Freesurfer April 2021

freesurfer@nmr.mgh.harvard.edu

104 participants
144 discussions

Re: [Freesurfer] Freeview slow on CentOS 8 Stream
by fsbuild 05 May '21

05 May '21

External Email - Use Caution Hello Torkil, Not sure what version of Freesurfer you are using, but if it’s an older release, it could be interesting to compare the performance with one of the latest development builds (not a release) from https://secure-web.cisco.com/11eosYMqxQIzJXYwfskbMMIPybJKGeVS7FnO….  There’s an archive and RPM for CentOS7 and an archive for a CentOS8 build. - R. On Apr 27, 2021, at 04:18, Torkil Svensgaard <torkil(a)drcmr.dk> wrote:       External Email - Use Caution        Hi RuopengThe users all agree it is GUI responsiveness. Everything else can run just stellar on the very same desktop, matlab etc, at the same time as freeview stalls.Mvh.TorkilOn 26/04/2021 19.16, Wang, Ruopeng wrote:Hi Torkil,Can you tell what part of the program slows down the most? Data loading? GUI responsiveness? Image/3D rendering? Or just in general? If it is the rendering, maybe try updating the graphics card driver to the latest?Best,RuopengOn Apr 26, 2021, at 6:06 AM, Torkil Svensgaard <torkil(a)drcmr.dk> wrote:       External Email - Use CautionHiWe have an older Ubuntu 16.04 HPC installation on which Freeview runsjust fine. We also have a brand new CentOS 8 Stream HPC installationwith much better hardware on which Freeview slows to a crawl after a bitof use.There's no error as such, it just slows to the point of being unusable.Any suggestions on how to fix it, or pinpoint the cause?Thanks,Torkil_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://secure-web.cisco.com/1ZSo3b7UZQvI87wlIWMxXiY8FNo9ppP_EMAuoLl2dyKZaXHHwwd8FIbgg_K7F0-UhXFuTt9dgR8j4eAFXChTX-nq8X3jtFYPllkw4s2D1PpOPgXfXko-sYDOv6xrQVkRqceKsnnQ4O3xc1bxvH33S1CtvdOsW20IhTVg_xHqpFDDpYAQEo_92j2xDkmSlAuIAPWjL_h8rl-Tz8ZuuU3isFx7bg6sk8PTqKIfMh0FIJCAQuXdn8n2036b7gr3K7raNuHqxutEnCTdr2EfLDZbT6g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://secure-web.cisco.com/1ZSo3b7UZQvI87wlIWMxXiY8FNo9ppP_EMAuoLl2dyKZaXHHwwd8FIbgg_K7F0-UhXFuTt9dgR8j4eAFXChTX-nq8X3jtFYPllkw4s2D1PpOPgXfXko-sYDOv6xrQVkRqceKsnnQ4O3xc1bxvH33S1CtvdOsW20IhTVg_xHqpFDDpYAQEo_92j2xDkmSlAuIAPWjL_h8rl-Tz8ZuuU3isFx7bg6sk8PTqKIfMh0FIJCAQuXdn8n2036b7gr3K7raNuHqxutEnCTdr2EfLDZbT6g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2FfreesurferThe information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://secure-web.cisco.com/1iIikemoA9DiusPW-kySeM7Lhv0S5lGLLVKXGGn…. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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QA in longitudinal processing
by Malo Gaubert 03 May '21

03 May '21

External Email - Use Caution Hello FreeSurfer developers, I am trying to apply longitudinal processing on T1w MRI data for two timepoints (~8 months between the two TP) in adolescents in order to perform vertex-based analyses. I am following the online tutorial here for the preprocessing: https://secure-web.cisco.com/15SLKllO1EVTB4t08TfZPIkp1fVCDUdF94m0DqoL4seAFO… Thus I launched the creation of BASE followed by the LONGITUDINAL. Everything went well for recon-all for these 3 steps. Now, I want to do the QA on the data and I have two questions regarding this QA: 1/ For one subject, for the two timepoints, the white and pial surface are entering in the left lateral ventricle as displayed in figure 1 (session 1 of the subject; cross-sectional), while the aseg is fine (this area is considered as Lateral ventricle, see figure 2 attached). What correction could I apply for this case ? 2/ For some subjects, there is a small shift between the pial of the two sessions (or the white; see figure 3=display of the norm of my norm and pial/white for the two timepoints (long)) and/or some weird/non straight lines for pial or white (see figure 3, especially between temporal pole and the rest of the brain). What could be the error in this case? Could it be related to some bad quality of T1w images? 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.0.tar.gz 2) Platform: Ubuntu 18 (Virtual Machine on remote server) 3) uname -a: Linux ubuntu18-cbrain-042020 4.15.0-135-generic #139-Ubuntu SMP Mon Jan 18 17:38:24 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Any help would be appreciated. Best, Malo

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Out of memory from longitudinal segmentation of hippocampus
by Wei Shao 03 May '21

03 May '21

External Email - Use Caution Hello, Dear FreeSurfer expert. I was tried to use longitudinal segmentation of T1 scans for the longitudinal analysis. but there is a problem making Unknown map to reduced label 13 Computing hyperparameters for estimation of Gaussian parameters Error using permute Out of memory. Type HELP MEMORY for your options. Error in myMRIread>myMRIread_aux (line 99) Error in myMRIread (line 63) Error in SegmentSubfieldsT1Longitudinal (line 904) MATLAB:nomem @#@FSTIME 2021:04:24:13:57:21 run_SegmentSubfieldsT1Longitudinal.sh N 17 e 249.25 S 49.95 U 759.76 P 324% M 1532492 F 249 R 4682496 W 0 c 134624 w 550491 I 3940880 O 1217536 L 1.24 1.04 1.58 @#@FSLOADPOST 2021:04:24:14:01:30 run_SegmentSubfieldsT1Longitudinal.sh N 17 4.04 3.43 2.47 Linux gra-login1 3.10.0-1127.8.2.el7.x86_64 #1 SMP Tue May 12 16:57:42 UTC 2020 x86_64 GNU/Linux longitudinal subfields exited with ERRORS at Sat Apr 24 14:01:31 EDT 2021 For more details, see the log file /home/weishao/long_BAY12019/scripts/long-hippocampal-subfields-T1.log I have checked the space: Description Space # of files /home (user weishao) 44G/53G 147k/500k Could you tell me what I should do? Thanks Best, Cheer

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Adjusting statistical thresholds
by Craggs, Jason G. 30 Apr '21

30 Apr '21

External Email - Use Caution Greetings, My lab is just starting to incorporate --------------------------------- Jason G Craggs, Ph.D. Assistant Professor SHP/Physical Therapy University of Missouri 801 Clark Hall Columbia, MO 65211-4250 Phone: 573-884-9345 http://secure-web.cisco.com/1om_TcLlijTCIxWjYEa6ZCmlDCHTYDbIVGkmP1P4GYQcHf0… https://secure-web.cisco.com/1JbmhTp91hlfULAboEisj8WyTXDFMj6B4CaELpCFBBOqiY… https://secure-web.cisco.com/1CbHVR5iuhveJeIkIZ5D4FvzjVWbH9WIXYYSwS8KhWc3W4…

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[ERROR] mri_fill: could not find any points where lh and rh wm are nbrs
by Maria Baena Perez 30 Apr '21

30 Apr '21

External Email - Use Caution Dear Freesurfer experts, When I run "recon-all -autorecon2-cp post_005_5" I get the following error: ----------------------------------------------- Fill Wed Apr 28 15:02:30 CEST 2021 /usr/local/freesurfer/subjects/post_005_5/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.03550 -0.03726 0.02428 -5.20844; 0.04020 1.20081 0.24439 -18.80629; -0.03042 -0.27019 1.02611 9.81696; 0.00000 0.00000 0.00000 1.00000; reading colortable from MGH file... colortable with 14176 entries read (originally /usr/local/freesurfer/FreeSurferColorLUT.txt) voxel to talairach voxel transform 1.03550 -0.03726 0.02428 -5.20844; 0.04020 1.20081 0.24439 -18.80629; -0.03042 -0.27019 1.02611 9.81696; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... mri_fill: could not find any points where lh and rh wm are nbrs No such file or directory Linux sleep2014 4.10.0-27-generic #30~16.04.2-Ubuntu SMP Thu Jun 29 16:07:46 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s post_005_5 exited with ERRORS at Wed Apr 28 15:02:37 CEST 2021 To report a problem, see http://secure-web.cisco.com/1h89mJlBFS4Sw6GwbJ46-9RztVTwv-aPIoayZx7zzoQGZBh… We have checked the aseg.auto_noCCseg.mgz and the wm.mgz and everything seems to be correct. I`m using freesurfer v6.0. Could you help me to solve this problem? Many thanks Maria

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FreeSurfer results for Allen Brain Atlas donors?
by Keith Jamison 29 Apr '21

29 Apr '21

External Email - Use Caution I just came across this page that describes freesurfer outputs for the 6 Allen Brain Atlas donors: https://secure-web.cisco.com/1tWRubEIGq1Vc2e5IRFbcyZbKrPn8IuChYlWsqD8Clzjen… There's a recent note saying the data has been moved to a sharepoint server. Access to that server appears to be restricted. Is that data still publicly available somewhere? Thanks! -Keith Jamison

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mris_anatomical_stats
by Nils B. 29 Apr '21

29 Apr '21

External Email - Use Caution Dear Supportteam, I have a short question concerning the data produced by mris_anatomical_stats. The description on the anatomical structures is really short so I just wanted to ask if the precentral stats are for the precentral gyrus? Best regards, Nils -- Nils Böer Research Assistant with Bachelor Degree (WHB) *Psychology and Movement Science* University of Paderborn Department of Sports and Health Warburger Str. 100 33098 Paderborn Room: Sp 1.401 Email: nils.tobias94(a)gmail.com / nboeer(a)mail.uni-paderborn.de <nils.tobias94(a)gmail.com> Web: https://secure-web.cisco.com/1UEsGq-Ov55CfhmCUKI5WtiYJLPy4Xa6a_QJXCVgG6B5Cm… https://secure-web.cisco.com/16rRO6pleZ5M3Nwh65k5t2q9-oc2lO4-G17OfjKbbTveLY… <https://secure-web.cisco.com/1UEsGq-Ov55CfhmCUKI5WtiYJLPy4Xa6a_QJXCVgG6B5Cm…>

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Several open positions at Harvard University: Research Coordinator and 2-3 Research Assistants
by Gaab, Nadine 27 Apr '21

27 Apr '21

The Gaab Lab (http://secure-web.cisco.com/1i5_mEfuDXw4ZnX2b7Yr6ifS53LF6292DEznzfT-RFDAW2F…<http://secure-web.cisco.com/1i5_mEfuDXw4ZnX2b7Yr6ifS53LF6292DEznzfT-RFDAW2F…>) at Harvard works at the intersection of neuroscience, education, EdTech, and policy. We focus on typical/atypical learning trajectories with a special focus on language and reading development and the role of the environment in shaping these trajectories. We are seeking a full-time Lab Coordinator to oversee the daily operations of the lab AND 2-3 research assistants 1. The Lab Coordinator will be responsible for: * Organization and implementation of administrative systems and procedures * Coordinating the day-to-day running of the lab: developing and overseeing project timelines, coordinating in-person and virtual meeting logistics, preparing agendas, assembling meeting materials, documenting meetings, acting as the administrative contact to all stakeholders, managing correspondence, managing contact information, developing and maintaining methods for organizing information including files, databases, and other systems * Preparation of IRB documentation and submissions in conjunction with the Principal Investigator and/or other members of the research team * Serving as a member of the Leadership Team: coordinating the activities of the various national and international project work streams, supporting and managing logistics of professional development learning opportunities * Supporting researchers with implementing research activities * Management of the lab budget and other financial administrative tasks * Coordination of hiring and temporary payroll of graduate students, staff, or temps * Supervising and coordinating the work of support staff, students, interns, and temps * Will have an opportunity to contribute to stimuli design, data analyses and/or publications To qualify, you must have: A Bachelor's or Master's degree in psychology, cognitive science, neuroscience, education, or a related field and three years of relevant work experience. Excellent written and verbal communication skills, office organization, attention to detail and use of current technologies is a must. Strong interpersonal skills including the ability to communicate with faculty, students, and administrators at all levels is required. Demonstrable pre-existing interest in cognitive neuroscience and/or education research desired. This position demands initiative and the ability to work flexibly on multiple tasks simultaneously under minimal supervision. Must be self-motivated and able to work in a fast-paced, changing environment. Start will be ASAP. We will prioritize applicants who are interested in a two-year commitment. All interested applicants should email a resume/CV and cover letter to gaablab(a)gse.harvard.edu<mailto:gaablab@gse.harvard.edu> with the subject line "Lab Coordinator Position" 1. The Research Assistants will be responsible for: * MRI/fMRI scanning and behavioral testing of young children, infants, and their parents in-person and in virtual settings * Subject recruitment, scheduling and assessments for various research studies, which may include close interaction with or conducted in schools and daycare centers in the Boston area and in national/international settings * Implementation and maintenance of analysis software * Preparation of IRB documentation and submissions in conjunction with the Principal Investigator and/or other members of the research team * Conducting data collection activities and preparing analytical reports regarding results of studies * Will have an opportunity to contribute to stimuli design, data analyses and/or publications To qualify, you must have: A Bachelor's degree in psychology, cognitive science, neuroscience, education, or a related field and two years of relevant work experience (relevant coursework may count towards experience). Comfort with a heterogeneous computing environment (Linux/Unix, Mac, and Windows) as well as some programming experience preferred; knowledge of psychological experiment software (E Prime, Presentation, etc.) and/or fMRI analyses software very helpful. Demonstrable pre-existing interest in cognitive neuroscience desired; knowledge of neuroanatomy or statistics extremely helpful. Prior experience working with infants and small children (e.g., in a preschool or daycare setting or within a research project) will be a plus. Must be self-motivated and able to work in a fast-paced, changing environment and must like working with children. Start will be ASAP. All interested applicants should email a resume/CV and cover letter to gaablab(a)gse.harvard.edu<mailto:gaablab@gse.harvard.edu> with the subject line "Research Assistant Position" "Nothing in science has any value to society if it is not communicated." Anne Roe (1904-1991) Nadine Gaab, PhD Associate Professor of Education Harvard Graduate School of Education Harvard University Larsen Hall (Office 504) 14 Appian Way, Cambridge, MA 02138 nadine_gaab(a)gse.harvard.edu<mailto:nadine_gaab@gse.harvard.edu> http://secure-web.cisco.com/1i5_mEfuDXw4ZnX2b7Yr6ifS53LF6292DEznzfT-RFDAW2F…<http://secure-web.cisco.com/1MgJ1UrEdJVtNYVHndUJcEarK7ykI4zCp2mtXfDv-yk_qdp…> Twitter: Nadine Gaab (@GaabLab)

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Freeview slow on CentOS 8 Stream
by Torkil Svensgaard 27 Apr '21

27 Apr '21

External Email - Use Caution Hi We have an older Ubuntu 16.04 HPC installation on which Freeview runs just fine. We also have a brand new CentOS 8 Stream HPC installation with much better hardware on which Freeview slows to a crawl after a bit of use. There's no error as such, it just slows to the point of being unusable. Any suggestions on how to fix it, or pinpoint the cause? Thanks, Torkil

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Freeview issues with surfaces
by Pål Gunnar Larsson 26 Apr '21

26 Apr '21

External Email - Use Caution I have made a new install of everything, now running Ubuntu 20.04 with Virtualbox 6.0 and Freesurfer 7.1. Freesurfer crashes with : "nquads=10158084, nvertices=529 terminate called after throwing an instance of 'int' Aborted (core dumped)" If I try to open surface lh.area or lh.thickness. Others like lh.pial and lh.inflated works nicely. I have tried this with one of "my" patients and bert with same result. Suggestions? Pål Pål G. Larsson M.D., PhD. not sensitive

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Freesurfer April 2021