Freesurfer

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30068 discussions

Request to Post Job Position on Freesurfer listserv
by Otero Ospina, Andrea 14 Oct '24

14 Oct '24

External Email - Use Caution Hi, I hope this message finds you well. We would like to post the following job position on the Freesurfer listserv. Could you please assist us with this request? Department of Psychiatry and Behavioral Sciences Postdoctoral Associate Position in Human Neuroimaging University of Miami Miller School of Medicine, Miami, Florida, USA The Gabbay Laboratory within the Department of Psychiatry at the University of Miami Miller School of Medicine is seeking highly motivated postdoctoral scholars in the field of human neuroimaging. Available positions will focus on analyzing fMRI and proton MR spectroscopy data as well as acquiring or processing related MRI and biological measures. Candidates should either have completed or be near completing a PhD in neuroscience, psychology, cognitive neuroscience, radiology, engineering, biostatistics, or a related field, and should have a strong background in quantitative analysis. Proficiencies with at least one major neuroimaging software suite (e.g. FSL, AFNI, SPM, Freesurfer, Caret, Connectome Workbench, etc.) and Unix/Linux environment are expected. Familiarity with Matlab, Python, and/or R programming languages is a plus. The primary responsibilities for this postdoctoral fellow will be to run scans, analyze neuroimaging data from multiple ongoing and recently concluded research projects, and write manuscripts. Under the mentorship of Vilma Gabbay, MD and Benjamin Ely, PhD, postdoctoral scholars will be expected to advance clinical and methodological knowledge through their postdoctoral training. Our lab is dedicated to the study and treatment of mood, anxiety, and substance use disorders in adolescent and high-risk adult (e.g. HIV+) populations using innovative neuroimaging and immunological methodologies. The neuroimaging program features high-resolution data acquisition and analysis techniques modeled on the Human Connectome Project (HCP) and is committed to the highest standards for magnetic resonance imaging and spectroscopy. The lab is funded by four ongoing NIH R01 neuroimaging studies (R01MH120601, R01DA054885, R01MH128878, and R01MH131207) and several smaller grants, providing unparalleled funding for active and exploratory studies. Major research topics include longitudinal studies of adolescent mood and anxiety disorders; comorbidity of depression, cannabis use, and HIV infection; and an intervention study aimed at improving well-being among healthcare workers with parental responsibilities during the COVID-19 pandemic. Project abstracts with further details can be found on NIH RePORTER. Resources available on-campus and through long-standing collaborations include multiple research-dedicated 3T MRI scanners (Siemens Skyra/Vida/Prisma) with cutting-edge accelerated and multi-echo fMRI sequences, high-performance scientific computing clusters, and an extensive library of analytic and statistical software. The PIs are fully committed to fostering the trainee's research independence through publication of first-authored manuscripts in top journals and mentorship in grant applications. In addition to assisting with the PI’s proposals, the successful applicant will be highly encouraged to develop and pursue funding for their own research project through federal (e.g. NIH F32) or foundation grant programs by the end of their first year. Please send a CV, statement of interest, and contact information for three references to axo833(a)med.miami.edu<mailto:axo833@med.miami.edu>. University of Miami is an equal opportunity employer, and all qualified candidates will be given equal consideration. Priority will be given to candidates available to start sooner. Compensation will be proportional to experience and will follow standard postdoctoral fellowship rates posted by University of Miami. Best, Andrea Otero, M.D. Clinical Research Coordinator Department of Psychiatry and Behavioral Sciences University of Miami — Miller School of Medicine Email: axo833(a)med.miami.edu<mailto:njh115@med.miami.edu> Phone: 305-243-7086 [cid:97820b9a-5459-48c5-b510-70a6fc22a6b5] [cid:a06cc866-1bdb-4959-a3ec-4c95e614aaf9]<https://secure-web.cisco.com/1NtHyStrjuOSWOO5EbcV14g1jIPuoLRF1sxsbaI79RQ5Jg…> Book time to meet with me<https://secure-web.cisco.com/1NtHyStrjuOSWOO5EbcV14g1jIPuoLRF1sxsbaI79RQ5Jg…>

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mri_segstats for lobar intensity values
by Julie Ottoy 11 Oct '24

11 Oct '24

External Email - Use Caution Hi Freesurfer team, I want to calculate the average PET intensity values per lobe. I want to use the lobar annotations as outlined here in 'lobe mapping': https://secure-web.cisco.com/1Opn2TyIP5_MF5tP6PRtaju8QtoITdCtzrmIlxZvYGO1bU… My PET images are volumetric in T1w MRI space. I have successfully created my lobes following this command: mri_annotation2label --subject $session --hemi lh --lobesStrict lobes However I'm getting an error with my next command: mri_segstats --annot $session/label/lh.lobes.annot --i $session/pet_surf/SUVR/SUVR_T1space.nii.gz --sum lh.pet_lobar.sum It is reading in the white surface, because I get this error: error: MRISread($path/$session/label/rh.lobes.annot/surf/--i.white): could not open file How should I run this command when reading from the volumetric PET image? Thank you, Julie

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Re: [Freesurfer] Error while opening Freeview on Linux
by fsbuild 11 Oct '24

11 Oct '24

External Email - Use Caution Try downloading and installing the freesurfer .deb or.rpm linux package installer that matches your OS .. from,https://secure-web.cisco.com/1Me3-1hl0gfMcAF2vBsI1JUBKuzDpNWmT5AWDIQZn… For example, on Rocky8 linux (uses RedHat lkie .rpm files),  install the .rpm file from where you downloaded it with, e.g., $ sudo yum install ./freesurfer-Rocky8-7.0.0-dev.x86_64.rpm On Ubuntu22 linux, i,e, uses debian like .pkg files), install the .deb file from where you downloaded it with,$ sudo apt install ./freesurfer_ubuntu22-7-dev_amd64.deb Those package installers should automatically install any missing libraries on you system like libpng12.so.  Downloading and expanding one of the freesurfer *.tar.gz archives will not do an actual install, i.e. won’t check for or try to install missing libraries on your system needed to run freesurfer. Then setup the freesurfer environment as listed here,https://secure-web.cisco.com/1BELDi9cDpanBzm2iGuNdHAswzIduLFc5gddCoywt… - R. On Oct 11, 2024, at 14:00, Harsh Srivastava <harsh.sriv(a)iitb.ac.in> wrote:        External Email - Use Caution        Dear Freesurfer team,I have Freesurfer installed on Linux. All Freesurfer commands work well, however, I am not able to open freeview. I get this error:freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directoryPlease let me know how it can be resolved.Warm regards,--  Harsh Srivastava (he/him), 23M0132 (2nd year), MTech Biomedical Engineering, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India._______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1Nteb0siX3-eisiJSbMFVKuyiiW1wlCIU90j5qryoeAjXJ…

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Re: [Freesurfer] Difficulty with downloading Tensorflow and using with SynthSeg
by fsbuild 11 Oct '24

11 Oct '24

External Email - Use Caution  You could try downloading and installing one of the freesurfer package installers, i.e.. on Linux the .rpm to .deb file that matches your OS, or on MacOS either the *x86_64*.pkg (Intel Macs) or *arm64*.pkg (Macs with M1, M2, … processors) that matches you machine ...from...https://secure-web.cisco.com/1B-Y6R_reuVQwDKeMGSdl7-e2TzqvCfjXmPbUtNUE3LgEgrgfj-hvlDZ0qydXe5FMyaoau4W867g0jlJCQIwBSi8MQKtA7eag5M53D1u7aaCBRL4MGNd7bZ46ojlcSrj-pSlRW3pPgTjUHpxMdfDMc4ap6wIwAvOxW41t2tivZ-o1EsqSe8i3DT4Q3o-PdHEGdfXUkxghQJz_vxnJziMs4-TnOJR3VhNH0uLGlUjv30Bl8dVBHgxCkGcDE6v7lhqQWG9OA5Ih6V7lbVsjv8KS698gyYmNydlNBGdq75HF5hVYTwC_N45DMPecMCHruJmZ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Fstable%2FThe python provided in the distribution already has packages installed and will automatically run when you type a command that runs a python script, e.g., mri_synthseg, from the command line.  Prior to that you need to setup the freesurfer shell environment as listed here,https://secure-web.cisco.com/14OSIP22yq-rfoLg4l3V2OcIYvWi4b3IkHZ6noxLG… - R. On Oct 11, 2024, at 13:53, Patel, Ronit <Ronit.Patel(a)pennmedicine.upenn.edu> wrote:        External Email - Use Caution        Hi Freesurfer Support, I hope all is well. I am hoping to download TensorFlow to utilize SynthSeg on my MRI scans, but there appears to be a strange problem when I try to download it. While I do have the correct version of python and numpy, it continues to say the correct version is unavailable and prevents TensorFlow from downloading.  At the same time, when I try to run synthseg and input the mri_synthseg function, the error I always get is 'Illegal Instruction: 4'. I am unsure what this means, as the input and output is clearly specified when I try this method. I had assumed it was simply because TensorFlow was not installed, but I was told it may be something else by my colleagues.  I greatly appreciate any help that can be provided! Sincerely,Ronit Ronit PatelClinical Research AssistantUniversity of Pennsylvania Department of Neurology | TBI Research Initiative <Screenshot 2024-10-11 at 1.45.56 PM.png>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Error while opening Freeview on Linux
by Harsh Srivastava 11 Oct '24

11 Oct '24

External Email - Use Caution Dear Freesurfer team, I have Freesurfer installed on Linux. All Freesurfer commands work well, however, I am not able to open freeview. I get this error: _freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory_ Please let me know how it can be resolved. Warm regards, -- Harsh Srivastava (he/him), 23M0132 (2nd year), MTech Biomedical Engineering, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India.

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Difficulty with downloading Tensorflow and using with SynthSeg
by Patel, Ronit 11 Oct '24

11 Oct '24

External Email - Use Caution Hi Freesurfer Support, I hope all is well. I am hoping to download TensorFlow to utilize SynthSeg on my MRI scans, but there appears to be a strange problem when I try to download it. While I do have the correct version of python and numpy, it continues to say the correct version is unavailable and prevents TensorFlow from downloading. At the same time, when I try to run synthseg and input the mri_synthseg function, the error I always get is 'Illegal Instruction: 4'. I am unsure what this means, as the input and output is clearly specified when I try this method. I had assumed it was simply because TensorFlow was not installed, but I was told it may be something else by my colleagues. I greatly appreciate any help that can be provided! Sincerely, Ronit Ronit Patel Clinical Research Assistant University of Pennsylvania Department of Neurology | TBI Research Initiative

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NIH R25 Course : Training in Advanced Statistical Methods in Neuroimaging and Genetics, Salt Lake City, Utah, April 7-18, 2025.
by ROBERT CARY WELSH 11 Oct '24

11 Oct '24

External Email - Use Caution Hi everybody, We are still taking applications for our NIH funded 2025 session of the course, “Training in Advanced Statistical Methods in Neuroimaging and Genetics”. We hope you pass this email on to your local neuroimaging community. The in-person course starts on Monday, April 7th, 2025, finishing on April 18th, 2025 and is held in Salt Lake City, Utah, United States at the University Guest House Conference Center. Our course also includes an ongoing (throughout the year) continuing education portion. Over an intensive 2-weeks, about 8 hours per day, you will experience a balanced mixture of lectures and hands-on computer labs. More information and registration at : neurostatsbootcamp.org<http://secure-web.cisco.com/1dSR9cVnA26HZj9TFTNx2QeK5CzA2Z239Hu-w9rxQ34-TSM…> All students receive a $750 subsidy, reducing the cost from $3000 to $2250. Strictly financial need scholarships are also offered (that offset even more tuition). Tuition includes hotel accommodations at the University Guest House (arrival on April 6 with departure on April 18), breakfast, lunch, day time snacks, three dinners out as a group, and the planned evening activities. All course attendees will arrange for their own transportation to Salt Lake City. The course cost does include a daily pass to the Salt Lake City Trax light rail/commuter system. (Please note that the course instructors' effort is supported by the NIH grant thus avoiding that cost being passed on to the course attendees. This course is strictly not-for-profit.) Because of the limited size and advanced nature of the course, attendance is by application only – please make sure to fully read the website instructions. In general, applicants should be a US citizen, permanent resident, or working with an appointment at a US institution, though we do have the ability to accommodate 3 to 6 individuals that do not meet this criteria. We anticipate the total class size to be between 24 and 30 students. There are opportunities for scholarships which can partially offset hotel accommodations. These are based on true financial need and you will be instructed how to apply if you are admitted to the course. We look forward to seeing you in SLC in 2025! Priority application deadline is Oct 25, 2024; decisions around Dec 13th. Late application deadline is Nov 22, 2024; decisions by Jan 3th, 2025. For more information email us at neurostats(a)g.ucla.edu<mailto:neurostats@g.ucla.edu> Robert and Anna ------------------------------ Robert Welsh, PhD Course Director, Training in Advanced Statistical Methods in Neuroimaging and Genetics rcwelsh(a)g.ucla.edu<mailto:rcwelsh@g.ucla.edu> (preferred) robert.c.welsh(a)utah.edu<mailto:robert.c.welsh@utah.edu> Anna Docherty, PhD Associate Course Director, Training in Advanced Statistical Methods in Neuroimaging and Genetics anna.docherty(a)utah.edu<mailto:anna.docherty@utah.edu> Christina Caldera Course Administrator neurostats(a)g.ucla.edu<mailto:neurostats@g.ucla.edu>

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Re: [Freesurfer] mri_glmfit error: matrix is rank-deficient by 18
by fsbuild 10 Oct '24

10 Oct '24

External Email - Use Caution  I’m not sure it will make a difference, but you could try downloading, installing and running one of the current development builds for the Silicon Mac.  You could try this download link, https://secure-web.cisco.com/1knximumtc7HGhko0zDsKDfS2Nqhp3y3blHXGS-mPKcRQ-… - R. On Oct 4, 2024, at 12:20, Shawn Flanagan <shawn..flanagan(a)rosalindfranklin.edu> wrote:        External Email - Use Caution        Hi FreeSurfer Developers, I am attempting to compute group analysis as described in the FS tutorial and it appears to run but with the following message at the end for each contrast: Writing results   CON-ACLleft     maxvox sig=-2.57471  F=9.30914  at  index 155198 0 0    seed=1728409464 Computing efficiency /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4..13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13..2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18   CON-ACLright     maxvox sig=2.75772  F=10.1304  at  index 31842 0 0    seed=1728409464 Computing efficiency /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18   CON-ACLtar     maxvox sig=2.22177  F=7.75177  at  index 69873 0 0    seed=1728409464 Computing efficiency /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13..2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13..2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx: vnl_qr<T>::solve() : matrix is rank-deficient by 18 mri_glmfit done I have searched the list and no similar errors have been reported. Does anyone have thoughts or insights about this? If it is helpful, I have attached the fsgd file, contrast files, script file, and a representative mri_glmfit log file.  1) FreeSurfer Version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb84602) Platform: Mac Studio M23) Script:  #!/bin/tcsh set study = $argv[1] foreach hemi (lh rh)   foreach smoothness (0 5 10 15 20 25)     foreach meas (volume thickness)         mri_glmfit \         --y ${hemi}.${meas}.${study}.${smoothness}.mgh \         --fsgd FSGD/${study}.fsgd dods \         --C Contrasts/CON-ACLleft.mtx \         --C Contrasts/CON-ACLright.mtx \         --C Contrasts/CON-ACLtar.mtx \         --surf fsaverage ${hemi} \         --cortex \         --glmdir ${hemi}.${meas}.${study}.${smoothness}.glmdir \         --eres-save     end   end end Appreciate your time and advice! Best, Shawn --  Shawn Flanagan, PhDAssociate ProfessorDirector, Human Performance LaboratoryDepartment of Podiatric Medicine and SurgeryDr. William M. Scholl College of Podiatric MedicineNeuroscience ProgramSchool of Graduate and Postdoctoral Studiesshawn.flanagan(a)rosalindfranklin.edu <CON-ACLleft.mtx><CON-ACLright.mtx><CON-ACLtar.mtx><mri_glmfit.log><BBACL.fsgd><runGLMs.sh>_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1UTFsfZM2c36YeGLIQ25Bild7hRzYEEJsr_HuaallFxuHt…

2 1

Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file
by fsbuild 09 Oct '24

09 Oct '24

External Email - Use Caution  Hello Noga, You can download a stable dev build that should have that change from,https://secure-web.cisco.com/1XcEIgMflApxwmjZQJXk88BihZ8JMhKTtQrRQlv37… - R. On Oct 9, 2024, at 12:28, Hoffmann, Malte,PhD <MHOFFMANN(a)mgh.harvard.edu> wrote:Thanks for attaching the files. The transform you have there is in NiftyReg format and needs to be converted to LTA with `lta_convert --inniftyreg temp_trans.lta --outlta out.lta --src temp_moving.nii.gz --trg temp_target.nii.gz` before you can apply it with `mri_convert`. SynthMorph's switch from NiftyReg to LTA format did note make it into FreeSurfer 7.4.1. It'll be in the FreeSurfer dev build, the upcoming 7.5 release, and the latest SynthMorph from the Docker Hub. ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of noga.kertes(a)campus.technion.ac.il <noga.kertes(a)campus.technion.ac.il> Sent: Wednesday, October 9, 2024 11:57 To: Freesurfer support list Subject: Re: [Freesurfer] FreeSurfer -  extract rigid   parameters      from    .lta    file        External Email - Use Caution Sorry, I forgot to attached it. Target, moving, moving_mask and the .lta file are attached Thank you! Noga ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Hoffmann, Malte,PhD <MHOFFMANN(a)mgh.harvard.edu> Sent: Wednesday, October 9, 2024 17:07 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file [You don't often get email from mhoffmann(a)mgh.harvard.edu. Learn why this is important at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1aGYNcgfZMwQslXNnJ7kYnWXxaCWBZ67TmzqCmIgJn25S9… ] I am not sure what happened, but it looks like `mri_convert` doesn't like the shear in your voxel-to-world matrix. Any chance you can share the input images and mask? The LTA didn't make it to my side, as it was likely removed by the mailing list. ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of noga.kertes(a)campus.technion.ac.il <noga.kertes(a)campus.technion.ac.il> Sent: Wednesday, October 9, 2024 03:57 To: Freesurfer support list Subject: Re: [Freesurfer] FreeSurfer - extract rigid    parameters      from    .lta    file        External Email - Use Caution Hi, I want to use mri_synthmorph to rigid register a moving image to a fixed image therefore I ran the following command: mri_synthmorph -m rigid -t temp_trans.lta -o temp_moved.nii.gz temp_moving.nii.gz temp_target.nii.gz The file `temp_trans.lta` is attached. Afterwards, I want to use `temp_trans.lta` to register the mask of the moving image therefore I use mri_convert in the following way: `mri_convert -at temp_trans.lta temp_moving_mask.nii.gz temp_moved_mask.nii.gz -rt nearest` But the following error message appears: reading from temp_moving_mask.nii.gz... WARNING: MRIsetRas2VoxFromMatrix(): voxels sizes are inconsistent   (1.172,1) (1.172,1) (1.5,1) This is probably due to shear in the vox2ras matrix Input Vox2RAS ------ 1.00000   0.00000   0.00000   0.00000; 0.00000   1.00000   0.00000   0.00000; 0.00000   0.00000   1.00000   0.00000; 0.00000   0.00000   0.00000   0.00000; TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) INFO: Reading transformation from file temp_trans.lta... Reading transform with LTAreadEx() error: Cannot allocate memory error: LTAalloc(-240): could not allocate xforms And the temp_moved_mask.nii.gz  is not generated Thanks, Noga ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Hoffmann, Malte,PhD <MHOFFMANN(a)MGH.HARVARD.EDU> Sent: Wednesday, October 9, 2024 03:22 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file [You don't often get email from mhoffmann(a)mgh.harvard.edu. Learn why this is important at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1aGYNcgfZMwQslXNnJ7kYnWXxaCWBZ67TmzqCmIgJn25S9XXs6EJAqJzja2kOD7uNlBBuQvN0R9ni7eLhkLDg4_phMZw1wZFmfB6oXOFQfqmhYk-DKH_k-jtqQgVmS2tlkgCCJrJCiDC8nU2_KR2V7w3babdvZZgRAhijYS0X8cDuTgw7GTW7-MiTzWrXp6nyhnFIOhnSnJNW_KmSvhvxuPt7ACfiaI5p6CDy0N5-Rc4N7FWL8WX7NNg3ZkiPQ-Rowe_EMvqgzR26EmBOwxqYF-QxewJUyZjCsyAcYd0eMFy6xCfrKZ8VoeKjg_cYmfknUI3_cAFFzjp65u04Y9IG-A/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification%26lt;https://secure-web.cisco.com/19NIoews75g1MQJ7WWQgztI5gweAmpQkQi8uHDJfmZXHSP8HUGH7_bvQqUTEoz8xzbjxP56p3EiZLA6ji9SEemJ4O-GthL3LJMbFzgaz4xipjMcvKQwQE-j0FffyMTy9EAFDolsrScpDPxWOpYTQiFyU8ZZAzcLuoHjuTDkEhDocW2_upcuLthXs27wEKw5KgVxqh5bCjcHOs7zgksXz57BO7YzY29NZOYBEryExu7u_IyOhx-0MOuK1Hj1w61Ktfvjv_yjRqi52ZdQnUGByxw05qfod0AjqE1lHOxm19jsfrAMfUbpD2ht3X0DCK28R-AFTKQfi97SC0C_zX8JGIcg/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification><https://secure-web.cisco.com/1Jlfhefm_fgaKLPMvwBU0qMCaEmAbT-kVGoiC9E2P4Fhs9vsfl5tW-whUqKVLxc9rEsqpAy2oz4e8SktwK6JKrI8uJgK8463tPihvarHZ_LNYXlgVNDoeCldyEvlAiZH3OOPesr_UwxnzCDUYVn73j4B9s11cqUd2QejYp6R8HuWljGrp3lFpMwP491SwMJ60-xl9No3zmpS6_HYD-MbVGYFR1zB2TRpgSo7r3DldE3JQcYh7SoYv5sTfbxiTzRCcj0vzzO7MYu0g1G_aaMj3xBM45Zlvds1rkom7tRCoJofWkf7t-yyP7SyA0a0vwZ_n/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification%253Chttps%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F19NIoews75g1MQJ7WWQgztI5gweAmpQkQi8uHDJfmZXHSP8HUGH7_bvQqUTEoz8xzbjxP56p3EiZLA6ji9SEemJ4O-GthL3LJMbFzgaz4xipjMcvKQwQE-j0FffyMTy9EAFDolsrScpDPxWOpYTQiFyU8ZZAzcLuoHjuTDkEhDocW2_upcuLthXs27wEKw5KgVxqh5bCjcHOs7zgksXz57BO7YzY29NZOYBEryExu7u_IyOhx-0MOuK1Hj1w61Ktfvjv_yjRqi52ZdQnUGByxw05qfod0AjqE1lHOxm19jsfrAMfUbpD2ht3X0DCK28R-AFTKQfi97SC0C_zX8JGIcg%252Fhttps%25253A%25252F%25252Faka.ms%25252FLearnAboutSenderIdentification%26data%3D05%257C02%257Cnoga.kertes%2540campus.technion.ac.il%257Ce7c8f8b282d041fcd0c208dce86c1253%257Cf1502c4cee2e411c9715c855f6753b84%257C1%257C0%257C638640798087421907%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C0%257C%257C%257C%26sdata%3DhbEkqPBFqr1ydE1cDiXYGg3HzPem4b9lZVaK4lqicg0%253D%26reserved%3D0%253E> ] Hi Noga, Could you elaborate on the issue you're experiencing with the LTA and send an example? Thanks, Malte ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of noga.kertes(a)campus.technion.ac.il <noga.kertes(a)campus.technion.ac.il> Sent: Tuesday, October 8, 2024 05:06 To: Freesurfer support list Subject: Re: [Freesurfer] FreeSurfer - extract rigid parameters from    .lta    file        External Email - Use Caution Thanks You for the response! Another issue I encountered was with the .lta file that is being generated using mri_synthmorph. I want to use the .lta file with mri_convert to transform some another image with the same transform. However, the .lta file that is being generated by mri_synthmorph contain only the transformation without any other imformation (like the .lta file that mri_robust_register generate) The command I ran: mri_synthmorph -m rigid -t temp_trans.lta -o temp_moved.nii.gz temp_moving.nii.gz temp_target.nii.gz Thanks! Noga ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve(a)mgh.harvard.edu> Sent: Tuesday, October 1, 2024 17:12 To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file You don't often get email from dgreve(a)mgh.harvard.edu. Learn why this is important<MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1HvZ3tfDVTBTHYJC9wnYNUaCWBxCPEh_yB5HQNB2JSWlD8… Yes, 3 translation, then 3 rotation, then 3 scale, then 3 shear The translations depend upon the coordinate system, so they are kind of arbitrary; they are simply the last column of the matrix in the LTA On 10/1/2024 4:19 AM, noga.kertes@campus.technion.ac.il<mailto:noga.kertes@campus.technion.ac.il> wrote:        External Email - Use Caution Thanks you for the help! I ran this command and got the following output: -14.7814 8.24088 7.81518 0.998388 4.87218 3.29326 1 1 1 0 -7.45058e-09 -5.58794e-09 What does each number represent? Are the first three numbers representing translations? If so, and if they are supposed to be in millimeters, the values seem excessively high, even though the actual translation appears to be much smaller. However, when inspecting the resulting image, the registration seems to have been successful. Do you have any thoughts on why it could happen? Thanks again, Noga ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@MGH.HARVARD.EDU><mailto:dgreve@MGH.HARVARD.EDU> Sent: Monday, September 30, 2024 17:02 To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FreeSurfer - extract rigid parameters from .lta file You don't often get email from dgreve@mgh.harvard.edu<mailto:dgreve@mgh.harvard.edu>. Learn why this is important<MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1J52q-H-8YrKgC4MraUgYbyuk_pNsWLH07KCbcf3dtM-x3… Use mri_coreg --mat2par file.lta On 9/29/2024 5:48 AM, noga.kertes@campus.technion.ac.il<mailto:noga.kertes@campus.technion.ac.il> wrote:        External Email - Use Caution Hello FreeSurfer Developers, I am using mri_robust_register to register a moving volume to a fixed one. The algorithm outputs the rigid transformation in a .lta file. I need to extract the rigid parameters (3 rotation angles in degrees and 3 translation parameters in millimeters). However, the transformation in the file doesn't seem right, as the translation parameters appear to be very large (I assume the values in the last column of the transformation are in millimeters). The moved image doesn’t seem to translate by more than a few millimeters. Is there a command for converting the .lta file into rotation and translation parameters? If not, could you provide more information on how to manually convert it using the transformation in the .lta file? Freesurfer version: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 Thank you, Noga _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1tJ1ZotcCzZXNlOhoYTRHUGuZIKdF8fY1taI-SUAMMmkCQ… External e-mail, be judicious when opening attachments or links _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1tJ1ZotcCzZXNlOhoYTRHUGuZIKdF8fY1taI-SUAMMmkCQ… External e-mail, be judicious when opening attachments or links _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1tJ1ZotcCzZXNlOhoYTRHUGuZIKdF8fY1taI-SUAMMmkCQ… The 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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1KUFwJKPhB5IOtyzDv63S47hlK9NOCYHnyBt4sraQh1Keh… <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1KUFwJKPhB5IOtyzDv63S47hlK9NOCYHnyBt4sraQh1Keh… . 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External e-mail, be judicious when opening attachments or links _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1tJ1ZotcCzZXNlOhoYTRHUGuZIKdF8fY1taI-SUAMMmkCQ… The 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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1KUFwJKPhB5IOtyzDv63S47hlK9NOCYHnyBt4sraQh1Keh… <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1KUFwJKPhB5IOtyzDv63S47hlK9NOCYHnyBt4sraQh1Keh… . 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. External e-mail, be judicious when opening attachments or links _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1PXqq5_-v5TeLWuEI4_T2b00Ch_pGFyGzqkl1URoXpzUR8…

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FreeSurfer - extract rigid parameters from .lta file
by noga.kertes＠campus.technion.ac.il 09 Oct '24

09 Oct '24

External Email - Use Caution Hello FreeSurfer Developers, I am using mri_robust_register to register a moving volume to a fixed one. The algorithm outputs the rigid transformation in a .lta file. I need to extract the rigid parameters (3 rotation angles in degrees and 3 translation parameters in millimeters). However, the transformation in the file doesn't seem right, as the translation parameters appear to be very large (I assume the values in the last column of the transformation are in millimeters). The moved image doesn’t seem to translate by more than a few millimeters. Is there a command for converting the .lta file into rotation and translation parameters? If not, could you provide more information on how to manually convert it using the transformation in the .lta file? Freesurfer version: freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 Thank you, Noga

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