Freesurfer March 2023

freesurfer@nmr.mgh.harvard.edu

104 participants
154 discussions

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

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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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recon-all not parcellating
by Carlos Estévez Fraga 10 Mar '23

10 Mar '23

External Email - Use Caution Dear Freesurfer team, I am trying to run recon-all -all in the cluster but unfortunately I am unable to obtain the parcellated images (exact command is recon-all -parallel -openmp $NSLOTS -s ${j} -i ${j}_corrected.nii.gz -all -cw256) I have run the script different times with different subjects and it just stops abruptly always in the same point, after WM segmentation, see below the recon-all-status.log for one subject (same in all of them, it stops after WM segmentation) I tried it on my laptop and in my desktop computer and it works, but not in the cluster... Any chance you know why this may be happening? Best regards, Carlos #@# MotionCor Tue Mar 7 22:10:08 GMT 2023 #@# Talairach Tue Mar 7 22:10:18 GMT 2023 #@# Talairach Failure Detection Tue Mar 7 22:13:37 GMT 2023 #@# Nu Intensity Correction Tue Mar 7 22:13:37 GMT 2023 #@# Intensity Normalization Tue Mar 7 22:16:54 GMT 2023 #@# Skull Stripping Tue Mar 7 22:18:15 GMT 2023 #@# EM Registration Tue Mar 7 22:20:49 GMT 2023 #@# CA Normalize Tue Mar 7 22:22:45 GMT 2023 #@# CA Reg Tue Mar 7 22:23:44 GMT 2023 #@# SubCort Seg Tue Mar 7 23:07:13 GMT 2023 #@# CC Seg Wed Mar 8 00:00:24 GMT 2023 #@# Merge ASeg Wed Mar 8 00:03:01 GMT 2023 #@# Intensity Normalization2 Wed Mar 8 00:03:01 GMT 2023 #@# Mask BFS Wed Mar 8 00:04:47 GMT 2023 #@# WM Segmentation Wed Mar 8 00:04:48 GMT 2023 #@# Fill Wed Mar 8 00:07:28 GMT 2023 -- *Dr Carlos Estevez-Fraga, MD, PhD* Senior Clinical Research Fellow Department of Neurodegenerative Diseases UCL Queen Square Institute of Neurology London, UK *Mail:* c.fraga(a)ucl.ac.uk *Phone*: +44 7788 926 982

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acces to virtual machine archive
by Free Surfer 10 Mar '23

10 Mar '23

External Email - Use Caution Hello, I have just downloaded the virtual machine and ubuntu package. Could you send me a password for unpack archive with virtual machine image, and for ubuntu account? Thanks so much in advance!

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Request: Password VirtualBox Vm Images
by Fislage, Marinus 09 Mar '23

09 Mar '23

External Email - Use Caution Dear all, I would like to kindly ask for the password related to the VM zip archive: https://secure-web.cisco.com/1f7WVlIuUEn_Vllgaj670_9Zm1yN5Kl0O5jr8VA3slmuHC… Thank you very much! Kindest regards, Marinus

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Re: [Freesurfer] Segmentation fault (core dumped)
by fsbuild 09 Mar '23

09 Mar '23

External Email - Use Caution As Yujing said, the 5.1.0 release is quite old (dating back to CentOS4) and binary backwards compatibility cannot be expected to work indefinitely going forwards to newer versions of the OS.  I ran a simple mri_surf2surf command from 5.1.0 on CentOS7 and it crashed immediately.    I then tried the same command using the freesurfer 5.3.0 release built for CentOS6 and it worked on CentOS7. You can download freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz from https://secure-web.cisco.com/1S9OGgcf17zFMWWXjC8lPSf7mq4hk6Ou69iX…, or see the direct link  https://secure-web.cisco.com/1O5P1_jnLPrOGdYkXFNDEb2y-k3m7evHo5fe2uNzyoNAaKSkB3Nt1_wXhgDLemrYevJFPQsp5tpz_wdWUjWhVTD9p6CNaNieHzYFY7XvcOkTsvaaxQ14203xL-zEAR2Eav2sKtvuxzucTJqIFKJcJxwO4tU1LWxZbL8HSzpbAx4gHo4SUez6Lwz1bZarwjhy7YEdn5NslhRbXzeF8MIl4YiwsVYH1XGmK-teHPP1FTJiVcnLV6oEDyz9jwP0uUf5tP9RGIWsdKBnItP4JbrHc-fZumOroSi_i6GuKCOsp-IouIjFOvOowWaI6ldL4IOMcIeaqNW-BG-wO4CN5ByZFrg/https%3A%2F%2Fftp.nmr..mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F5.3.0%2Ffreesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz%26nbsp;  The 5.3.0 release notes are here, https://secure-web.cisco.com/19Gm_LLMuws0ked03zCf5tnQ6jPznJWqxPj… Please be aware we post this caveat on our download page saying that numeric/floating point results can differ when you switch to a different freesurfer release or newer version of the OS, Important Note: When processing a group of subjects for your study, it is essential to process all your subjects with the same version of FreeSurfer, on the same OS platform and vendor, and for safety, even the same version of the OS. While we continue to work to ensure that results match across platforms, there are none-the-less system-level libraries that are OS dependent. An exception to this rule is that you may view and edit files across any platform or version, and run some post-processing tools (outside the recon-all stream) if you check with us first (for instance you may run the longitudinal processing with newer versions). I would expect the above to be true if you switch from the 5.1.0 release to the 5.3.0 release. So if you must continue to run 5.1.0, then I would try to run it on the (same) version of the OS you used where it previously worked.  One way to do that is with a virtual machine (VM) hosting the (old) OS.   It looks like we have a virtual machine image with freesurfer 5.1.0 installed available from under https://secure-web.cisco.com/11VzvQh0Sbki3c91H_Wr1_Sbun-1WBJp0X7…;  That virtual disk image file (..vdi), https://secure-web.cisco.com/1f9gnsQF3U_bgE7wRs0_PPUaeSlPgrJxG-afglho7qOnEI6IK3x6Q74lVczCqUz814qnE3gT4GO-FHPsn6fv4NwsG7SMQykR-ghIZUMdjGSmckggj6M5NAUe9S37AMJzV215rTC59h7VmVa-paqybjKPfVK-VAtQ2oUwks-053E4KC89mt53wvYjRuyAhnLrA0JFdOGOuMo-8KrX_ENyyGH2zzQJtiTEGmBnnMpKIGFw9QCAfWRqmgMi_BDHy7lmAxYnWCVd_XdH1VJ1HqLhBIonwjm5X2caNf1OTebriIZfm2h5IupSjvLGZMRF43ej87-9ybXcYkIZ6L_qBDq_D-A/https%3A%2F%2Fftp.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F5.1.0%2Ffreesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full.vdi,  should still run in virtual box on your CentOS7 machine.   My guess would be it is a CentOS4 VM image with freesurfer 5.1.0 installed but I don’t know how that matches up to any previous version of the OS you used to successfully run freesurfer 5.1.0. - R. On Mar 9, 2023, at 20:17, Huang, Yujing <YHUANG43(a)mgh.harvard.edu> wrote:Hi Tracy, I looked at your recon-all.log.  There are total of 19 runs.  The first 4 runs from 2015 and 2016 finished without errors. They were all run on hippocampus.umd.edu. The later failed ones with segmentation fault were run a different machine - seahorse.umd.edu. Since you are using Freesurfer 5.1 built for centos4, I’m wondering if there are some compatibility issues. Can you try running it on hippocampus.umd.edu? I did notice that you tried 6.0.0 and 7.1.1 but those runs reported a different error. Best, Yujing From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Tracy RigginsSent: Thursday, March 9, 2023 6:26 PMTo: freesurfer@nmr.mgh.harvard.edu; Allard, Tamara Lynn <tallard@terpmail.it-prod-webhosting.aws.umd.edu>Subject: [Freesurfer] Fwd: Segmentation fault (core dumped)         External Email - Use Caution        YujingAny insight on this?Thanks,Tracy---------- Forwarded message ---------From: Tracy Riggins <riggins(a)umd.edu>Date: Mon, Mar 6, 2023, 10:44 PMSubject: Re: Segmentation fault (core dumped)To: <freesurfer(a)nmr.mgh.harvard.edu> Yujing Yes, we have run this successfully with other participants (although it was a while ago).Attached is the recon-all.logthanks for your help!Tracy On Sun, Mar 5, 2023 at 1:21 PM Tracy Riggins <riggins(a)umd.edu> wrote:Greetings FS experts: We are trying to run recon-all -s -qcache on a handful of brains processed in freesurfer v5.1.0.   (it's an old dataset...5.1 makes the most sense for our purpose.) The error is below: <image001.png> --------------------------------------#@# 1/1 HMN080 Fri Mar  3 12:14:44 EST 2023 -------------------------------------mri_surf2surf --srcsubject HMN080 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.51930/HMN080.1.mgh --sval /export/data/seahorse_ncdl/HMN/data/HMN080/surf/lh.thickness --sfmt curv --noreshape --no-cortexSegmentation fault (core dumped)Linux seahorse.umd.edu 3.10.0-1160.80.1.el7.x86_64 #1 SMP Sat Oct 8 18:13:21 UTC 2022 x86_64 x86_64 x86_64 GNU/Linuxrecon-all -s HMN080 exited with ERRORS at Fri Mar  3 12:14:48 EST 2023 Can you assist?  OR perhaps tell us where to find the core dump file, which may have more information?-- Tracy Riggins, Ph.D.Pronouns: she/her/hersAssociate Professor of Psychology4094 Campus Drive, Biology/Psychology Building 2147JUniversity of Maryland, College Park, MD 20742Zoom Meeting ID: 6751666548*****************************************************Research info:  MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/16uU9Voo_CziLp-ng0Dkh27qT2SP4MKOfHHDUkD… has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1OFC1dVVEqctiVCBhWLVpuWAqvx-VAFmj5QcsN… lives matter in academiaLGBTQIA+ Ally _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer March 2023