Freesurfer October 2024

freesurfer@nmr.mgh.harvard.edu

44 participants
51 discussions

Obtaining eTIV/ICV value after recon-any processing
by Mahir Khan 14 Oct '24

14 Oct '24

External Email - Use Caution Hi, I am trying the recon-any processing stream on some clinical imaging. I am having trouble finding the eTIV or ICV value that is typically reported as an output in the normal recon-all processing stream. I noticed in the stats/brainvol.stats file that there is a “BrainSeg” measure that is around what is expected as an eTIV value - is this the eTIV value to use in downstream analyses? Best, Mahir -- Mahir Khan PhD Student, Neuroscience Graduate Program Neural Plasticity & Neurorehabilitation Lab University of Southern California Email: mhkhan(a)usc.edu <mailto:mhkhan@usc.edu>

1 0

Hardware selection for utmost performance of Freesurfer
by Jin Liu 14 Oct '24

14 Oct '24

External Email - Use Caution Hello Freesurfer team, Our lab is considering purchasing a new workstation, typically for running Freesurfer at the current stage. The best we can get would be a Dell model with 23 physical cores (46 logical cores) 256 Gb RAM Ubuntu Nvidia box, but we are confused if the hardware processing capacity will significantly improve Freesurfer performance or will even not support Freesurfer functions. We are aware that number of cores can lead to an exponential growth in speed using parallel processing. Is there an upper limit to this increase? We also know that having a larger RAM can improve the performance of Freeview and we also wonder if it reaches marginal effects for a 256 Gb RAM, and if having a Nvidia box would make a difference. Thanks, Jin

1 0

[WARNING: ATTACHMENT UNSCANNED]Issue with WM surface fill
by Bronwyn Overs 14 Oct '24

14 Oct '24

External Email - Use Caution Dear Freesurfer Support, I'm reviewing a specific MRI image that I have processed with Freesurfer V5.3. I'm concerned about a potential issue with voxels missing from the WM surface. This appears to impacting the pial boundaries and lateral ventricle labels in the aseg from slices 56-99. For reference, I attached 5 images (both wm and brainmask surfaces) that are each 5 slices apart. Happy to upload the whole series of images if this would be helpful. Would you recommend filling in some of the voxels near the lateral ventricles? My concern is that I am unsure where the ventricle begins, as I suspect the gyrus at the rh pericalcarine surface is not being properly labelled and identified in the pial surface. Any advice you can provide will be greatly appreciated. Kind regards, Bronwyn Overs Senior Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1725 [ http://secure-web.cisco.com/1PhyqjBKyb2oDl07vqwWhBygB_5YJLdeJ41dvzkSKapr3Gu… | neura.edu.au ] [ https://secure-web.cisco.com/1Nq-N5jOYtG9ZB4Dl8PisdSUykSQS1VbMzYkTSuKxvkBDE… | Twitter ] | [ https://secure-web.cisco.com/1wYi0bZZPKh6dadEH9ixKmgt3NP7bvL1I_HLfiwg9s6h5-… | Facebook ] | [ http://secure-web.cisco.com/1yUpg4OTzIo3qIvjsCh2VZmcvRXG4uvBgKotJ3qtYmng5K2… | Subscribe ]

2 3

Request to Post Job Position on Freesurfer listserv
by Otero Ospina, Andrea 14 Oct '24

14 Oct '24

External Email - Use Caution Hi, I hope this message finds you well. We would like to post the following job position on the Freesurfer listserv. Could you please assist us with this request? Department of Psychiatry and Behavioral Sciences Postdoctoral Associate Position in Human Neuroimaging University of Miami Miller School of Medicine, Miami, Florida, USA The Gabbay Laboratory within the Department of Psychiatry at the University of Miami Miller School of Medicine is seeking highly motivated postdoctoral scholars in the field of human neuroimaging. Available positions will focus on analyzing fMRI and proton MR spectroscopy data as well as acquiring or processing related MRI and biological measures. Candidates should either have completed or be near completing a PhD in neuroscience, psychology, cognitive neuroscience, radiology, engineering, biostatistics, or a related field, and should have a strong background in quantitative analysis. Proficiencies with at least one major neuroimaging software suite (e.g. FSL, AFNI, SPM, Freesurfer, Caret, Connectome Workbench, etc.) and Unix/Linux environment are expected. Familiarity with Matlab, Python, and/or R programming languages is a plus. The primary responsibilities for this postdoctoral fellow will be to run scans, analyze neuroimaging data from multiple ongoing and recently concluded research projects, and write manuscripts. Under the mentorship of Vilma Gabbay, MD and Benjamin Ely, PhD, postdoctoral scholars will be expected to advance clinical and methodological knowledge through their postdoctoral training. Our lab is dedicated to the study and treatment of mood, anxiety, and substance use disorders in adolescent and high-risk adult (e.g. HIV+) populations using innovative neuroimaging and immunological methodologies. The neuroimaging program features high-resolution data acquisition and analysis techniques modeled on the Human Connectome Project (HCP) and is committed to the highest standards for magnetic resonance imaging and spectroscopy. The lab is funded by four ongoing NIH R01 neuroimaging studies (R01MH120601, R01DA054885, R01MH128878, and R01MH131207) and several smaller grants, providing unparalleled funding for active and exploratory studies. Major research topics include longitudinal studies of adolescent mood and anxiety disorders; comorbidity of depression, cannabis use, and HIV infection; and an intervention study aimed at improving well-being among healthcare workers with parental responsibilities during the COVID-19 pandemic. Project abstracts with further details can be found on NIH RePORTER. Resources available on-campus and through long-standing collaborations include multiple research-dedicated 3T MRI scanners (Siemens Skyra/Vida/Prisma) with cutting-edge accelerated and multi-echo fMRI sequences, high-performance scientific computing clusters, and an extensive library of analytic and statistical software. The PIs are fully committed to fostering the trainee's research independence through publication of first-authored manuscripts in top journals and mentorship in grant applications. In addition to assisting with the PI’s proposals, the successful applicant will be highly encouraged to develop and pursue funding for their own research project through federal (e.g. NIH F32) or foundation grant programs by the end of their first year. Please send a CV, statement of interest, and contact information for three references to axo833(a)med.miami.edu<mailto:axo833@med.miami.edu>. University of Miami is an equal opportunity employer, and all qualified candidates will be given equal consideration. Priority will be given to candidates available to start sooner. Compensation will be proportional to experience and will follow standard postdoctoral fellowship rates posted by University of Miami. Best, Andrea Otero, M.D. Clinical Research Coordinator Department of Psychiatry and Behavioral Sciences University of Miami — Miller School of Medicine Email: axo833(a)med.miami.edu<mailto:njh115@med.miami.edu> Phone: 305-243-7086 [cid:97820b9a-5459-48c5-b510-70a6fc22a6b5] [cid:a06cc866-1bdb-4959-a3ec-4c95e614aaf9]<https://secure-web.cisco.com/1NtHyStrjuOSWOO5EbcV14g1jIPuoLRF1sxsbaI79RQ5Jg…> Book time to meet with me<https://secure-web.cisco.com/1NtHyStrjuOSWOO5EbcV14g1jIPuoLRF1sxsbaI79RQ5Jg…>

1 0

mri_segstats for lobar intensity values
by Julie Ottoy 11 Oct '24

11 Oct '24

External Email - Use Caution Hi Freesurfer team, I want to calculate the average PET intensity values per lobe. I want to use the lobar annotations as outlined here in 'lobe mapping': https://secure-web.cisco.com/1Opn2TyIP5_MF5tP6PRtaju8QtoITdCtzrmIlxZvYGO1bU… My PET images are volumetric in T1w MRI space. I have successfully created my lobes following this command: mri_annotation2label --subject $session --hemi lh --lobesStrict lobes However I'm getting an error with my next command: mri_segstats --annot $session/label/lh.lobes.annot --i $session/pet_surf/SUVR/SUVR_T1space.nii.gz --sum lh.pet_lobar.sum It is reading in the white surface, because I get this error: error: MRISread($path/$session/label/rh.lobes.annot/surf/--i.white): could not open file How should I run this command when reading from the volumetric PET image? Thank you, Julie

1 0

Re: [Freesurfer] Error while opening Freeview on Linux
by fsbuild 11 Oct '24

11 Oct '24

External Email - Use Caution Try downloading and installing the freesurfer .deb or.rpm linux package installer that matches your OS .. from,https://secure-web.cisco.com/1Me3-1hl0gfMcAF2vBsI1JUBKuzDpNWmT5AWDIQZn… For example, on Rocky8 linux (uses RedHat lkie .rpm files),  install the .rpm file from where you downloaded it with, e.g., $ sudo yum install ./freesurfer-Rocky8-7.0.0-dev.x86_64.rpm On Ubuntu22 linux, i,e, uses debian like .pkg files), install the .deb file from where you downloaded it with,$ sudo apt install ./freesurfer_ubuntu22-7-dev_amd64.deb Those package installers should automatically install any missing libraries on you system like libpng12.so.  Downloading and expanding one of the freesurfer *.tar.gz archives will not do an actual install, i.e. won’t check for or try to install missing libraries on your system needed to run freesurfer. Then setup the freesurfer environment as listed here,https://secure-web.cisco.com/1BELDi9cDpanBzm2iGuNdHAswzIduLFc5gddCoywt… - R. On Oct 11, 2024, at 14:00, Harsh Srivastava <harsh.sriv(a)iitb.ac.in> wrote:        External Email - Use Caution        Dear Freesurfer team,I have Freesurfer installed on Linux. All Freesurfer commands work well, however, I am not able to open freeview. I get this error:freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directoryPlease let me know how it can be resolved.Warm regards,--  Harsh Srivastava (he/him), 23M0132 (2nd year), MTech Biomedical Engineering, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India._______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1Nteb0siX3-eisiJSbMFVKuyiiW1wlCIU90j5qryoeAjXJ…

1 0

Re: [Freesurfer] Difficulty with downloading Tensorflow and using with SynthSeg
by fsbuild 11 Oct '24

11 Oct '24

External Email - Use Caution  You could try downloading and installing one of the freesurfer package installers, i.e.. on Linux the .rpm to .deb file that matches your OS, or on MacOS either the *x86_64*.pkg (Intel Macs) or *arm64*.pkg (Macs with M1, M2, … processors) that matches you machine ...from...https://secure-web.cisco.com/1B-Y6R_reuVQwDKeMGSdl7-e2TzqvCfjXmPbUtNUE3LgEgrgfj-hvlDZ0qydXe5FMyaoau4W867g0jlJCQIwBSi8MQKtA7eag5M53D1u7aaCBRL4MGNd7bZ46ojlcSrj-pSlRW3pPgTjUHpxMdfDMc4ap6wIwAvOxW41t2tivZ-o1EsqSe8i3DT4Q3o-PdHEGdfXUkxghQJz_vxnJziMs4-TnOJR3VhNH0uLGlUjv30Bl8dVBHgxCkGcDE6v7lhqQWG9OA5Ih6V7lbVsjv8KS698gyYmNydlNBGdq75HF5hVYTwC_N45DMPecMCHruJmZ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Fstable%2FThe python provided in the distribution already has packages installed and will automatically run when you type a command that runs a python script, e.g., mri_synthseg, from the command line.  Prior to that you need to setup the freesurfer shell environment as listed here,https://secure-web.cisco.com/14OSIP22yq-rfoLg4l3V2OcIYvWi4b3IkHZ6noxLG… - R. On Oct 11, 2024, at 13:53, Patel, Ronit <Ronit.Patel(a)pennmedicine.upenn.edu> wrote:        External Email - Use Caution        Hi Freesurfer Support, I hope all is well. I am hoping to download TensorFlow to utilize SynthSeg on my MRI scans, but there appears to be a strange problem when I try to download it. While I do have the correct version of python and numpy, it continues to say the correct version is unavailable and prevents TensorFlow from downloading.  At the same time, when I try to run synthseg and input the mri_synthseg function, the error I always get is 'Illegal Instruction: 4'. I am unsure what this means, as the input and output is clearly specified when I try this method. I had assumed it was simply because TensorFlow was not installed, but I was told it may be something else by my colleagues.  I greatly appreciate any help that can be provided! Sincerely,Ronit Ronit PatelClinical Research AssistantUniversity of Pennsylvania Department of Neurology | TBI Research Initiative <Screenshot 2024-10-11 at 1.45.56 PM.png>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Error while opening Freeview on Linux
by Harsh Srivastava 11 Oct '24

11 Oct '24

External Email - Use Caution Dear Freesurfer team, I have Freesurfer installed on Linux. All Freesurfer commands work well, however, I am not able to open freeview. I get this error: _freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory_ Please let me know how it can be resolved. Warm regards, -- Harsh Srivastava (he/him), 23M0132 (2nd year), MTech Biomedical Engineering, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India.

1 0

Difficulty with downloading Tensorflow and using with SynthSeg
by Patel, Ronit 11 Oct '24

11 Oct '24

External Email - Use Caution Hi Freesurfer Support, I hope all is well. I am hoping to download TensorFlow to utilize SynthSeg on my MRI scans, but there appears to be a strange problem when I try to download it. While I do have the correct version of python and numpy, it continues to say the correct version is unavailable and prevents TensorFlow from downloading. At the same time, when I try to run synthseg and input the mri_synthseg function, the error I always get is 'Illegal Instruction: 4'. I am unsure what this means, as the input and output is clearly specified when I try this method. I had assumed it was simply because TensorFlow was not installed, but I was told it may be something else by my colleagues. I greatly appreciate any help that can be provided! Sincerely, Ronit Ronit Patel Clinical Research Assistant University of Pennsylvania Department of Neurology | TBI Research Initiative

1 0

NIH R25 Course : Training in Advanced Statistical Methods in Neuroimaging and Genetics, Salt Lake City, Utah, April 7-18, 2025.
by ROBERT CARY WELSH 11 Oct '24

11 Oct '24

External Email - Use Caution Hi everybody, We are still taking applications for our NIH funded 2025 session of the course, “Training in Advanced Statistical Methods in Neuroimaging and Genetics”. We hope you pass this email on to your local neuroimaging community. The in-person course starts on Monday, April 7th, 2025, finishing on April 18th, 2025 and is held in Salt Lake City, Utah, United States at the University Guest House Conference Center. Our course also includes an ongoing (throughout the year) continuing education portion. Over an intensive 2-weeks, about 8 hours per day, you will experience a balanced mixture of lectures and hands-on computer labs. More information and registration at : neurostatsbootcamp.org<http://secure-web.cisco.com/1dSR9cVnA26HZj9TFTNx2QeK5CzA2Z239Hu-w9rxQ34-TSM…> All students receive a $750 subsidy, reducing the cost from $3000 to $2250. Strictly financial need scholarships are also offered (that offset even more tuition). Tuition includes hotel accommodations at the University Guest House (arrival on April 6 with departure on April 18), breakfast, lunch, day time snacks, three dinners out as a group, and the planned evening activities. All course attendees will arrange for their own transportation to Salt Lake City. The course cost does include a daily pass to the Salt Lake City Trax light rail/commuter system. (Please note that the course instructors' effort is supported by the NIH grant thus avoiding that cost being passed on to the course attendees. This course is strictly not-for-profit.) Because of the limited size and advanced nature of the course, attendance is by application only – please make sure to fully read the website instructions. In general, applicants should be a US citizen, permanent resident, or working with an appointment at a US institution, though we do have the ability to accommodate 3 to 6 individuals that do not meet this criteria. We anticipate the total class size to be between 24 and 30 students. There are opportunities for scholarships which can partially offset hotel accommodations. These are based on true financial need and you will be instructed how to apply if you are admitted to the course. We look forward to seeing you in SLC in 2025! Priority application deadline is Oct 25, 2024; decisions around Dec 13th. Late application deadline is Nov 22, 2024; decisions by Jan 3th, 2025. For more information email us at neurostats(a)g.ucla.edu<mailto:neurostats@g.ucla.edu> Robert and Anna ------------------------------ Robert Welsh, PhD Course Director, Training in Advanced Statistical Methods in Neuroimaging and Genetics rcwelsh(a)g.ucla.edu<mailto:rcwelsh@g.ucla.edu> (preferred) robert.c.welsh(a)utah.edu<mailto:robert.c.welsh@utah.edu> Anna Docherty, PhD Associate Course Director, Training in Advanced Statistical Methods in Neuroimaging and Genetics anna.docherty(a)utah.edu<mailto:anna.docherty@utah.edu> Christina Caldera Course Administrator neurostats(a)g.ucla.edu<mailto:neurostats@g.ucla.edu>

1 0

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer October 2024