Freesurfer March 2021

freesurfer@nmr.mgh.harvard.edu

106 participants
144 discussions

Troubleshooting: Soft Failures
by 崔鹏程 18 Mar '21

18 Mar '21

External Email - Use Caution Hi FreeSurfer experts, Recently, I used Fresurfer's recon-all toprocess our own T1 MRI brain volumes which is 0.7 m3 isotropic. For most young brain cases, FS performs very well, the segmention is great. But for almost every elderly brain case, the segmention is inaccurate visibly. The figure is the same slice of T1 data and aseg. mgz , the GM is mislabeled as wm-hypointensities. I found some solutions to this problem. But these solutions all require manual editing, which will take a long time. Is there a way to automatically solve this problem by setting some parameters? Thank you for your attention and your help! Cui

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Which pial surface to trust, with or without -FLAIR option
by Xiaojiang Yang 17 Mar '21

17 Mar '21

External Email - Use Caution Dear FS developers, I have run FS’s recon-all on many cases, with and without -FLAIR options. I found the pial surface results (?h.pial) I obtained without -FLAIR option fit to the original image (subjected/mri/orig.mgz) much better than those with -FLAIR option, at least from my visual judgment. See https://secure-web.cisco.com/1jL9MUfd9oLXR_SVyZl8-wPztrX70T9SJxxJaJElRv5e-D… for one example. I know -FLAIR option was introduced to improve the quality of pial surface segmentation. Now for many cases, my intuition is that -FLAIR option decreases the pial quality. My questions are: - Is this intuition correct? - Should I trust the pial surface that’s obtained with or without -FLAIR option in general? In addition, when I use the -FLAIR option, I sometimes get failed when running recon-all. After I did some manual edits to the brainmask image, and re-run the recon-all: recon-all -autorecon-pial -subjid <subjectID> I can get recon-all successful. But if I run recon-all without -FLAIR option, I can get successful results without needing to manually edit the brainmask image. So my last question is: - Should I just run recon-all without -FLAIR option, or, with -FLAIR option + manual edit + re-run with -autorecon-pial? Which is better? Thank you very much! John

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Difference between V1_exvivo.label and v1.predict.label?
by Lee Subin Kristine 17 Mar '21

17 Mar '21

External Email - Use Caution Dear FreeSurfers, I am wondering what is the difference between V1 labels obtained from V1_exvivo.label and v1.predict.label, and what is more exact? When visualizing resutls from both labels, V1_exvivo.label occupies a larger portion than v1.predict label. Thanks, Kristine

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mri_vol2surf; --projfrac-avg and --projfrac-max
by Horn, Mitchell Jacob 17 Mar '21

17 Mar '21

Dear FS Experts, When using --projfrac-max or --projfrac-avg, how is the “min” component defined? If I specify: --projfrac-max -2 1 0.1 Is the min (-2) simply 2x the thickness at each vertex below/inside the GM/WM boundary? Thanks in advance! Mitch

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Post-doctoral Position in Human Perceptual Neuroscience at NYU
by Wu, Yuan hao 17 Mar '21

17 Mar '21

External Email - Use Caution The Perception and Brain Dynamics Laboratory (PI: Biyu J. He, Ph.D.) at New York University is currently recruiting for a post-doctoral fellow to study neural mechanisms of human perception and the interaction between perceptual and cognitive systems. We are looking for a candidate with independent critical thinking, strong analytical and quantitative skills, and good interpersonal skills. We are especially interested in candidates with experience in using advanced neuroimaging data analyses to test theories in perceptual/cognitive neuroscience, and/or candidates with experience in large-scale computational modeling. Our laboratory is located on the medical campus of New York University in Manhattan, NY, and is affiliated with the Neuroscience Institute, Departments of Neurology, Neuroscience & Physiology, and Radiology. The position is expected to start in fall 2021. We provide competitive salary and benefits that adjust for cost of living in New York City. To apply, please send a CV, a cover letter, a statement of scientific and career goals, and names and contacts of three referees to Prof. Biyu Jade He (email: biyu.jade.he(a)gmail.com<mailto:biyu.jade.he@gmail.com>) with the subject line “post-doctoral application 2021”. --------------------------------- Yuan-hao Wu, Ph.D. Postdoctoral Researcher Neuroscience Institute New York University Langone Medical Center New York, NY 10016 ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =================================

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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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Freesurfer March 2021