Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30083 discussions

Re: [Freesurfer] Freeview segmentation fault on Mac OS X High Sierra
by fsbuild 17 Mar '21

17 Mar '21

External Email - Use Caution Hello Mikael. I don’t see a crash report/attachment with your posting.  You could just cut and paste the error output from the terminal followed by a cut and paste of the first page of the crash report directly into the actual email - if you like. - R. On Mar 17, 2021, at 08:47, Mikael Novén <mikael.noven(a)ling.lu.se> wrote:        External Email - Use Caution        Dear experts,I recently updated to FreeSurfer 7.1.1 but this caused Freeview to stop working. I can neither use the terminal command ”freeview” or open it through the .app in Finder. I get a ”Segmentation fault: 11”. I attach the crash report below. XQuartz works (I can run ”xclock” and similar programs). Any help with getting Freeview to work is much appreciated. Kind regards,Mikael Novén_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Software Engineering job annoucement at LCN in the Martinos Center (MGH)
by Douglas N. Greve 17 Mar '21

17 Mar '21

The Lab for Computational Neuroimaging (LCN) at the Martinos Center at MGH is seeking a highly motivated software engineer to be responsible for maintaining and testing existing software as well as to help implement new algorithms in C++ and Python. Members of LCN develop software for the analysis of structural, functional, and diffusion MRI and PET of the human brain. LCN is best known for FreeSurfer (surfer.nmr.mgh.harvard.edu) a brain anatomical analysis package that is used by thousands of researchers around the world. LCN is a dynamic and diverse lab composed of members from a wide range of backgrounds. The software engineer will work closely with researchers and other software engineers to build, improve, test, support, and document the software as well as add new features. The successful applicant should be proficient in C++ and Python with basic knowledge of git, unix scripting, and machine learning. More details and requirements as well as job application portal can be found at: https://partners.taleo.net/careersection/ghc/jobdetail.ftl?job=3128985&tz=G… <https://partners.taleo.net/careersection/ghc/jobdetail.ftl?job=3128985&tz=G…> Primary work location: MGH, 13th Street, 149 13th Street, Charlestown 02129 Massachusetts General Hospital is an Equal Opportunity Employer.//By embracing diverse skills, perspectives, and ideas, we choose to lead. Applications from protected veterans and individuals with disabilities are strongly encouraged.

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Freeview segmentation fault on Mac OS X High Sierra
by Mikael Novén 17 Mar '21

17 Mar '21

External Email - Use Caution Dear experts, I recently updated to FreeSurfer 7.1.1 but this caused Freeview to stop working. I can neither use the terminal command ”freeview” or open it through the .app in Finder. I get a ”Segmentation fault: 11”. I attach the crash report below. XQuartz works (I can run ”xclock” and similar programs). Any help with getting Freeview to work is much appreciated. Kind regards, Mikael Novén

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Meylin overlay
by バキット・ムダシル 17 Mar '21

17 Mar '21

External Email - Use Caution Dear freesurfer experts, Is there a way to import the individual surface myelin maps from the human connectome project database to freesurfer and use them as overlays? Or can we create them in freesurfer? Mudathir

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Hypothalamus segmentation output
by Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 17 Mar '21

17 Mar '21

External Email - Use Caution Dear Freesurfer experts, Hope that you all are well and stay safe. I would like some help figuring out the code to open the output for the hypothalamus segmentation (via freeview). Does anyone have this info? I didn't find it on the website. Thank you so much! All the best, Alex

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Re: [Freesurfer] freesurfer install error
by fsbuild 16 Mar '21

16 Mar '21

External Email - Use Caution It reads like you are trying to install on an Ubuntu system, e.g., Ubuntu 18 or Ubuntu 20? On Ubuntu you can try the install command,$ sudo apt install libjpeg62 Also it would be good to know what freesurfer release you are installing, e.g., 7.1.1. Something may not be right with your environment for remote X programs.  I would check you have the DISPLAY environment variable setup in your xshell or xmanager setup.  On my terminal DISPLAY is set to, $ echo $DISPLAY:0 I don’t know how xshell and xmanager setup your X environment, but I would first try running a simple X windows program like xeyes and get that to work (displays a pair of eyes that track the cursor) before running tksurfer, etc. - R. On Mar 16, 2021, at 07:17, 1248742467 <1248742467(a)qq.com> wrote:        External Email - Use Caution        Hello, FsAfter installing FreeSurfer, use tkregister2, tkmedit, tkurfer, and recon all -- help to verify whether the installation is successful. The first and fourth commands are OK, but the second and third commands display the same error: glut: fatal error in tksurfer.bin : could not open display:  localhost:17.0.I use xshell as a terminal, and I have installed xmanager. I used to be able to use it, but now I have problems.And when I use the Freeview command, an error is reported as follows: freeview.bin : error while loading shared libraries:  libjpeg.so .62: cannot open shared object file: No such file or directoryDo you know how to solve the above problems?Looking forward to your reply_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Help
by Murray Howerth 16 Mar '21

16 Mar '21

External Email - Use Caution I am new to this platform and would like some direction as how to obtain adjusted cerebellar volumes, specifically lobular cerebellum structure. With thanks, M

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Aseg missing frontal portions - subcortical okay?
by Laurel Quinlan 16 Mar '21

16 Mar '21

External Email - Use Caution Hi Freesurfer Team, I am checking over the aseg on one of my subjects and notice that there are large portions of cortex missing anteriorly. The omission does not seem to affect any subcortical structures. Do you think that the subcortical values extracted from this subject are okay, even if there is cortex missing? Thanks! Laurel Quinlan Research Specialist Center for Healthy Minds University of Wisconsin-Madison

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Flip image (resize)
by Ramesh Babu 16 Mar '21

16 Mar '21

External Email - Use Caution Dear Experts, The fMRI data, when viewed in SPM, some images have 3x3x4 voxel dimensions and some images have -3x3x4. Should I flip the image (using resize option) so that all images will have the same dimensions? or Should I leave it without flipping? Please give your suggestions. Regards Ramesh

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Absolute volume difference between Freesurfer 6.0 and 7.1
by Lee, Sang Hoon 16 Mar '21

16 Mar '21

External Email - Use Caution I recently installed version 7.1, and I compared absolute volumes with version 6.0, and I realized that there are some significant differences in some brain structures (e.g. Hippocampus and amygdala). In some cases, the differences are more than 7%-14%. I understand that I should not be mixing the version when I process my datasets, but can you let me know what the main reason for the differences is, and how much should I expect? thank you. Sang

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