Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30055 discussions

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…

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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… . 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 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

3 9

Re: [Freesurfer] error: Bad CPU type in executable WMH FreeSurfer
by fsbuild 08 Oct '24

08 Oct '24

External Email - Use Caution OK, thanks for the screenshot.  The terminal output shows the wrong version of freesurfer is installed for your Intel machine.   The banner listed after running the SetUpFreesurfer.sh script lists: ——— freesurfer-macOS-darwin_arm64-dev-20240327-cfc18dd ————— The “darwin_arm64" text means it is a build for one of the Silicon Macs with an M1, M2, M3, etc. processor - which cannot run on a Mac with an Intel processor.  It should instead list "darwin_x86_64". I suggest notifying whoever maintains your lab machines that they need to install the Intel freesurfer .pkg file for any Intel Macs in the lab.  Also that build from March of 2024 is neither a stable release or a newer development build that has gone thru additional testing since March. I would try installing a more recent/stable development build from September of 2024 ...For Intel Macs install,https://secure-web.cisco.com/1MzogCxGrRPYJVbIArUflYtH3GJ_tHDYDVrAKy… Silicon Macs install,https://secure-web.cisco.com/1GZ-150MGTRrpB2zDKb2JZ446yiTuiNhyi9UdQ… - R. On Oct 8, 2024, at 09:14, Johnson, Ian <ian.p.johnson(a)yale.edu> wrote:        External Email - Use Caution        I am having some trouble running those commands, but this is the lab computer "About Mac". Best,Ian JFrom: fsbuild <fsbuild(a)contbay.com> Sent: Monday, October 7, 2024 6:22 PM To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] error: Bad CPU type in executable WMH FreeSurfer Please send along a screenshot of what you see when you select from the upper right hand corner Apple pull down menu —> About this Mac.   You may not have the resources to run some of the python commands. After you setup the fressurfer shell environment, please send along the output from these commands in the terminal window,$ which python<your output>$ python --version<your output> - R. On Oct 7, 2024, at 16:54, Johnson, Ian <ian.p.johnson(a)yale.edu> wrote:        External Email - Use Caution        I am running Sequoia 15.0.1.From: fsbuild <fsbuild(a)contbay.com> Sent: Monday, October 7, 2024 4:36 PM To: freesurfer@nmr.mgh..harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] error: Bad CPU type in executable WMH FreeSurfer  Please let us know the operating system name and revision running on the machine. - R. On Oct 7, 2024, at 16:13, Johnson, Ian <ian.p.johnson(a)yale.edu> wrote:        External Email - Use Caution        Hello Free Surfer Pros, I am trying to run WMH-Synth-Seg on a different machine (2.4GHz Quad-Core Intel Core i5, Intel Iris Plus Graphics 655 1536 MB). I am getting the error message: "line 30: /Applications/freesurfer/dev/python/bin/python3: Bad CPU type in executable" Is this machine too old to run WMH FreeSurfer? Best,Ian Johnson, B.A.Clinical Research AssociateDivision of Neurocritical Care & Emergency NeurologyYale School of MedicineE: ian.p.johnson@yale.edu_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Freeview error with QT
by fsbuild 08 Oct '24

08 Oct '24

External Email - Use Caution  If you installed freesurfer using the .deb or .rpm installers on linux, or the .pkg file on the Mac - then you should have a working Qt setup, e..g., to run freeview.   In particular on linux, if you didn’t use the .rpm or.deb freesurfer package installers then you could be missing system xcb, x11, etc. libraries that are needed for freeview to work with Qt and display images.   The error message you list could be caused by missing system libraries on linux.    But you should not need Qt to run the mri_synthseg python script. If you need a linux installer, you can download the 7.4.1 release .deb and .rpm packages from,https://secure-web.cisco.com/1sN_hNN-x87-4yiZtnv5-EtjWLD52fsmIqh3fH64n… If you don’t mind using a development build, you can download a newer version of freesurfer with the installers from,https://secure-web.cisco.com/1K7FNswoPaZy3t7lSU1dptGdx4qhGJml50ASI_flM… - R. On Oct 8, 2024, at 14:05, Eashrat Muniya <eashrat.muniya(a)acmit.at> wrote:        External Email - Use Caution        Dear all, i am  facing this issue with QT but i am sure i have put all the environment variable for QT correctly. Can someone help me solve this issue? In the end I want to use the Synthseg.  Any help is appreciated!  Thanks!  Regards Eashrat  <Screenshot 2024-10-08 194846.png>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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PVC on DCE MRI
by Shen, Qian 08 Oct '24

08 Oct '24

External Email - Use Caution Hi Dr Greve, We are looking to apply voxelwise PVC on our dynamic contrast-enhanced (DCE) MRI data using methods implemented in PETSurfer. Our DCE MRI data voxelsize =1x1x5mm, and we have used the Patlak model to estimate the transfer coefficient (Ktrans). We are interested in both GM and WM signals. I have a few specific questions regarding the applicability and execution of PVC in our case: 1. Given that the Müller-Gärtner (MG) method assumes constant WM signals and zero CSF signals (which is more suited to PET studies), it seems this may not be optimal for us. Would the RBV or Meltzer (MZ) methods be more appropriate for our DCE MRI data? 2. Should PVC be applied to the 4D dynamic DCE data before dynamic modeling, or directly to the 3D Ktrans map after modeling? 3. Does the point spread function (PSF) of the MRI scanner cause more PVE than the TFE? Additionally, I have one more question about the outputs of the MG PVC method. Could you clarify the role of mgx.gm in the results? Does it the combination of mgx.ctxgm and mgx.subctxgm? Looking forward to your reply. Thank you in advance, Shen

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