Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

how to load flat surface in freeview
by Francesca Strappini 17 Mar '22

17 Mar '22

External Email - Use Caution Dear Freesurfer experts, I'm trying to load the flat surface that I created with this command line: mris_flatten -w 10 lh.full.patch.3d lh.full.flat.patch.3d I tried loading the patch inside freeview but I got this error message: [francesca@GIOVE surf]$ tksurferfv sub01_mprage lh inflated freeview -f /home/francesca/freesurfer/subjects/sub01_mprage/surf/lh.inflated:curvature=/home/francesca/freesurfer/subjects/sub01_mprage/surf/lh.curv -viewport 3d ASSERTION FAILED: /home/rd521/space_freesurfer/build/docker_centos8/trunk/rd521-7.2.0/utils/mrisurf_metricProperties.cpp:4248 mris->dist_nsize == 0 ASSERTION FAILED: /home/rd521/space_freesurfer/build/docker_centos8/trunk/rd521-7.2.0/utils/mrisurf_metricProperties.cpp:4248 mris->dist_nsize == 0 Errore di accesso al segmento di memoria (creato file core) And I tried to run this command line but nothing happened: [francesca@GIOVE surf]$freeview -f lh.inflated:patch=lh.full.flat.patch.3d Thank you, Francesca -- Francesca Strappini, Ph.D. Psychology Department Sapienza University of Rome Via dei Marsi 78, Rome 00185 Italy Tel.: +39 392 151 4029 E-mail: francesca.strappini(a)uniroma1.it <francescastrappini.stud(a)uniroma1.it>

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Re: [Freesurfer] 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 Thanks for the tip Ruopeng! Just tried MobaXterm. Nice piece of software! I had to enable hardware acceleration (mobaXterm -> settings -> X11 -> OpenGL acceleration -> Hardware) for freeview to work at all, but it worked-now the configure overlay window does not freeze. Two draw backs though: -Rendering behaves weirdly. Every now and then (within few seconds), while just moving the mouse, the brain just disappears, and only reappears when I rotate it by click-and-drag. It does not prevent one to get something done, but it is frequent enough to be quite disturbing :-( -Graphics seem to only go through the (moba)Xserver when the wsl is launched from within mobaXterm. When launching wsl through other means (e.g. command prompt), freeview does open but the window outline looks different and the initial problem is back, as if graphics go through another Xserver... (and by the way, I completely removed Xming !) I am generally confused with Xserver stuff, but does the last point suggest that wsl in Windows 11 (build 22000) has its own Xserver-like capability? Would make sense with Windows upping its game for the integration wsl graphics into the windows desktop (https://secure-web.cisco.com/1WiSJsgR_rkzEwjyT1ydiRFw_EKqkfi02STKKjfu1AoEsO…) Any more advice on either (1) getting moba render to work more smoothly, (2) having wsl actually use Xming or (3) having freeview and native wsl graphics live happily together? Thanks a lot for the help and Good night! Sébastien

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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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