Freesurfer

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30076 discussions

FW: Postdoc position
by Fischl, Bruce 16 Mar '22

16 Mar '22

FYI -----Original Message----- From: Oula <oulap(a)drcmr.dk> Sent: Wednesday, March 16, 2022 10:08 AM To: Fischl, Bruce <BFISCHL(a)mgh.harvard.edu>; Iglesias Gonzalez, Eugenio <e.iglesias(a)ucl.ac.uk> Subject: Postdoc position External Email - Use Caution Hi guys, The postdoc position in the LF&NIH project is now open for applications. If you could forward the link below to relevant people and/or mailing lists that would be great! https://secure-web.cisco.com/1U2oCq8kSMeg-3aK_uWqtCIWlVo5rPCPsF2RuvaWlsAoqj… Cheers, Oula

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Re: [Freesurfer] Freesurfer on Windows - password
by fsbuild 15 Mar '22

15 Mar '22

External Email - Use Caution Sending you the info to your email shortly. - R. On Mar 15, 2022, at 06:22, Lara Marie Ehrlich <Lara.Ehrlich(a)ruhr-uni-bochum.de> wrote:       External Email - Use Caution        Dear Freesurfer Team,my name is Lara Ehrlich and I have recently been trying to utilize Freesurfer on my Windows Computer. I was able follow the instructions provided on https://secure-web.cisco.com/1Chmd6b0yn-khMjmu5rbyEXEiSH5kC9zE_NZ_B… I was unable to log into the desktop of the virtual machine/ubuntu because it requires a password for the “developer” account. I noticed in  previous mailing archives this password was sent privately – could I also receive this password by chance? Thank you for your help in advance.Sincerely,Lara E._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Running mri_watershed with previously generated brainmask
by Sliva, Danielle 15 Mar '22

15 Mar '22

External Email - Use Caution Hello FreeSurfer Experts, I’m attempting to generate inner/outer skull and skin surfaces using mri_watershed in order to compute a forward operator in MNE (don’t have FLASH for mri_make_bem). The issue I have is that the outer skull surface is incorrect and looks more like the skin surface, including a large amount of neck. Upon closer inspection, this seems to be due to large chunks of dura included in the brainmask (mostly in the area superior to the interhemispheric fissure), pushing the surface out too far. To fix this, I tried running recon-all -skullstrip with various flags, and found that a lower watershed threshold with the -gcut flag worked really well to remedy this problem, producing an accurate brainmask and brain.mgz files (after re-running -autorecon2). My understanding was that this change to brain.mgz should have then improved the surfaces generated when subsequently running the watershed algorithm- however a new brain.mgz file that looked like the original incorrect volume (before using gcut) was instead generated. I’ve searched the list and similar issues have been reported (see ”e.g.”, below), but I have not yet found a solution - is it possible to use the brainmask or brain.mgz file that I already have when running mri_watershed to generate skin and skull surfaces? There is a -mask flag to “mask a volume with the brain mask”- does this mean that it finds the existing brainmask.mgz file generated by autorecon1? I tried using it, but the brain.mgz file generated was not restricted to the voxels included in the previously generated brainmask. Please clarify the usage of this flag. Alternatively, is it possible to somehow use gcut when running mri_watershed on its own (as opposed to being run as part of recon-all -skullstrip)? Or to create the skin and skull surfaces when running recon-all -skullstrip with the -gcut flag? I am using freesurfer 7.1.1 on OSX Mojave E.g. - others reporting similar issue: https://secure-web.cisco.com/1xwUD8H2ELqmT-XJg96ZsminARQ0lHfB96Ll9HKpRLV0qU… https://secure-web.cisco.com/1JkDmZCv6uauCpr2tI2Yaw1OLcLrdPSvI9AMarDaaIy20t… https://secure-web.cisco.com/1cACd5dT5U95tvMeIiQb6mqBCDQWypNk0zlZRiSVFkBzr1… Many thanks in advance, Danielle -- Danielle D. Sliva PhD Candidate, Jones Lab Dept. of Neuroscience Brown University

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Freesurfer on Windows - password
by Lara Marie Ehrlich 15 Mar '22

15 Mar '22

External Email - Use Caution Dear Freesurfer Team, my name is Lara Ehrlich and I have recently been trying to utilize Freesurfer on my Windows Computer. I was able follow the instructions provided on https://secure-web.cisco.com/1Chmd6b0yn-khMjmu5rbyEXEiSH5kC9zE_NZ_BfnEM0uY9… Unfortunately I was unable to log into the desktop of the virtual machine/ubuntu because it requires a password for the “developer” account. I noticed in previous mailing archives this password was sent privately – could I also receive this password by chance? Thank you for your help in advance. Sincerely, Lara E.

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Freeview error on centos7
by Wen Wen 14 Mar '22

14 Mar '22

External Email - Use Caution Dear Freesurfer experts, I’m running Freeview on a centos7 computer and having the issue of loading surface data and 1mm volume data. The error message is *Segmentation fault (core dumped).* This issue remains no matter I work locally or remotely. However, 2mm volume data can be visualized successfully in either way. I've tried running glxgears, which gave me a pop-up window showing 3 interlocking wheels (red/green/blue). Below is the graphic card information obtained from lspci | grep VGA if helps. 01:00.0 VGA compatible controller: NVIDIA Corporation GP102GL [Quadro P6000] (rev a1) 42:00.0 VGA compatible controller: ASPEED Technology, Inc. ASPEED Graphics Family (rev 41) Thanks in advance for your help. Best, Wen

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Custom Freeview Color Map (not Lookup Table)
by Keator, David (Psychiatry & Human Behavior) 14 Mar '22

14 Mar '22

External Email - Use Caution Hi, I’d like to load in a custom color map to be used in color percentile-scaled functional images into FreeView (version 3.0; Build Aug 11, 2020). I can’t seem to find a reference for defining and loading a custom color map. I have done this for custom lookup tables and that’s all fine but now I’d like to define a ~256 RGB colors and use that in place of the standard color maps (e.g. Jet, NIH, PET, etc.). Thanks, Dave David Keator, M.S., Ph.D. Research Professor Psychiatry and Human Behavior Operations Director Neuroscience Imaging Center University of California, Irvine Irvine Hall rm. 163 – Zot 3960 Irvine, CA. 92697 Office: 949-824-7870 ________________________________ This message may contain confidential information and is for the sole use of the intended recipient(s). If you are not the intended recipient, do not use, distribute, or copy this e-mail. Please notify the UC Irvine Health – Compliance and Privacy Office via email at hacompliance(a)uci.edu or by phone 888-456-7006 immediately if you have received this e-mail in error. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.

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Developmental neuroimaging postdoc positions
by Signe Bray 14 Mar '22

14 Mar '22

External Email - Use Caution The Department of Radiology in the Cumming School of Medicine at the University of Calgary is accepting applications for two Postdoctoral Scholar positions in Developmental neuroimaging and Computational modeling of mental illness risk. Both are 2-year positions with the possibility of extension. Postdocs will work with Drs. Signe Bray and Emma Towlson on projects related to precisely measuring brain development, characterizing brain alterations related to risk for neurodevelopmental and mental health conditions, e.g., related to perinatal complications, and early detection to support early intervention. Depending on interest, the postdocs may play a role in study design and data collection, data processing, analysis, methods development and computational modeling. Applicants must be nearing completion of a PhD or have completed a PhD in the last three years and should have a background in neuroimaging, psychology, neurosciences, physics, biomedical engineering, network neuroscience or a related discipline. It is highly desirable that applicants have experience conducting research in an interdisciplinary environment. Our labs and the University of Calgary are committed to equity, diversity and inclusion (EDI; https://secure-web.cisco.com/1Czb8F65qNPPaPzpvfwMNPke7cVunR3I0AKy6N8bdnMfNJ…) and we encourage applicants from diverse backgrounds to apply. Interested candidates should submit a letter of interest and CV to slbray(a)ucalgary.ca. The University of Calgary is Canada’s leading next-generation university – a living, growing and youthful institution that embraces change and opportunity with a can-do attitude. Located in the nation’s most enterprising city, the university is making tremendous progress on its Eyes High journey to be recognized as one of Canada’s top five research universities, grounded in innovative learning and teaching and fully integrated with the community it both serves and leads. The University of Calgary inspires and supports discovery, creativity and innovation across all disciplines, and champions transdisciplinary approaches. For more information, visit *ucalgary.ca* <http://secure-web.cisco.com/138dcsY7eZIt2nQy0vWSYF3ZuKQU6w1BACuk2noojTvHwfc…>. Calgary is one of the world's cleanest cities and has been named one of the world's most livable cities for years. Calgary is a city of leaders – in business, community, philanthropy and volunteerism. Calgarians benefit from the strongest economy in the nation and enjoy more days of sunshine per year than any other major Canadian city. Calgary is less than an hour’s drive from the Rocky Mountains and boasts the most extensive urban pathway and bikeway network in North America.

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Linear mixed model for longitudinal data
by Julian Macoveanu 14 Mar '22

14 Mar '22

External Email - Use Caution Dear Kersten, Thank you for your answer, I have some follow-up questions to the first two points before I can move on. 1) Regarding family-relation, since three random effects may not work, did you mean that a simpler model with 2 random effects (intercept and family ID, thus leaving out slope which I assume is time from baseline) would work? While forgetting family ID is an option, it would be a model that may attract criticism. 2) Regarding multiple comparison correction, I understand how to perform the procedure you suggested (second option) to simply calculate the corrected p threshold using pcor = -log10(pth) and then use pcor as threshold for the sig.mgh. However after running FDR2: [detvtx,sided_pval,pth] = lme_mass_FDR2(F_lhstats.pval,F_lhstats.sgn,lhcortex,0.05,0); While detvtx is not empty (a few vertexes survived) and the pth value is calculated to 1.00000e-30 and therefore pcor to 30. This doesn’t seem right. What is also strange is that I saw a few times a more reasonable pth in the range of e-5 using the exact same data and procedure. I cannot replicate this in the same analysis in R2021, now I only get the e-30 (I only tried left cortex thickness so far). Best, Julian

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recon-all outpputs for deep learning
by REEM ABU BAKR BAHATHIQ 13 Mar '22

13 Mar '22

External Email - Use Caution Hello Freesurfer experts I want to apply deep learning to structural brain images processed by Recon-all. My goal is to demonstrate the morphological variation(e.g., gray matter volumes or cortical thickness) of brain regions in structural magnetic resonance imaging using convolutional neural networks (CNN). Then interpret those models on the basis of the region of interest. But I'm still distracted by the model input . I searched before but still couldn't decide which Recon-all output I should use to perform the task. I think I'll use the folder(mri) but I'm not sure which file. can any one guide me . Thanks,

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Re: [Freesurfer] Ubuntu VM Developer Password request?
by fsbuild 12 Mar '22

12 Mar '22

External Email - Use Caution Sending the info to your email shortly. - R. On Mar 12, 2022, at 09:52, Dean, Owen <Owen_Dean(a)urmc.rochester.edu> wrote:        External Email - Use Caution        Dear the Freesurfer Team, I am writing to request the Ubuntu VM Developer password for the Freesurfer version? Thank you!Sincerely, OwenOwen DeanUniversity of Rochester School of Medicine and Dentistryhe, him, his_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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