rrkPFwya2Y3o-Kg07_nIggSZ9oXXbinUuAdIwcI0iRqe6KosyMKzWJq_kkReHZMfQMDhUHX3sHlUgUCEkU4XEOVVn-u2KtOf9LJ4sVNsGrNoauhQO_onuf_mvcuPTFxx8o39H4zCrl3lYXguL-r0BVaoORQIfA7PHqlLGpQ6qwCRVzlLs7A8q_mmDyyBbnpSu-VuQ5AtLTNeBRL5wKhCcIzIM4cSYpsztm9q1QVbHUuobd8L4mlLPi8jdsfTbOr0AiELvxbRPWPA_17c3xezx4gOAo7leN4se5Lw_dJq88bFxbg/http%3A%2F%2Fwww.mcs.anl.gov%2Fpetsc%2Fpetsc-as%2Fdocumentation%2Ftroubleshooting.html%23Signal[0]PETSC
> ERROR:
> or try
> http://secure-web.cisco.com/1JsIV3v6H8VSyBNnbIppnqmNOkuk-noOC5m-VFsDLuqNWwPz-rO-J1FzW6RPFhzjZ_DXULTjfDx7Tl3HkIFUWssfo_12FO0ZDaoyOkaJJ9NA3KDFT-WUV0Vs02nlPzcZsSaxemALkmavfAuE5-faK5-MEB5BmObdCUTf9A-8aEVtc3hW_Pd4BapjsUgSwXmzP5SIr4EIvObSju9mketw_eQ6rgURbuk78DM5GPWoKe1RErdc8mN8OMlJQXHLLfcPHZppsgwx7JIiD6kyDjxXzidtVNKt5K8snPYU12Id4NiL_KDUUCsAAtaunRZcJC9Lv/http%3A%2F%2Fvalgrind.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 agc01 by moana004 Fri
> Mar 10 11:22:48 2023
> [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
> libGL error: unable to load driver: swrast_dri.so
> libGL error: failed to load driver: swrast
> [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://secure-web.cisco.com/1Bgfp-85Thmw5Xhnu5rrkPFwya2Y3o-Kg07_nIggSZ9oXXbinUuAdIwcI0iRqe6KosyMKzWJq_kkReHZMfQMDhUHX3sHlUgUCEkU4XEOVVn-u2KtOf9LJ4sVNsGrNoauhQO_onuf_mvcuPTFxx8o39H4zCrl3lYXguL-r0BVaoORQIfA7PHqlLGpQ6qwCRVzlLs7A8q_mmDyyBbnpSu-VuQ5AtLTNeBRL5wKhCcIzIM4cSYpsztm9q1QVbHUuobd8L4mlLPi8jdsfTbOr0AiELvxbRPWPA_17c3xezx4gOAo7leN4se5Lw_dJq88bFxbg/http%3A%2F%2Fwww.mcs.anl.gov%2Fpetsc%2Fpetsc-as%2Fdocumentation%2Ftroubleshooting.html%23Signal[0]PETSC
> ERROR:
> or try
> http://secure-web.cisco.com/1JsIV3v6H8VSyBNnbIppnqmNOkuk-noOC5m-VFsDLuqNWwPz-rO-J1FzW6RPFhzjZ_DXULTjfDx7Tl3HkIFUWssfo_12FO0ZDaoyOkaJJ9NA3KDFT-WUV0Vs02nlPzcZsSaxemALkmavfAuE5-faK5-MEB5BmObdCUTf9A-8aEVtc3hW_Pd4BapjsUgSwXmzP5SIr4EIvObSju9mketw_eQ6rgURbuk78DM5GPWoKe1RErdc8mN8OMlJQXHLLfcPHZppsgwx7JIiD6kyDjxXzidtVNKt5K8snPYU12Id4NiL_KDUUCsAAtaunRZcJC9Lv/http%3A%2F%2Fvalgrind.org
> on linux or man libgmalloc on Apple to find
> memory corruption errors
>
Re: [Freesurfer] Post-Doctoral position available in human neuroimaging and sensory testing at the University of Minnesota School of Dentistry
External Email - Use Caution A gentle reminder that this post doctoral position is still open for applications. Thank you. On Mon, Sep 14, 2020 at 2:28 PM Estephan Moana Filho wrote: > *POSITION OVERVIEW* > > > > The Division of TMD & Orofacial Pain (OFP) at the University of Minnesota > School of Dentistry (UMN SOD) is seeking a highly motivated Post-Doctoral > Associate in the field of human neuroimaging and sensory testing for an > NIH/NIDCR funded project studying brain-related mechanisms in painful > temporomandibular disorders (TMD). The focus of this position will be on > acquisition and analysis of neuroimaging data, as well as performing > quantitative sensory (QST) and endogenous pain modulation (EPM) testing. > > This project is led by Dr. Estephan J. Moana-Filho, a dentist-scientist > within the TMD & OFP division, who provides clinical care to OFP patients > and is interested in expanding the knowledge about brain mechanisms in OFP > conditions with a focus on painful TMD. The methods to be used include > multimodal magnetic resonance imaging (MRI) based on the Human Connectome > Project (HCP) sequences (structural, resting and stimulus-evoked BOLD fMRI, > diffusion) combined with sensory testing and psychosocial/behavioral > measures (QST, EPM, questionnaires, clinical measures, etc.). Our goal is > to further our understanding of brain structural and functional networks > involved in sensory processing, and potentially underlying central > sensitization features present in painful TMD. > > > > *Duties and Responsibilities*: > > The Post-Doctoral Associate’s responsibilities will include, but are not > limited to: > > 1. Implement multimodal MRI data analysis pipelines (structural and > functional connectivity, stimulus-evoked fMRI, diffusion-based tractography > and volumetry/cortical thickness measures) based on the HCP pre-processing > pipelines (Glasser et al., 2013). > > 2. Perform sensory/EPM testing in human participants following > standardized protocol (Rolke et al., 2006) > > 3. Acquire neuroimaging data following the HCP neuroimaging approach > (Glasser et al., 2016), including stimulus-evoked fMRI. > > 4. Model and analyze complex datasets including neuroimaging, sensory > and clinical data. > > > > *Required qualifications*: > > 1. PhD in neuroscience, biomedical engineering, oral biology, > psychology, cognitive science, or a related field. > > 2. Strong proficiencies with one or more major neuroimaging software > suites (e.g., FSL, Freesurfer, Connectome workbench, AFNI, SPM, etc.) and > Unix/Linux environment. Familiarity with R, Python, and/or Matlab > programming languages is a plus*.* > > 3. Quantitative and statistical skills, including strong programming > skills and comfort with diverse computing environments such as > high-performance computing systems. > > 4. Comfortable with interacting with human participants. > > 5. Demonstrated ability to complete projects as evidenced by > first-author publication(s). > > 6. Proficient writing skills, motivated and driven to publish in > peer-reviewed journals. > > > > In addition to these requirements, the ideal candidate should have a > passion for self-learning, be inquisitive, critical problem-solving skills > and initiative to seek out the resources necessary to achieve the project’s > goals. > > > > The Moana-Filho lab is part of a vibrant pain research community at the > UMN, with access to several resources including: > > · The Center of Magnetic Resonance Research (CMRR), a world class > MRI research center with several research dedicated MRI scanners including > three 3T Prisma, 7T and 10.5T human scanners. > > · The UMN Minnesota Supercomputing Institute (MSI), an > interdisciplinary research resource supporting high-performance computing > services. The latest MSI’s system is among the top 10 university-owned > supercomputers in the nation, with a peak performance of over 670 Tflops > and an additional 105 Tflops from a dedicated GPU subsystem. Its main > cluster is also equipped with 40 high memory nodes to accommodate large > memory requirements. These memory nodes feature 1 TB of memory and large > solid state drives for ultra-high performance input/output. All systems are > connected to high-performance parallel storage systems, with a current > capacity of approximately 3 PBytes. MSI staff manage and operate these > resources, offering full support to users in developing and optimizing > workflows. > > > > Applications will be reviewed on an ongoing basis. Funding is available as > a one-year appointment with the possibili
[Freesurfer] Post-Doctoral position available in human neuroimaging and sensory testing at the University of Minnesota School of Dentistry
External Email - Use Caution *POSITION OVERVIEW* The Division of TMD & Orofacial Pain (OFP) at the University of Minnesota School of Dentistry (UMN SOD) is seeking a highly motivated Post-Doctoral Associate in the field of human neuroimaging and sensory testing for an NIH/NIDCR funded project studying brain-related mechanisms in painful temporomandibular disorders (TMD). The focus of this position will be on acquisition and analysis of neuroimaging data, as well as performing quantitative sensory (QST) and endogenous pain modulation (EPM) testing. This project is led by Dr. Estephan J. Moana-Filho, a dentist-scientist within the TMD & OFP division, who provides clinical care to OFP patients and is interested in expanding the knowledge about brain mechanisms in OFP conditions with a focus on painful TMD. The methods to be used include multimodal magnetic resonance imaging (MRI) based on the Human Connectome Project (HCP) sequences (structural, resting and stimulus-evoked BOLD fMRI, diffusion) combined with sensory testing and psychosocial/behavioral measures (QST, EPM, questionnaires, clinical measures, etc.). Our goal is to further our understanding of brain structural and functional networks involved in sensory processing, and potentially underlying central sensitization features present in painful TMD. *Duties and Responsibilities*: The Post-Doctoral Associate’s responsibilities will include, but are not limited to: 1. Implement multimodal MRI data analysis pipelines (structural and functional connectivity, stimulus-evoked fMRI, diffusion-based tractography and volumetry/cortical thickness measures) based on the HCP pre-processing pipelines (Glasser et al., 2013). 2. Perform sensory/EPM testing in human participants following standardized protocol (Rolke et al., 2006) 3. Acquire neuroimaging data following the HCP neuroimaging approach (Glasser et al., 2016), including stimulus-evoked fMRI. 4. Model and analyze complex datasets including neuroimaging, sensory and clinical data. *Required qualifications*: 1. PhD in neuroscience, biomedical engineering, oral biology, psychology, cognitive science, or a related field. 2. Strong proficiencies with one or more major neuroimaging software suites (e.g., FSL, Freesurfer, Connectome workbench, AFNI, SPM, etc.) and Unix/Linux environment. Familiarity with R, Python, and/or Matlab programming languages is a plus*.* 3. Quantitative and statistical skills, including strong programming skills and comfort with diverse computing environments such as high-performance computing systems. 4. Comfortable with interacting with human participants. 5. Demonstrated ability to complete projects as evidenced by first-author publication(s). 6. Proficient writing skills, motivated and driven to publish in peer-reviewed journals. In addition to these requirements, the ideal candidate should have a passion for self-learning, be inquisitive, critical problem-solving skills and initiative to seek out the resources necessary to achieve the project’s goals. The Moana-Filho lab is part of a vibrant pain research community at the UMN, with access to several resources including: · The Center of Magnetic Resonance Research (CMRR), a world class MRI research center with several research dedicated MRI scanners including three 3T Prisma, 7T and 10.5T human scanners. · The UMN Minnesota Supercomputing Institute (MSI), an interdisciplinary research resource supporting high-performance computing services. The latest MSI’s system is among the top 10 university-owned supercomputers in the nation, with a peak performance of over 670 Tflops and an additional 105 Tflops from a dedicated GPU subsystem. Its main cluster is also equipped with 40 high memory nodes to accommodate large memory requirements. These memory nodes feature 1 TB of memory and large solid state drives for ultra-high performance input/output. All systems are connected to high-performance parallel storage systems, with a current capacity of approximately 3 PBytes. MSI staff manage and operate these resources, offering full support to users in developing and optimizing workflows. Applications will be reviewed on an ongoing basis. Funding is available as a one-year appointment with the possibility of extension. Salary will be competitive and commensurate with experience. In case of any questions, please feel free to contact Dr. Moana-Filho (moana004 at umn dot edu ). To apply, click on “External Applicants” under the banner “Apply now!” and search for Job Opening 337497: https://humanresources.umn.edu/content/find-job ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] dt_recon using weighted least squares for diffusion tensor estimation
Dear freesurfer experts, As far as I understand, dt_recon uses linear least squares method as default to estimate the diffusion tensor. Is it possible to use weighted linear least squares in dt_recon? Thank you. Estephan Moana-Filho, DDS, MS, PhD Clinical Fellow, Oral Maxillofacial Pain Program Center for Pain Research and Innovation UNC School of Dentistry Re: [Freesurfer] Diffusion tensor estimation method ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Desikan-Killiany parcellations of SI+SII and IPL
Dear Freesurfer experts, Is it a fair assumption that the Desikan-Killiany parcellations of the postcentral gyrus is roughly equivalent to SI+SII, and that the supramarginal gyrus ≈ inferior parietal lobule? I used SI, SII and IPL ROI masks in some FSL analyses, and would like to use similar ROIs for Freesurfer results. Thank you. Estephan Moana-Filho, D.D.S., M.S. Ph.D. Candidate Clinical Fellow, Oral Maxillofacial Pain Program Center for Pain Research and Innovation UNC School of Dentistry mo...@unc.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Incomplete skull striping but correct segmentation
I had some subjects processed through the standard recon-all pipeline that had some remaining skull just below the frontal lobe (superior part of the orbit). The segmentation as checked in tkmedit appeared to be ok, i.e. it was not considering the skull parts as white matter. The reconstructed cortical surfaces also appeared to be good in tksurfer. Playing with the watershed value did not provide much improvement, and I assume that to clean up the images adequately I would have to do so by hand. My question is: should I be concerned about improving skull stripping for these subjects, given the good segmentation and cortical reconstruction obtained? Thank you. Estephan Moana, DDS Graduate Student Oral Biology PhD Program - Neurobiology track School of Dentistry, UNC- Chapel Hill 2140 Old Dental Building, CB# 7455 Rm 2140 Chapel Hill, NC 27599 Phone: (919) 966-5680 Fax: (919) 966-5339 mo...@email.unc.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FSL-FS results integration
Hello Freesurfer people, I am following the FSL-Fressurfer tutorial from the June course to look at my data on both applications. I successfully was able to register my FEAT output (non-smoothed) to the FS anatomical. My questions are for the following steps: 1. Is there a difference between resampling individual run COPE's to a common surface instead of resampling subject-level GFEAT COPE's (in native space)? If they are equivalent the second option seems to be less cumbersome when typing the mris_preproc command - is this a correct conclusion? 2. When I display individual functional runs or GFEAT results over the subject's surface, I am basically looking at FEAT/GFEAT results, correct? So when I run a surface_based group analysis using mri_glmfit how similar/different are these results from those of a group-level FEAT analysis, assuming that I used a simple one-sample group mean and fixed-effects for both analyzes? Thank you. Estephan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Making nice images using FreeSurfer
Hello FreeSurfer experts, I am playing with displaying FEAT output over the 3D pial surface provided by FS. I was wondering if somebody knows how to: 1. See both hemispheres side-by-side at the same time (both pial and inflated, if possible); 2. Make a video of the output 3D brain rotating at a certain axis (x,y or z), and maybe transitioning from pial to inflated surface. This may not really matters for scientific purposes, but it should produce some wows during lectures and thesis defense (my goal). AFNI does it, but its rendering option makes the image grainy, resulting in a video with poor resolution. Thank you. Estephan Moana, DDS Graduate Student Oral Biology PhD Program - Neurobiology track School of Dentistry, UNC- Chapel Hill 2140 Old Dental Building, CB# 7455 Chapel Hill, NC 27599 Phone: (919) 966-5680 Fax: (919) 966-5339 mo...@email.unc.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FSL to FreeSurfer registration
Thanks for you input Michael. For some reason, I only saw your answer after Dougla's response. Assuming that I do not want to do volume-based analysis and just want nice pics of my blobs over a 3D brain, would Michael's suggestion work? If so, what is the next step after using fslroi, as the input for reg-feat2anat is a feat directory (an not a single example_func file)? An unrelated question: is there a way to get the FreeSurfer mailing list via a RSS feed? This would be help decrease the amount of emails in my inbox... Thanks again. Estephan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FSL to FreeSurfer registration
Thanks Nick, this helps a lot! Estephan Nick Schmansky wrote: Estaphan, It turns out the freesurfer mailing list does support RSS feeds: http://www.mail-archive.com/freesur...@surfer.nmr.mgh.harvard.edu/maillist.xml Nick On Thu, 2009-09-24 at 13:25 -0400, Nick Schmansky wrote: Estephan, I can ask our IT people about an RSS feed. Another option is to turn-on digest mode under the mailing list options. Freesurfer emails would arrive in once-a-day bundles. https://mail.nmr.mgh.harvard.edu/mailman/options/freesurfer Nick On Thu, 2009-09-24 at 12:35 -0400, Estephan Moana wrote: Thanks for you input Michael. For some reason, I only saw your answer after Dougla's response. Assuming that I do not want to do volume-based analysis and just want nice pics of my blobs over a 3D brain, would Michael's suggestion work? If so, what is the next step after using fslroi, as the input for reg-feat2anat is a feat directory (an not a single example_func file)? An unrelated question: is there a way to get the FreeSurfer mailing list via a RSS feed? This would be help decrease the amount of emails in my inbox... Thanks again. Estephan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FSL to FreeSurfer registration
Hello all, I took the FS course last June at the OHBM in San Francisco, and am now playing with it to get to know it better. One of the slides on the talk about FSL-FS integration mentioned that the input data (from FEAT) for the reg-feat2anat command should have not been smoothed prior to registering to FS. Considering that FEAT 1st level analysis has a default of 5mm spatial smoothing (and that's what I used on my data), it seems counterintuitive to need to run a 1st level analysis again so the output files are not spatially smoothed. So my questions are: 1) having the example_func file spatially smoothed will necessarily hinder a proper registration to the FS anatomical?; 2) if so, should I re-run all my FEAT 1st level analysis without smoothing or is there any other way? I know this is quite a beginners question, but I could not find the answers on the FS FAQ or the mailing list archives. I appreciate any light on this. Regards, Estephan Moana, DDS Graduate Student Oral Biology PhD Program - Neurobiology track School of Dentistry, UNC- Chapel Hill 2140 Old Dental Building, CB# 7455 Chapel Hill, NC 27599 Phone: (919) 966-5680 Fax: (919) 966-5339 Cell: (612) 702-3295 mo...@email.unc.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
