Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Multiple Freesurfer(s)
by Giulio Degano 07 May '21

07 May '21

External Email - Use Caution Hi all, I am trying to install multiple Freesurfer versions on a Linux server (academic purposes, Linux Ubuntu 20.04). I was able to install 7.1 and 5.3 (I used two different folders) and I also got the licenses. While 7.1 runs with no problem, for 5.3 recon-all keeps giving the "invalid license file error". I am probably missing something. Thanks in advance Best Giulio Degano

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Job ad: MRI physicist
by Keith Schneider 07 May '21

07 May '21

External Email - Use Caution The Center for Biomedical and Brain Imaging (CBBI) is a core imaging facility at the University of Delaware dedicated to scientific research. It is equipped with a Siemens Prisma 3T MRI scanner, Bruker 9.4T small bore MRI scanner, TMS, and MRI-compatible EEG. It supports a wide range of scientific investigations through imaging of humans, animals and materials. Under general direction of the CBBI Manager, the MRI Physicist is responsible for supporting the operations of the Siemens and Bruker MRI scanners. The MRI Physicist is expected to contribute to both research and training efforts that will include pulse sequence programming, parameter and image quality optimization, protocol design, scanner operation, technical support and user training. The candidate will be expected to maintain a broad knowledge of state-of-the-art MRI technology and equipment. The incumbent must have excellent communication and organizational skills, the ability to positively interact with a diverse group of MRI users, and a strong motivation to learn new MRI techniques. MAJOR RESPONSIBILITIES: • Pulse sequence programming on Bruker 9.4T and Siemens 3T MRI scanners • Assist users on appropriate choice and use of coils • Technical liaison for obtaining sequences or protocols for non-standard imaging (e.g. cardiac, musculoskeletal) from Siemens and other sites • File reports as needed for WIP sequences and Siemens MRA • Ensure data quality from the viewpoint of machine fundamentals • Technical support 9.4T and 3T scanners • Protocol design and testing for 9.4T scanner, including imaging of live animals and awake animals; as-needed for 3T • Routine quality assurance for 9.4T and 3T MRI scanners • Train users, including students, on use of 9.4T and 3T MRI scanners • Help users optimize pulse sequence parameters to maximize SNR and avoid imaging artifacts • Consult on image analysis, as needed • Review journals and abstracts to keep abreast of new developments • Collaborate with ongoing research as needed; may have independent research projects if desired • Consult users about imaging details for manuscript preparation and grant applications, as needed • Perform miscellaneous job-related duties as assigned QUALIFICATIONS: • PhD in MR physics or MS with equivalent experience • expert understanding of MR physics, image acquisition, signal processing, imaging processing and image reconstruction • MR pulse sequence programming • Experience with Bruker and Siemens MRI scanners • MRI scanning experience with both humans and animals—willing to handle animals • Ability to design experiments, optimize MRI protocols, troubleshoot image artifacts, analyze data, and interpret results • Knowledge of functional MRI, DTI, MRS, T1/T2 relaxation and perfusion • Siemens IDEA and ICE certification (or ability to obtain) http://careers.udel.edu/cw/en-us/job/493998/mri-physicist-research-office <http://careers.udel.edu/cw/en-us/job/493998/mri-physicist-research-office> For further information, contact me. keith ----- Keith Schneider Director, Center for Biomedical and Brain Imaging Associate Professor Department of Psychological and Brain Sciences University of Delaware

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error at 3d normalization pass 1 of 2 stage with MP2RAGE data
by Corinna Bauer 05 May '21

05 May '21

External Email - Use Caution Hello all, I am trying to run recon-all on MP2RAGE data from Philips and it exits with errors at this point: 3d normalization pass 1 of 2 error: No such file or directory error: MRInormFindControlPoints: could not find enough control points error: No such file or directory error: MRInormFindControlPoints failed Command exited with non-zero status 253 The log file is attached. The input file was the MPRAGE generated on the scanner console (i.e. not the T1 map). I attached a screenshot of orig.mgz viewed in fsleyes. Any thoughts? Thanks! Corinna

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help with SAMSEG
by Alberto Del Cerro Leon 05 May '21

05 May '21

External Email - Use Caution Hello Freesurfer team, my group is interested in using the SAMSEG tool to evaluate white matter lesions in MCI patients. We would like to use a personalized atlas for the measure. We suppose that we need to use the flag --atlas but we don`t know if we need a generic atlas or we need an atlas at each subject' spaces. Thanks in advance for your help.

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Freesurfer version 7 reconall -autorecon2-wm error
by Jewelia K. Yao 05 May '21

05 May '21

External Email - Use Caution Hi Freesurfer Developers, I am trying to run reconall -autorecon2-wm using Freesurfer version 7 after making some minor edits to the wm.mgz file. I've tried it on multiple subjects and still get the same error (recon-all.log attached) when mri_fill starts to run: reading segmented volume aseg.presurf.mgz removing CC from segmentation Looking for area (min, max) = (350, 1400) area[0] = 1276 (min = 350, max = 1400), aspect = 0.46 (min = 0.10, max = 0.75) no need to search using seed (127, 124, 151), TAL = (1.0, 23.0, 4.0) *** Error in `mri_fill': double free or corruption (!prev): 0x0000000001c65070 *** reconall -autorecon2-wm runs well with Freesurfer version 6, but since the data was run through reconall with version 7, I was hoping to to use it for autorecon as well. I couldn't find any similar errors (specific to version 7) in the list. Does anyone know if this error is specific to version 7 and if there's any way to troubleshoot? Thanks! Jewelia

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make_average_subject without Talairach transform
by Trisanna Sprung-Much 05 May '21

05 May '21

External Email - Use Caution Hi there I’d like to know if it is possible to create an average volume and average surface of several subjects without having to incorporate the Talairach transform and no transform at all. Thank you, Trisanna Sprung-Much Research Associate McGill University MD Anderson Cancer Centre --

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Error with mris_convert
by バキット・ムダシル 05 May '21

05 May '21

External Email - Use Caution Hi, I manually made annotation files on an inflated surface of 40 subjects. The labels that makes these annotfiles are 13 in total but not present in all subjects every time, some can be missing depending on the brains surface morphology. I made the ctab files manually in the label folder in eluding an unknown label in the first line. I tried to convert one of the annotfiles into gii format and got the following error: mris_convert --annot $SUBJECTS_DIR/spl_01/label/lh.par.annot $SUBJECTS_DIR/spl_01/surf/lh.white ~/Desktop/spl_01/lh.par.gii reading colortable from annotation file... colortable with 14 entries read (originally none) Segmentation fault: 11 What this error exactly means, and how I can solve this issue. Thanks Mudathir

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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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Error 3d normalization pass 1 of 2 white matter peak
by Camerino, I.L. (Ileana) 04 May '21

04 May '21

External Email - Use Caution Dear Freesurfer experts, I am running recon all on a T1 image that already gave me many problems. After I solved the last one (adding control points in white matter) I finally got a new error. The command I run is: echo "cd $PWD; ./recon_all_sub056.sh" | qsub -N "reconall_sub056" -l walltime=48:00:00,mem=150gb. Error is: 3d normalization pass 1 of 2 white matter peak found at 110 Cannot allocate memory Linux dccn-c047.dccn.nl 4.19.94-300.el7.x86_64 #1 SMP Thu Jan 9 16:15:13 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux 150gb is more memory than I ever used while running recon all on other data, so I doubt that adding more memory will help. Please could someone give me any hint on how can I solve this error? Thank you in advance Ileana Camerino PhD candidate Donders Institute for Brain, Cognition and Behaviour Centre for Cognition Spinozabuilding Room B02.25 Montessorilaan 3, 6525 HR Nijmegen The Netherlands Tel. +31-24 3612618

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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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