Freesurfer March 2022

freesurfer@nmr.mgh.harvard.edu

86 participants
124 discussions

Atlas of primary motor and auditory cortex
by Jingyi Wang 16 Mar '22

16 Mar '22

External Email - Use Caution Hello Freesurfer experts, I ran the recon-all command and got all the .label files for the segmentations of the cortical areas. However, I have some questions about the label for primary motor and auditory cortex. - I found two types of labels associated with the primary motor cortex: lh.L_M1.label and lh.BA4a_exvivo.label. Are they both valid, and the lh.BA4a_exvivo.label segmentations are finer parcellation than the other one? - What's the primary auditory cortex .label file? Thanks in advance! ________________________ Jingyi Wang Postdoctoral Scholar LEAP Neuro Lab Psychological & Brain Sciences University of California, Santa Barbara

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complete unfinished steps of recon all
by Hossein Rahimzadeh 16 Mar '22

16 Mar '22

External Email - Use Caution Hello FreeSurfer Developers, Due to the fact that the freesurfer runs for a long time, the computer is turned off several times during the run due to electricity fluctuations. How to complete unfinished steps of recon-all. I tried to continue the analysis with the command "recon-all -make all -s subject, but" I got the following error: ERROR: -make is no longer supported 1)freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b 2)linux ubuntu 20.04 3)two recon-all.log of two subjects have attached Best regards, Hossein Rahimzadeh Biomedical Engineering, MSc. Shahid Beheshti University of Medical Sciences, Tehran, Iran.

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bug: freeview's "configure overlay" window frozen (Ubuntu18 in wsl2 on Windows 11)
by Sebastien Proulx 16 Mar '22

16 Mar '22

External Email - Use Caution Dear Freesurfers, I just installed Freesurfer (freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b) on Ubuntu (Ubuntu 18.04.6 LTS) running in Windows 11's wsl2. So far Freeview is running fine-I can load volumes and surfaces, and add an overlay to a surface-but configuring an overlay fails: the "configure overlay" window freezes at opening and even the x button to close the window does not work. No error message on the command terminal. Is this a known bug? Any fix or workaround? Thanks and Have a very good day! Sébastien

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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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Freesurfer March 2022