Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 discussions

Re: [Freesurfer] Passcode for FreeSurfer VM
by fsbuild 23 May '22

23 May '22

External Email - Use Caution Sending the info to your email shortly. - R. On May 16, 2022, at 06:07, Aleksandra Petrovskaia <alexvalpetrovskaya(a)gmail.com> wrote:        External Email - Use Caution        Dear all,I hope you are doing well. I am an intern at the University of Gothenburg, Sweden,  could you please provide me with a passcode for FreeSurfer VM image? I would like to use this version: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1K6vBdJsncsO4FArAm6uohxZsPHj-p7u1Ssztq… wishes,AlexandraБез вирусов. MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1i9mfmQBWSvZ95AjICCQzNHTSucxu_A-YuQ2d_G… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mri_surf2surf error
by Zhang, Fan 19 May '22

19 May '22

External Email - Use Caution Hello Everyone, I am trying to run mri_surf2surf. But I got some errors saying "no such file or directory" while in fact there are files in the pathway. I was able to run this previously, so I am not sure if this is relevant to the recent upgrade of the Mac operation system (12.2.1). My FreeSurfer version is (Darwin-OSX-stable-pub-v6.0.0-2beb96c). Does anyone know how to resolve this? Thank you so much for the help! Fan mri_surf2surf --hemi lh --s fsaverage5 --sval lh.CCn_band.Seed1_20220314.V1.13subjs.mgh --fwhm 13 --tval lh.CCn_band.Seed1_20220314.V1.13subjs.13.mgh sysname Darwin hostname Hans-iMac-Pro.local machine x86_64 user fanzhang srcsubject = fsaverage5 srcval = lh.CCn_band.Seed1_20220314.V1.13subjs.mgh srctype = trgsubject = fsaverage5 trgval = lh.CCn_band.Seed1_20220314.V1.13subjs.13.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 13 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /Applications/freesurfer/subjects/fsaverage5/surf/lh.sphere.reg Loading source data MRIallocSequence(0, 0, 0, 0): bad parm No such file or directory Segmentation fault: 11

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questions about ThalamicNuclei.sh, segmentHA_T1.sh, segmentBS.sh
by Wenjun Huang 19 May '22

19 May '22

External Email - Use Caution Hi, I'm attempting to use segmentThalamicNuclei.sh( https://secure-web.cisco.com/1RV2omTbdlZNcuz2LjtNOfF_gXU-a1Zh7ZafxTa7vX-y1Z… ),segmentHA_T1.sh( https://secure-web.cisco.com/1LhDcP1FH1KgfwvDWIRfvii3lB4d3_LJAyFBfDkPRA2sC_…) segmentBS.sh ( https://secure-web.cisco.com/1Zcp3K-vS0QBfdAhIw0PbtQM6onkntbEtV2RlFJ3B_lENy…) But I have done all the recon-all on version 6.0. So I wonder if it's ok if I run recon-all on 6.0v and do the three segments on 7.2v within one project? I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Many thanks, Wenjun 1) FreeSurfer version(recon-all): freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55 2) aFreeSurfer version(segmentThalamicNuclei.sh,segmentHA_T1.sh,segmentBS.sh): freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b 3) Platform: Ubuntu 18.04 LTS(Bionic Beaver) 4) uname -a: Linux lipalab-Precision-5820-Tower 5.4.0-100-generic #113~18.04.1-Ubuntu SMP Mon Feb 7 15:02:59 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

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fspalm: mri_surfcluster error: could not read surface /home/lipalab/Desktop/hwj/GLM/children/fsaverage/surf/lh.white
by Wenjun Huang 19 May '22

19 May '22

External Email - Use Caution I'm attempting to use fspalm ( https://secure-web.cisco.com/1zRz_KYc-Z02lCLizE3BUB2We3AfuiVlIxzRg5VijNOs5j…) and I copied fspalm, mri_volcluster, and mri_surfcluster into $FREESURFER_HOME/bin. But get error: MRISread(): could not open file mri_surfcluster: could not read surface /home/lipalab/Desktop/hwj/GLM/children/fsaverage/surf/lh.white---------------------------------------------------- Reading source surface /home/lipalab/Desktop/hwj/GLM/children/fsaverage/surf/lh.white And after I copy mri_volcluster, and mri_surfcluster into $FREESURFER_HOME/bin, I got this error when I run mri_glmfit-sim. I wonder if it's because of my freesurfer's version? And if it works for me if I get a newer version, will it be ok if I recon-all, mri_glm-stim, mri_glmfit-sim on 6.0v and do the fspalm on 7.2v within one project? I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, I've attached the fspalm.log and in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a 2) Platform: Ubuntu 18.04 LTS(Bionic Beaver) 3) uname -a: Linux lipalab-Precision-5820-Tower 5.4.0-100-generic #113~18.04.1-Ubuntu SMP Mon Feb 7 15:02:59 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux 4) fspalm.log and perm.th40.abs.mri_glmfit-sim.log: see attached

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Password Request Ubuntu
by Soto, Valentine C 18 May '22

18 May '22

External Email - Use Caution Hello, I am trying to download the virtual image for Ubuntu to utilize the windows VirtualBox FreeSurfer software. There's a password protecting the download, and I believe this is the email to request access from. Can I get the password for the file? Freesurfer 7.2.0 release in Ubuntu 18.04.06: FS_7_2_0_Ubuntu_18_04_06.ova.7z<https://secure-web.cisco.com/1R0ie-9Mo-_ypVxMaHm07Tjd_A2gwb7FA-6sned-VCSHW4…> Sincerely, Valentine Soto, B.S. (he/him) Lulu Merle Johnson Fellow, University of Iowa Interdisciplinary Graduate Program in Neuroscience Neurodevelopment and Psychopathology Lab

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Re: [Freesurfer] Password
by fsbuild 18 May '22

18 May '22

External Email - Use Caution Sending the info ro your email shortly. - R. On May 18, 2022, at 06:08, Pål Gunnar Larsson <pall(a)ous-hf.no> wrote:        External Email - Use Caution        Hello Has downloaded FS_7_2_0_Ubuntu_18_04_06.ova.7z Can you please send me a password? Best Pål G. Larsson M.D., PhD.Senior Medical OfficerDepartment of NeurosurgeryDivision of Surgery and Clinical Neuroscience Oslo University HospitalPo.box 4950 Nydalen0424 OsloNorwayTel:  (+47) 23074407Mobile: (+47) 93429791E-mail: pall@ous-hf.no Ikke sensitiv _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Freesurfer Passcode
by fsbuild 18 May '22

18 May '22

External Email - Use Caution Sending the info to your email shortly. - R. On May 16, 2022, at 17:43, Utsav Shrestha (shrstha3) <shrstha3(a)memphis.edu> wrote:        External Email - Use Caution        Hello all,I would like to request for a passcode for FS_7_2_0_Ubuntu_18_04_06.ova.7z as being instructed in the wiki. Thank you for your time!With Regards,Utsav ShresthaBiomedical EngineeringClass of 2024Research AssistantThe University of MemphisMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://http://secure-web.cisco.com/1FX5E_3Dju9d12sGP3CXRycSkIsmTlfB2FGP7… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Password
by Pål Gunnar Larsson 18 May '22

18 May '22

External Email - Use Caution Hello Has downloaded FS_7_2_0_Ubuntu_18_04_06.ova.7z Can you please send me a password? Best Pål G. Larsson M.D., PhD. Senior Medical Officer Department of Neurosurgery Division of Surgery and Clinical Neuroscience Oslo University Hospital Po.box 4950 Nydalen 0424 Oslo Norway Tel: (+47) 23074407 Mobile: (+47) 93429791 E-mail: pall(a)ous-hf.no<mailto:pall@ous-hf.no> Ikke sensitiv

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Problems with identifying fornix using TRACULA
by Morgan Botdorf 17 May '22

17 May '22

External Email - Use Caution Hi all, We recently processed our DWI data (school-aged children) using the updated version of TRACULA (Freesurfer 7.2). We were mainly interested in using this version because of the addition of the fornix to the atlas. After processing the data, we noticed a lot of really small volumes for fornix and noticed that TRACULA had a hard time overall in defining this tract in our dataset. We know that this is a hard tract to define, and we were wondering if there are any suggestions for improving the identification of this tract using TRACULA? <mbotdorf(a)terpmail.umd.edu> Thank you, Morgan Botdorf -- Morgan Botdorf, Ph.D. Postdoctoral Researcher The Changing Brain Lab University of Pennsylvania mbotdorf(a)sas.upenn.edu <mbotdorf(a)terpmail.umd.edu>

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Opening for PhD position based in Tours (Loire Valley, France)
by briend 17 May '22

17 May '22

External Email - Use Caution Dear colleagues, Apologies for double posting, The INSERM-U1253 & University of Tours research unit based in Tours (Loire Valley, France) invites applications for a PhD position to begin in the Fall of 2022 on the reward and interoceptive systems in autism. The main objective of the current PhD proposal is to identify impaired social processing in autism and AD across the last two dimensions. To do that, first, this project will explore the neural activity of the reward system in these patients via functional magnetic resonance imaging. Then, we will probe the deficit of interoception present in these disorders. This sensory modality will also be examined in relation to social processes, within an innovative device of immersive reality (the CAVE: computer automatic virtual environments). Applicants should hold a Master's degree (or equivalent) in one of the following disciplines: computational or cognitive neuroscience, computer science, cognitive science or related. Prior experience in the field of computational neuroscience and/or neuroimaging are of advantage. Sound knowledge of statistics and programming are essential. The candidate’s main missions will be to program, run and analyze behavioral and neuroimaging tests with individual with autism and healthy controls, involving interoceptive tasks and cognitive tests. A good command of written and spoken English is requested of all applicants. Knowledge of French language is beneficial. Prospective candidates should also contact directly Frederic Briend (frederic.briend(a)univ-tours.fr) and/or Marianne Latinus (marianne.latinus(a)univ-tours.fr) by June 2, 2022. Please include the following documents in your application (as a single PDF-file): Cover letter, curriculum vitae, at least one recommendation letter. The position should start in October 2022. For more information, and to apply (deadline: June 2, 2021): Follow this link*, and the how to section here**. Frederic Briend * https://secure-web.cisco.com/1_4aOFbrupfS8UnwlBMZogdhCEcKWAuwy5IJXTH8J0v0Sl… ** https://secure-web.cisco.com/1PI-W3CqSafquqExDKKVrmQEWfUneXHmYuwkE3xSpUzo-W…

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