Freesurfer December 2021

freesurfer@nmr.mgh.harvard.edu

56 participants
87 discussions

QXcbConnection
by Carina Forster 30 Dec '21

30 Dec '21

External Email - Use Caution Dear Freesurfer community, I am using Windows 11 and Ubuntu on WSL2 to access freesurfer. I installed Xming. Unfortunately I get the following error msg when I try to open freeview: QXcbConnection: Could not connect to display 172.20.16.1 Could not connect to any X display. I added my IP adress to the HOST file as suggested but that doesn't help. I also played around with export DISPLAY (setting it to my IP adress, setting it to 0.0 etc). Nothing helped. This is the Xming log (I thought that might help). *Xming :0 -multiwindow -clipboard -acXdmcpRegisterConnection: newAddress 172.20.16.1winAdjustVideoModeShadowGDI - Using Windows display depth of 32 bits per pixelwinAllocateFBShadowGDI - Creating DIB with width: 1536 height: 864 depth: 32winInitVisualsShadowGDI - Masks 00ff0000 0000ff00 000000ff BPRGB 8 d 24 bpp 32glWinInitVisuals:1596: glWinInitVisualsglWinInitVisualConfigs:1503: glWinInitVisualConfigs glWinSetVisualConfigs:1581: glWinSetVisualConfigsinit_visuals:1055: init_visualsnull screen fn ReparentWindownull screen fn RestackWindowInitQueue - Calling pthread_mutex_initInitQueue - pthread_mutex_init returnedInitQueue - Calling pthread_cond_initInitQueue - pthread_cond_init returnedwinInitMultiWindowWM - HellowinInitMultiWindowWM - Calling pthread_mutex_lock ()winMultiWindowXMsgProc - HellowinMultiWindowXMsgProc - Calling pthread_mutex_lock ()glWinScreenProbe:1390: glWinScreenProbefixup_visuals:1303: fixup_visualsinit_screen_visuals:1336: init_screen_visuals(--) 5 mouse buttons found(--) Setting autorepeat to delay=500, rate=31(--) winConfigKeyboard - Layout: "00000407" (00000407)(--) Using preset keyboard for "German (Germany)" (407), type "4"Could not init font path element C:\Program Files (x86)\Xming/fonts/Type1/, removing from list!Could not init font path element C:\Program Files\Xming\fonts\dejavu, removing from list!Could not init font path element C:\Program Files\Xming\fonts\cyrillic, removing from list!Could not init font path element C:\WINDOWS\Fonts, removing from list!winInitMultiWindowWM - pthread_mutex_lock () returned.winInitMultiWindowWM - pthread_mutex_unlock () returned.winInitMultiWindowWM - DISPLAY=127.0.0.1:0.0winMultiWindowXMsgProc - pthread_mutex_lock () returned.winMultiWindowXMsgProc - pthread_mutex_unlock () returned.winMultiWindowXMsgProc - DISPLAY=127.0.0.1:0.0winProcEstablishConnection - HellowinInitClipboard ()winProcEstablishConnection - winInitClipboard returned.winClipboardProc - HelloDetectUnicodeSupport - Windows VistawinClipboardProc - DISPLAY=127.0.0.1:0.0winMultiWindowXMsgProc - XOpenDisplay () returned and successfully opened the display.winInitMultiWindowWM - XOpenDisplay () returned and successfully opened the display.winClipboardProc - XOpenDisplay () returned and successfully opened the display.* Anyone ideas on what could be the problem? Thank you so much. Best, Carina <https://secure-web.cisco.com/1ng5Zr4bbSkvs8cs0zHzZEKY6nqkvGCbjF81ZXgffmH7K1…> Virenfrei. http://secure-web.cisco.com/1m6lUHXphHkv8UYPf9uVnF4Ncx4_BrQJ-jK2FzNdqt0roB2… <https://secure-web.cisco.com/1ng5Zr4bbSkvs8cs0zHzZEKY6nqkvGCbjF81ZXgffmH7K1…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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GNU libc version
by Mohanad Arafe 29 Dec '21

29 Dec '21

External Email - Use Caution Hello, I am attempting to run recon-all on a simple NIFTI file in an HPC using FreeSurfer v6.0.0. I am running into the following problem: *GNU libc version: 2.17* *ERROR: Systems running GNU glibc version greater than 2.15* * require a newly formatted license file (it's free). Please* * download a new one from the following page:* I got a new license and I placed it in the FreeSurfer home directory but the issue remains. Thank you, Mohanad

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Re: [Freesurfer] Illegal Instruction Error
by fsbuild 27 Dec '21

27 Dec '21

External Email - Use Caution Hello Elizabeth, I don’t see anything wrong with how the 6.0..4/bin/bet2 binary is built. It would be interesting to see if the output is different with an older fsl version like 5.0.7. In a new/different terminal window you could setup your environment with 5.0.7 and then try again, $ setenv FSLDIR /usr/pubsw/packages/fsl/5.0.7$ setenv FSL_DIR "$FSLDIR" ..  .  . then source freesurfer setup or run .  .  . $ source $FSLDIR/etc/fslconf/fsl.csh - R. On Dec 27, 2021, at 15:34, Kaplan, Elizabeth <elizabeth_kaplan(a)brown.edu> wrote:        External Email - Use Caution        Hello All, I am running into an error when attempting to run the 'trac-all -prep -c" command. The error reads "/autofs/cluster/pubsw/2/pubsw/Linux2-2.3-x86_64/packages/fsl.64bit/6.0.4/bin/bet: line 399:  6625 Illegal instruction"I set my FSLDIR following the instructions on the FSL User guide and added these lines to my .bash_profile file. Any suggestions on how to navigate this issue? Thank you in advance!<trac-all.log><configuration.file.tutorial>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Developer password for Ubuntu log in
by fsbuild 27 Dec '21

27 Dec '21

External Email - Use Caution Sending the info to your email shortly ... - R. Sang-Han Choi (sanghanchoi(a)gmail.com) December 25, 2021 at 08:48         External Email - Use Caution        Dear FreeSurfer Manager I am currently setting up FreeSurfer using the Ubuntu VM by following (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1QGQZSIkEASZdRSKpPrM5N4xbfSHJd70xcSC-D-Mz_y96s…) But I can't log in because I don't have the developer password. Would it be possible to provide me with the password? Thank you! sincerely yours,  Sang-Han Choi _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1VfxXrSw7iLtZi9sYP-gRd5bC3fh4_lHDQYEoczrRjYYFW…

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Illegal Instruction Error
by Kaplan, Elizabeth 27 Dec '21

27 Dec '21

External Email - Use Caution Hello All, I am running into an error when attempting to run the 'trac-all -prep -c" command. The error reads "/autofs/cluster/pubsw/2/pubsw/Linux2-2.3-x86_64/packages/fsl.64bit/6.0.4/bin/bet: line 399: 6625 Illegal instruction" I set my FSLDIR following the instructions on the FSL User guide and added these lines to my .bash_profile file. Any suggestions on how to navigate this issue? Thank you in advance!

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Developer password for Ubuntu log in
by Sang-Han Choi 25 Dec '21

25 Dec '21

External Email - Use Caution Dear FreeSurfer Manager I am currently setting up FreeSurfer using the Ubuntu VM by following ( https://secure-web.cisco.com/146Qu5uXrq4DXeyoh_h2Rn9ul9DVRSvPNPQwb9piTjitro…) But I can't log in because I don't have the developer password. Would it be possible to provide me with the password? Thank you! sincerely yours, Sang-Han Choi

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Tracula error
by Nasiriavanaki, Zahra,M.D. 23 Dec '21

23 Dec '21

Hello, I’ve been running the trac-all -prep step and I faced this error: ConvertTransformFile 3 /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.mat /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.txt --hm --ras ConvertTransformFile: Command not found. Linux bee.nmr.mgh.harvard.edu<http://bee.nmr.mgh.harvard.edu> 3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Fri Dec 3 14:29:56 EST 2021 Could you please let me know what the problem is? I’m running it in dev environment. Thanks, Mona Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry | MGH/HMS Department of Radiology | MGH/HMS 149 13th Street, 149-2615 Boston, MA, USA, 02129

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trac-all -prep error
by Salar Dini, Elaheh 23 Dec '21

23 Dec '21

External Email - Use Caution Dear freesurfer developers and Dr. Yendiki, I am trying to run trac-all -prep -c dmriEla, dmriEla being my config file. I am attaching the config file here. If I perform registration-based correction with eddy_correct, doeddy=1, things start to run. However, if I use doeddy=2, model-based correction with eddy, I get the following error: ERROR: for B0 distortion correction with reverse-polarity DWIs ERROR: or for model-based eddy-current distortion correction, ERROR: must specify PE direction No Trac-all.log file is created. If needed, I can also send you a few anonymized slices from the acquired DTI series, so you can check the header. Moreover, I can send you the acquisition sequence properties as a PDF file if needed. Is there a way to fix this problem? In other words, can we do something to be able to use model-based correction instead of registration-based questions since it seems to be a more sophisticated method? I'm running freesurfer on Linux Centos7, the version of freesurfer is 7.2.0 and the installed package is freesurfer-linux-centos7_x86_64-7.2.0.tar.gz. I really do appreciate your time and help. Ela

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Postdoctoral Research Position in Brain Stimulation and Imaging
by Flanagan, Shawn D 23 Dec '21

23 Dec '21

External Email - Use Caution A postdoctoral position is available at the Neuromuscular Research Laboratory to study the neurophysiological basis of transcutaneous vagus nerve stimulation and its effects on cognitive function in healthy humans. The successful applicant will play a central role in the development and execution of the study and have opportunities to pursue follow-on / early career funding based on this work or other ongoing research initiatives. The research project involves extensive use of magnetic resonance imaging, high density electroencephalogram, transcranial magnetic stimulation and electromyography, neurophysiology signal acquisition and processing, psychometric testing (task switching, attention, acoustic startle modulation), and blood collection and analysis. Candidates must have a PhD with a strong background in behavioral neuroscience or neurobiology and a history of publication productivity. Proficiency in transcranial magnetic stimulation, electroencephalography, and magnetic resonance imaging is highly desirable. Proficiency with Matlab, R, Python, EEGlab, Freesurfer, DSI studio, Curry, BrainVoyager, Brainstorm, or FSL is desirable. The successful candidate is expected to have excellent oral and written communication skills, an interest in human research, and a strong inquisitive nature and initiative. Salary and benefits will be commensurate with NIH and University of Pittsburgh guidelines. To apply, please email curriculum vitae, names and contact information of three references, and a letter stating research interests to Dr. Shawn Flanagan (sdf29(a)pitt.edu<mailto:sdf29@pitt.edu>), Assistant Professor, Department of Sports Medicine and Nutrition, University of Pittsburgh. Applicants will only be contacted if invited to interview. --- Shawn Flanagan, Ph.D. Assistant Professor University of Pittsburgh School of Health and Rehabilitation Sciences Department of Sports Medicine and Nutrition Neuromuscular Research Laboratory Warrior Human Performance Research Center 3860 South Water Street Pittsburgh, PA 15203 sdf29(a)pitt.edu<mailto:sdf29@pitt.edu> Email 412.246.0460 Office 630.854.0547 Mobile Neuromuscular Research Laboratory<http://secure-web.cisco.com/1Mmlk3xwPMBRNBQp-JEyWAY_OblhIUOx3WlB44t6HWe2ZJ5…>

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Two Postdoc positions and one PhD studentship at Cardiff, UK
by Jiaxiang ZHANG 23 Dec '21

23 Dec '21

External Email - Use Caution [Apologize for cross-posting] Dear colleagues, We are seeking applicants for two postdoc positions (research associates) and one PhD studentship at Cardiff University Brain Research Imaging Centre (CUBRIC). The research associates will work on the neurocognitive mechanisms of human decision-making, integrating multimodal brain imaging (MEG, functional and diffusion MRI, and MRS) and computational modelling. The PhD will work on cohort data to understand information processing speed in humans. We encourage applicants from different disciplines, including cognitive neuroscience, imaging neuroscience, psychology, computer science, mathematics or physics. Job specs and application details are available online (see links below). For informal enquiries, please contact Dr Jiaxiang Zhang ( zhangj73(a)cardiff.ac.uk) with your CV. A. Postdoc positions (Deadline: Jan 14, 2022) https://secure-web.cisco.com/1_hEY9WeSONtg678hS7LTvoqOsXhkkTyoXpoIhQQFXbMJ9… B. 3-year PhD studentship (Deadline: March 11, 2022) https://secure-web.cisco.com/1Fj7Vwg6S2iQIng_VeEvZlnRPyLOOQiHQKhWduEs7Xhb5s… The successful candidates will be based at CUBRIC. CUBRIC houses a unique combination of state-of-the-art facilities and world-leading expertise, with 4 human MRI systems (2 x Siemens Prisma, 1 x Siemens Connectom, 1 x Siemens 7T), MEG, EEG, TMS, tDCS, clinical research units and testing labs. Further details of CUBRIC can be found on our web page ( http://secure-web.cisco.com/1bJGyDq0xWoxT3GoRScsNBQwYXAfJuJlfknpK6mU3e8UXK3… Dr. Jiaxiang Zhang Cardiff University Brain Research Imaging Centre (CUBRIC) School of Psychology Cardiff University Maindy Road, Cardiff, CF24 4HQ http://secure-web.cisco.com/1H2W3yXtCJTIM_dxk9Qa380uV6NWZ8h9nWLvwaq_miOaUpW… https://secure-web.cisco.com/19urc1hXCmOuFzBhNvrX5amqU3eJeEs3o4DvOwicqtt5xu… zhangj73(a)cardiff.ac.uk +44 (0)29 2087 0471

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Freesurfer December 2021