Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30065 discussions

Apply a nonlinear transform to a surface.
by Aaron Tanenbaum 13 Mar '23

13 Mar '23

External Email - Use Caution I am working on a project that will involve applying nonlinear work to a freesurfer surface. This project is in its infancy. I have not figured out all the details. The nonlinear transform will be in either FNIRT or ANTS format. Does anyone know how to do this?

4 5

Freeview error
by Estephan Moana Filho 13 Mar '23

13 Mar '23

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_nIggSZ9oXXb… ERROR: > or try http://secure-web.cisco.com/1JsIV3v6H8VSyBNnbIppnqmNOkuk-noOC5m-VFsDLuqNWwP… 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_nIggSZ9oXXb… ERROR: > or try http://secure-web.cisco.com/1JsIV3v6H8VSyBNnbIppnqmNOkuk-noOC5m-VFsDLuqNWwP… 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 11:22:50 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_nIggSZ9oXXb… ERROR: > or try http://secure-web.cisco.com/1JsIV3v6H8VSyBNnbIppnqmNOkuk-noOC5m-VFsDLuqNWwP… 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 11:22:51 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 > agc01:~ moana004$ > -- Estephan J. Moana-Filho, DDS, MS, PhD Assistant Professor Division of TMD, Orofacial Pain and Dental Sleep Medicine Graduate Faculty in Oral Biology Department of Diagnostic and Biological Sciences UMN School of Dentistry moana004(a)umn.edu 6-320d Moos Tower 515 Delaware St. SE Minneapolis, MN 55455-0329 Office: (612) 624-3338 Clinic: (612) 626-0140 Fax: (612) 626-0138 Clinical referrals: z.umn.edu/TMDrefer UMN profile: https://secure-web.cisco.com/1qDzqxV8A0saK5iVzOb_YFpj8bFrtMnaV7PlkTYT0_-gJx… ORCID ID: http://secure-web.cisco.com/1_aaPiXWbc5YByvuEhM2gYDWPGPbSIFVNqn8PmXWXc3hUEs… Publons: https://secure-web.cisco.com/1xpdcvUYZasLT9y5HJGpNs2tmC4cot__gVR6i_BeYNss6z… My Bibliography (NCBI): https://secure-web.cisco.com/107k1mETeQHnb4m4TKKH4M_6g4tY9rwD3cvRPnRFwNezv_… The information transmitted in this e-mail is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material, including "protected health information." If you are not the intended recipient, you are hereby notified that any review, retransmission, dissemination, distribution, or copying of this message is strictly prohibited. If you have received this communication in error, please destroy and delete this message from any computer and contact us immediately by return e-mail.

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Error using chol
by Caspar M. Schwiedrzik 13 Mar '23

13 Mar '23

External Email - Use Caution Hi! I am running into an issue with fast_selxavg3b. I am attempting a first level PPI analysis. The command is mkanalysis-sess -fsd bold -native -delay -2/2 -notask -TR 2 -polyfit 6 -analysis [xxx] -funcstem [xxx] -runlistfile mooneyppi.list -nuisreg motion.dat 6 -tpef tpef_dvars.dat -acfbins 5 -acffwhm 0 -mask [xxx] -force -nuisreg juice.dat 1 -nuisreg fixation.dat 1 -taskreg ppi.dat 4 I get the following error: GLS Residual Pass run 1 t= 0.0 Error using chol Matrix must be positive definite. Error in fast_selxavg3b (line 942) Wseg = inv(chol(toeplitz(acfrun))'); Before that, I am getting several warnings of this kind: > In fast_selxavg3b (line 895) Warning: Matrix is singular, close to singular or badly scaled. Results may be inaccurate. A few of them, but not run 1, have RCOND = NaN. This is with versions 7.2 and 5.3. I found one previous conversation on the mailing list regarding this error in the context of a resting state analysis, but no conclusion. Any advice would be appreciated. Thanks! Caspar

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white and pial surfaces of the hippocampus
by Khazar Ahmadi 13 Mar '23

13 Mar '23

External Email - Use Caution Dear FS experts, Id like to delineate WM and pial surfaces in the hippocampus and subsequently bin GM layers of it (like the approach that is commonly used for laminar analyses in V1 or other sensory cortices). I think the current output of recon-all does not contain WM/pial surfaces in subcortical regions. Have tried running the FS hippocampal module. It generates subfields (in .mgz format) and volume estimates but I cannot find any surface-based output. Is there a way to obtain pial and WM surfaces in this region? I have another question regarding surface-based representation of the subfields. Based on the paper by Sämann et al., 2020 (see the link below; Figure 6), I think it is possible to have surface-based visualization of the subfields using ENIGMA, but I could not find additional documentation on that. Any ideas on how to obtain surface-based segmentation of the hippocampus would be greatly appreciated. Thanks a lot, and best wishes, Khazar https://secure-web.cisco.com/162vGALDRGyKKidOcJ8MJ6vwNqV2G11ikgdRoQJk8awcbY… -- Khazar Ahmadi, PhD Postdoctoral Researcher, Institute of Cognitive Neuroscience, Department of Neuropsychology, Ruhr University Bochum, Bochum,Germany

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Freesurfer v. 7.3.2 careg error
by Simon Jones 13 Mar '23

13 Mar '23

External Email - Use Caution Dear Freesurfer Support, Under older versions of Freesurfer such as 7.2.0 I can split recon-all into two stages: recon-all -autorecon1 -noskullstrip -s sub -i sub.nii.gz Manually create brainmask.mgz recon-all -autorecon2 -autorecon3 -s sub Using freesurfer v. 7.3.2 this fails. I looked at the log file and in the -autorecon2 stage the steps go straight from mri_ca_normalize to mri_ca_label missing out mri_ca_register so no transforms/talairach.m3z file is created. I modified the second part to recon-all -autorecon2 -autorecon3 -careg -s sub and then it completed without error. Maybe this is intentional and there is another recommended way to do this multistage pipeline. Thanks, Simon

2 1

Virtual box password
by Scheffler, F, Dr [fredas＠sun.ac.za] 13 Mar '23

13 Mar '23

External Email - Use Caution Dear FreeSurfer dev community Can I please get the password for the freesurfer 7.2 virtual box? Thanks! Freda Scheffler PDRF The integrity and confidentiality of this email are governed by these terms. Disclaimer<https://secure-web.cisco.com/1qRaAYtTQzNeKbGdciQHv3yKlOaL9Y0kD6eO9ymfqjvQpZ…> Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings bere?l. Vrywaringsklousule<https://secure-web.cisco.com/1qRaAYtTQzNeKbGdciQHv3yKlOaL9Y0kD6eO9ymfqjvQpZ…>

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University of Michigan: Postdoctoral Position Available in Migraine/Pain Multimodal Neuroimaging & Neuromodulation
by Dajung Kim 12 Mar '23

12 Mar '23

External Email - Use Caution Dear all, The Headache and Orofacial Pain Effort (H.O.P.E.) Lab at the University of Michigan requests applications for a postdoctoral position to work on migraine, fibromyalgia, and TMD research programs funded mainly by the National Institute of Health. The programs use novel methodologies in neuroimaging and neuromodulation to investigate and target central mechanisms of chronic pain in vivo. Extensive knowledge of neuroimaging analysis software systems as well as programming experience is required, as is some level of comfort with novel neuromodulatory protocols. Previous research experience and publications with positron emission tomography (PET) and/or MRI-based neuroimaging methods and analyses are also needed. We are seeking applicants with advanced degrees and strong self-motivation to work in a highly creative, altruistic, and mentoring environment with students and residents from different departments across campus. The applicant will be exposed to several tech innovations, many developed in-house, for clinical translational pain research (e.g., migraine, TMD, dental and cancer pain), such as mobile technology, multimodal neuroimaging (PET, MRI, fNIRS, EEG) and neuromodulation montages (TMS and [HD]-tDCS). For more information: https://secure-web.cisco.com/1CMqPDyLmPprvRMmnI4Zo88-CVMepg39jQYutoIAAy36cB… Thank you, Alex DaSilva [image: image.jpeg] Alex F. DaSilva, DDS, DMedSc Tenured Professor Director, Learning Health Systems Diplomate of the American Board of Orofacial Pain Department of Biologic and Materials Sciences & Department of Psychology University of Michigan School of Dentistry Director, Headache & Orofacial Pain Effort (H.O.P.E.) *"Brain as the Target for Pain Research, Treatment, and Education"* *https://secure-web.cisco.com/1lMsdAEtVDoO3ssBwodWF4kjVBmRqHqsKCb5lXdfb2pWUxS6gEgQXNpoIKktg3X7QyuX2vaaDmtfWDhQ1G0EXXbCYNCfFyLw_IXYkXfzw0D8ZphXx1GCJhfvi-DeVv98d3fybJVL6HijHreruxluhFLS2mtL8-6DoVGPkf5NCnAkOiCuO3xlZhE9xFBwkc36wDDxLJ1hhxVBczSnzjvGOadkQGh4BQUSF7HFLet0AQUkwiy42wXhT_i5fGDmKxF8luDCxtLJubDxFf6PpAS9I7CYYShJZ44lFi4hPM8IoyOHkZhNtyUQVJpo2YNhUDB_edt6gbiddjANvho_MEMDCmg/https%3A%2F%2Fmedia.dent.umich.edu%2Flabs%2Fhope%2Fdev%2F <https://secure-web.cisco.com/1lMsdAEtVDoO3ssBwodWF4kjVBmRqHqsKCb5lXdfb2pWUx…>* Michigan Neuroscience Institute (MNI) 205 Zina Pitcher Pl, room 1021 Ann Arbor, MI 48109-5720 Office: 734 615-3807 Fax: 734 763-3453

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FS 7.2 VirtualBox 7z Password
by Chris Dering 11 Mar '23

11 Mar '23

External Email - Use Caution Dear FS experts, I am using the Oracle Virtual Box to install FS 7.2 on Windows. Could you send to me the passcode for the 7z archive?

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Pass code VirtualBox Ubuntu image Freesurfer 7.2.0
by Noël Staeren 10 Mar '23

10 Mar '23

External Email - Use Caution Hi, Is it possible to receive the pass code to open the image FS_7_2_0_Ubuntu_18_04_06.ova.7z for the FreeSurfer VirtualBox VM? Thank you very much, Noël

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Developmental Neuroscience Postdoc
by McQuaid, Goldie 10 Mar '23

10 Mar '23

External Email - Use Caution The JackLab <https://secure-web.cisco.com/1gfJ9h3fYCmtXdydHlATkZmg0283dqWsNow8So8uCSVtMO…> at George Mason University seeks a full-time postdoctoral fellow with experience in MRI to work on an NIMH Autism Centers of Excellence Network <https://secure-web.cisco.com/18vfzBjSVYLvbbKYIsn0_IYWxyVVm-B7m3yi_s-RHqE7lq…> project focused on understanding late diagnosis in autism. The successful candidate will work with a team of autistic and non-autistic investigators, Advisory Board members, and staff to ensure the success of this unique multimodal, mixed-methods project (with neuroimaging, qualitative, and quantitative data collection) developed in collaboration with the autistic community and focused on autistic well-being. Mason's MRI facility features state-of-the-art equipment, including a research-dedicated 3T Siemens Prisma, MRI simulator, and in-bore EEG and eye-tracking capabilities. This is a great opportunity for a candidate looking to advance in an autism-related career, as it will provide the opportunity to collaborate with field leaders throughout our network. Postdoctoral trainees on previous waves of data collection through this project have been successful in obtaining competitive NIH awards (e.g., K01, R01, etc.) and faculty positions. Our team is comprised of scientists of a variety of neurotypes, and autistic candidates are particularly encouraged to apply. Please see below for the official position description and link to the job ad/application portal. For full consideration, applicants must apply at https://secure-web.cisco.com/1smxNa677iZ9kZ3mJksyk5pLV8eIs6Suf8LhNeyr03P1k9…, complete and submit the online application; and upload a cover letter, curriculum vitae (CV), and a list of three professional references with contact information. Thank you! Allison Jack, PhD (she/her) ajack(a)gmu.edu Assistant Professor, Dept. of Psychology George Mason University *** *Job Posting:* https://secure-web.cisco.com/1smxNa677iZ9kZ3mJksyk5pLV8eIs6Suf8LhNeyr03P1k9… <https://secure-web.cisco.com/1smxNa677iZ9kZ3mJksyk5pLV8eIs6Suf8LhNeyr03P1k9…> *Developmental Neuroscience Postdoctoral Fellow – NIH Autism Center of Excellence Network* The JackLab in the Psychology Department at George Mason University is seeking a Postdoctoral Fellow to work on an NIH-funded Autism Center of Excellence (ACE) Network project focused on understanding late diagnosis in autism. This position is a 1-year, full time position, with potential for renewal throughout the life of the funded project. George Mason University has a strong institutional commitment to the achievement of excellence and diversity among its faculty and staff, and strongly encourages candidates to apply who will enrich Mason’s academic and culturally inclusive environment. *About the Position:* Our NIH-funded ACE Network project (R01MH100028, MPIs: Pelphrey, Kenworthy, & Jack) aims to understand and address disparities in diagnostic timing among autistic people, especially those potentially related to gender and sex assigned at birth. The successful candidate will work with a team of autistic and non-autistic investigators, Advisory Board members, and staff to ensure the success of this unique multimodal, mixed-methods project (with neuroimaging, qualitative, and quantitative data collection) developed in collaboration with the autistic community and focused on autistic well-being. This will be the third wave of data collection from the sex-balanced GENDAAR cohort (NDA Data Collection #2021), and will involve new recruitment of late-diagnosed autistic individuals who can enhance the cohort’s diversity with respect to race, ethnicity, gender identity, and other features (e.g., communication style, rurality). Under the supervision of Dr. Allison Jack at Mason, the fellow will facilitate project-related data collection and analysis as well as manuscript preparation. Specifically, they will assist with the collection of behavioral and neuroimaging data at Mason. Further, they will be involved preprocessing and analysis of both behavioral and magnetic resonance imaging (MRI) data and preparation of results from these analyses, as appropriate, for manuscript submissions and conference presentations. Commensurate with experience and interest, the fellow may also be involved in engagement with our Advisory Board; expansion of inclusive research practices; analyses in the domain(s) of machine learning, imaging genetics, and/or psychometrics; or other project-related activities. As an ACE Network, the project provides opportunities for the fellow to engage with field leaders in autism research across the country. The fellow will collaborate closely with the ACE Network research team at Children’s National Hospital Center for Autism Spectrum Disorders (CASD), led by Dr. Lauren Kenworthy, and our investigative partners at the Autistic Self Advocacy Network and the Autistic Women & Nonbinary Network. They will also assist with cross-site planning and coordination of MRI data collection and analysis in collaboration with our partners at the University of Virginia (Drs. Kevin Pelphrey & Jack Van Horn), Yale (Dr. Jim Duncan), and UCLA (Dr. Mirella Dapretto). Annual ACE Investigator Meetings hosted by NIH offer further opportunity for professional networking with leading autism researchers in the United States. A key value of our ACE project is inclusion of autistic individuals at all levels of research. We strongly encourage qualified candidates of all neurotypes, including autistic candidates, to apply. *Required Qualifications:* - Doctoral degree in psychology, neuroscience, psychiatry, or a related discipline; - Experience with MRI acquisition, preprocessing, and analytic methods; and - Experience in autism or a closely related neurodevelopmental condition. *Preferred Qualifications:* - Familiarity with work with adolescents; - Familiarity with use of MRI simulator/mock scanner and other practices to help acclimate individuals to the scanner environment; - Familiarity with BIDS format and fMRIPrep; - Extensive experience with one or more of: FSL, Freesurfer, and/or SPM; - Strong programming skills in Python, R, MATLAB, and/or linux/unix shell; and - Experience conducting analyses using a high performance computing cluster.

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Freesurfer