Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

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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Re: [Freesurfer] Ventricle segmentation issue - ventricle mislabeled as white matter
by Kang, Jee Won 22 Dec '21

22 Dec '21

External Email - Use Caution Hi Bruce, Again, so sorry if this message has been spammed to the mailing list; I kept getting messages that the body of the message was too big whenever I tried to send it with the attachments, so I'm instead sending along a dropbox link to the requested files from a subject with the described problem: https://secure-web.cisco.com/1bc6MB5a_uvCZt5sOF35dk1a-glsFH3pnjNrc9AoxTGiIk… Thank you for your insight and assistance with this! Sincerely, Jee Won ________________________________________ Message: 2 Date: Tue, 21 Dec 2021 15:31:42 +0000 From: "Fischl, Bruce" <BFISCHL(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Ventricle segmentation issue - ventricle mislabeled as white matter To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <BY5PR04MB6614B1B44ADDBBB00C9E7109EF7C9(a)BY5PR04MB6614.namprd04.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" External Email - Use Caution Hi Jee Won Can you send us the recon-all.log file? And ideally an example orig.mgz that we can try things on Cheers Bruce From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of Kang, Jee Won Sent: Tuesday, December 21, 2021 9:19 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] Ventricle segmentation issue - ventricle mislabeled as white matter External Email - Use Caution Hello all, I found a very common error in our data while I was correcting recons. The lateral ventricles (usually the horns) are being misclassified as white matter in aseg.mgz. This happened in around 1/3 of our 108 subjects. We were able to fix this issue by manually filling in the ventricles in aseg.presurf.mgz and re-running Freesurfer with the command autorecon2-noaseg -autorecon3, but this is obviously quite a labor-intensive fix for a substantial portion of our data. This was also the only way to fix the segmentation - filling in the mislabeled areas as 255 in the wm.mgz did not fix the problem. I'm not sure why Freesurfer is having issues here, as the areas it is mislabeling have very distinct intensity boundaries - the T1 intensity is usually between 20 and 45 in the areas that are being mislabeled. I've attached a screenshot of a subject's aseg.presurf.mgz who had this ventricle segmentation issue, and you can see that a large portion of the right ventricle has just not been segmented properly; the intensity of the area in the aseg.presurf.mgz and wm.mgz volumes is just 0, and it was 41 (R cerebral white matter) in aseg.mgz. Would you be able to provide some insight into why this might have been happening, and what we could do in the future to prevent such extensive manual editing in the future? I can also say that this data was processed with a T2 image as well, and supplying that flag didn't help with the segmentation issue. Thank you, Jee Won

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Postdoctoral Research Fellow position in Neuroimaging
by Aganj, Iman 20 Dec '21

20 Dec '21

The Laboratories for Computational Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging invites applications for a Postdoctoral Research Fellow position at the Massachusetts General Hospital and Harvard Medical School. The project will consist of human brain connectivity analysis, brain image segmentation, and/or multimodal MRI data harmonization, with application in studying Alzheimer's disease. The appointment is for two years with the possibility of a third year based on performance and the availability of funding. The project involves analyzing structural and functional brain networks through diffusion-weighted and functional MRI as well as brain structure segmentation, and examining the relationship of brain connections with different stages of dementia. The Research Fellow will be supervised by Dr. Iman Aganj, in close collaboration with Dr. Bruce Fischl. The candidate is required to have: * a Ph.D. in engineering, neuroscience, or a related field by the start date, * strong programming skills in MATLAB, Python, or a similar environment, and * a medical image analysis background. Familiarity and experience with any of the following will be a plus: neuroimaging, connectomics, medical image segmentation, diffusion-weighted MRI, functional MRI, MRI data harmonization, machine/deep learning, graph theory, dementia studies, mathematical modeling. Interested applicants are invited to send a cover letter describing research interests and experience, an up-to-date CV, and names and contact information of three references to: iaganj(a)mgh.harvard.edu<mailto:iaganj@mgh.harvard.edu> https://partners.taleo.net/careersection/ghc/jobdetail.ftl?job=3180937 Iman Aganj Assistant Professor of Radiology Harvard Medical School Associate Investigator Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital

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