Freesurfer

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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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Bigventricles segmentation
by Goodheart, Anna E.,MD, MSC 08 Oct '24

08 Oct '24

Hi FreeSurfer Team, I’m following up on a previous archived thread about trying to fix the segmentation of a scan with very large ventricles. Unfortunately, even with the -bigventricles flag I have a scan in which the posterior lateral ventricles are being included as white matter, and most of the corpus callosum is not being recognized. I tried editing the wm.mgz file without success. I’m using version 7.2.0. I’m happy to share images if helpful, or physically show someone if possible (I’m located in Building 149). Thank you very much! Anna -- Anna Goodheart, MD, MSc Massachusetts General Hospital Department of Neurology

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Freeview error with QT
by Eashrat Muniya 08 Oct '24

08 Oct '24

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 [cid:d7714658-35e6-49b4-aced-eb50fccb03d7]

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NIH funded postdoc position at Child Mind Institute
by Ting Xu 08 Oct '24

08 Oct '24

External Email - Use Caution Child Mind Institute is recruiting a Post Doctoral Fellowship interested in the study of brain structure and function connectome using multimodal neuroimaging techniques. Particular focus will be placed on brain development and cross-species comparison between human and nonhuman primates based on both in vivo and ex vivo MRI imaging data. This is an exempt full-time position (2-3 years) located in our New York headquarters office. Responsibilities: • Development, application, and refinement of analytic approaches for multimodal data, including, but not limited to, functional and structural imaging data. • Preprocess of functional and diffusion MRI datasets in human and nonhuman primates on high-performance computing infrastructures. Develop scientific-quality tests for evaluating the results of cutting-edge brain imaging analysis pipelines • Extend processing techniques used in analyzing brain imaging data and evaluate/compare novel approaches to the state-of-the-art in brain imaging research. • Preparation of manuscripts for publication in peer-reviewed scientific journals and assistance in grant applications in a timely fashion • Preparing data to be shared with research collaborators for experimentation and publication. • Assistance in the supervision of junior research staff (e.g., research assistants, data analysts) Qualifications: • Completed PhD in neuroscience, biomedical engineering, computer science, mathematics, biophysics, neuropsychology or related fields. • Significant prior neuroimaging experience with one or more imaging modalities (fMRI, DTI, MRI, EEG, MEG) • Strong skills in using one or more common functional neuroimaging packages (e.g., AFNI, FSL, FreeSurfer, SPM, etc.) • Strong programming experience in one or more languages (e.g., Python, R, Matlab etc.). • Ability to work as a member of a team as well as independently • Ability to work in a fast-paced environment • Interpersonal skills, as well as written and oral communication • A passion for the Child Mind Institute's mission For more information and apply, please visit: https://secure-web.cisco.com/1m0dzu-E1-XWjr-LWM70d-qHt3lOHzpu3awku2gpiDTwUn… If any questions, please reach out to the PI, Ting Xu (ting.xu(a)childmind.org ).

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

08 Oct '24

External Email - Use Caution 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

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mri_WMHsynthseg error: Killed 9
by Johnson, Ian 07 Oct '24

07 Oct '24

External Email - Use Caution Hello SynthSeg Experts, I am having an issue when I run mri_WMHsynthseg. I have run the program many times before without any issues. I recently closed my terminal while updating my Mac and reopened it to run WMHsynthseg. I have seen from previous posts that the "killed" error is because of an issue with RAM, but I have not run into this error in the past. The error occurs while on the "Pushing data through the CNN" step. There is no error message, terminal just prints "killed: 9" Best, Ian J

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Re: [Freesurfer] error: Bad CPU type in executable WMH FreeSurfer
by fsbuild 07 Oct '24

07 Oct '24

External Email - Use Caution  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@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

error: Bad CPU type in executable WMH FreeSurfer
by Johnson, Ian 07 Oct '24

07 Oct '24

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 Associate Division of Neurocritical Care & Emergency Neurology Yale School of Medicine E: ian.p.johnson(a)yale.edu

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