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30065 discussions

Extracting brain volume seperately
by 江一川(JIANG Yichuan) 22 Feb '23

22 Feb '23

External Email - Use Caution Dear Experts, How can I extract scalp, skull, csf, gray, and white volume, seperately. Best wishes,Yichuan Jiang

2 3

Re: [Freesurfer] segmenThalamicNuclei.sh exited with ERRORS
by fsbuild 22 Feb '23

22 Feb '23

External Email - Use Caution The best solution (which I think was previously emailed to you) is to have an admin/IT person update your system by doing the following: 1) Copy the link for the freesurfer release install package matching your Ubuntu system, e.g., 7.3.2 freesurfer release on Ubuntu 18, 20, 22, from https://secure-web.cisco.com/1yhwT1AT1siR71m0xkciflHcVEcWiQ2tB105s7o77YZsEO… 2) Download and install it with, $ wget <link copied from the web page above> .... say wget downloaded the file freesurfer_ubuntu18-7.3.2_amd64.deb  .... $ sudo apt-get install ./freesurfer_ubuntu18-7.3.2_amd64.deb That should install libncurses and anything else that's needed automatically.   Trying to piecemeal run commands to install individual system packages like libncurses is asking for more trouble. - R. On 2/22/23 10:54, Iglesias Gonzalez, Juan E. (JIGLESIASGONZALEZ(a)mgh.harvard.edu) wrote: Thanks for the interest in our software! Could you please try running this command from the terminal? sudo apt-get install libncurses5 Cheers, /Eugenio -- Juan Eugenio Iglesias http://secure-web.cisco.com/1KWPEVNu98oFkAEfRE8iBX30sj9pfVOIOS35SyW9UbpZ5sF…   From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of behçet ayyıldız <behcetayyildizz(a)gmail.com> Reply-To: Freesurfer support list <Freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, February 15, 2023 at 05:36 To: "Freesurfer(a)nmr.mgh.harvard.edu" <Freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] segmenThalamicNuclei.sh exited with ERRORS           External Email - Use Caution         Dear All,  I was using Linux Ubuntu to perform my analysis. However, they were changed with Linux ..... a couple of days ago. And while the segmentThalamicNuclei.sh command was running before the change, after the change it didn't run and I got the following message.     drodriguez@causal:/data_august/Daniela/Behcet/Freesurfer_pulvinar_OCD$ segmentThalamicNuclei.sh con_HaJa93 Setting ITK threads to 1 #-------------------------------------------- #@# Thalamic Nuclei processing Wed 15 Feb 2023 11:09:10 AM CET ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is ..:/sw/freesurfer/7.1.1//MCRv84//runtime/glnxa64:/sw/freesurfer/7.1.1//MCRv84//bin/glnxa64:/sw/freesurfer/7.1.1//MCRv84//sys/os/glnxa64:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/sw/freesurfer/7..1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64: /sw/freesurfer/7.1.1//bin/SegmentThalamicNuclei: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory 127 Linux causal.brain.mri.tu-muenchen.de 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux   Do you guys have any idea how to fix it ?   Thanks in advance.   -- Behçet Ayyıldız.. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1ZBVZ5ZFSgmC71czIQz4JvouTmwCxl02_s_J7s7c5bFqzK… 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 https://secure-web.cisco.com/1uQh2dF_tlYNnlReyb0WMNt1TLudo-l-6mkcvTuxmwVyoc… <https://secure-web.cisco.com/12zNRlJSicLgYfTc0OYTVbWFw67p4yuUW1gCGXLvqY60EZLB05C6R2lHBY3J0Gtv4gl3IfQyBofVg0B-vYhH6QczA7kQhDa4JkGtGaFh04VLDRkrWnQtFxs02mz9f0wFGdO4EzYTqNu0tqaOT5h4pEzcJFTFrQDbc6oDpeWWMOBJqPP2uMuJaAGzjknLwZ3kBZuUs0a9FPdL12Zi6u6HM-Dxm59CUSLPCjUVNMHfAa1ty9N70G2NfQyuK_4K9cN3q18FFgIlrG6OnkVxiHBoiEMdh3dd7RmhYAt7XXP9mAOrmpxwdmGE3L31CUXdrtEXE/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline%26gt; . 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.

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SEEKING A DYNAMIC POSTDOC TO INVESTIGATE BRAIN GUT MICROBIOME INTERACTIONS
by Arpana Annie Gupta 22 Feb '23

22 Feb '23

External Email - Use Caution > Dear Freesurfer Community, > > We are looking for a postdoc for this exciting position (2-3 years)- details below > > https://secure-web.cisco.com/1WHR8pdGZ0jD4fwtdRnmuQyzhK93d-z7GyJPzAcC5ZgWly… <https://secure-web.cisco.com/1WHR8pdGZ0jD4fwtdRnmuQyzhK93d-z7GyJPzAcC5ZgWly…> > > > https://secure-web.cisco.com/1hhsXFQO3_XzW7eqkp7i_t1kyJoD1KGKvCjC_NxMu-HJ2U… <https://secure-web.cisco.com/1hhsXFQO3_XzW7eqkp7i_t1kyJoD1KGKvCjC_NxMu-HJ2U…> > > The Goodman-Luskin Microbiome Center in the Division of Digestive Diseases at the University of California Los Angeles is seeking a full time Post-Doctoral Research Fellow for a U54-funded project studying sex-related differences in the brain-gut-microbiome interactions related to visceral pain. This project is focused on the sex-specific effect of gut microbial metabolites, and estrogen levels on ascending arousal pathways originating in distinct brainstem nuclei to change the activity and connectivity of brain networks involved in symptom generation in irritable bowel syndrome. > > As a part of an multidisciplinary research team the fellow will apply advanced computational, neuroimaging, biostatistical, and bioinformatics approaches to assess the interaction between various levels of biological data (e.g., microbiota, metabolites, sex hormones, multimodal brain and brainstem imaging data), clinical variables (symptom severity, widespread pain) and sex. > > There will be opportunities to develop translational and clinical neuroscience research skills (e.g., target discovery, individualized treatment development and biomarker/predictor development), in addition to state-of-the-art analytical skills to address basic and pathophysiological systems biology questions. > > The Goodman-Luskin Microbiome Center is an interdisciplinary, translational Center funded by the National Institutes of Health, and by philanthropic support. The overall research goals of the Center are to better understand the interactions between mind brain and body in health and disease, and to develop novel management strategies for optimal health and for complex chronic disorders. > > Center investigators are conducting clinical, translational and basic research with human populations, using interventions (e.g., diet, cognitive behavioral therapy) alongside deep phenotyping including neuroimaging, mutli-omics profiling (gut microbiome, metabolomics, inflammatory biomarkers, psychosocial and behavioral assessments. You will work directly with Arpana Gupta, PhD and Jennifer Labus, PhD and an array of faculty collaborators across UCLA, and beyond. > > There will be many opportunities to lead high impact publications starting on day one, working with existing rich and unique datasets in addition to creating new ones. Extensive mentorship will be provided to facilitate the transition to an independent research career. > > Duties and Responsibilities: > > The Post-Doctoral Fellow’s responsibilities will include, but are not limited to: > > Develop longitudinal multimodal MRI data analysis streams (functional connectivity, task-based fMRI, diffusion tractography and volumetrics). > Analyze complex multi-omics datasets including imaging, gut microbiome, metabolomics, behavioral and clinical data. > Prepare and submit manuscripts > Mentor graduate and undergraduate students > Be inquisitive, curious and publish! > Required Qualifications: > > Ph.D. in Neuroscience, Neuropsychology, Bioinformatics, Biostatistics, Engineering, Computer Science or a related field. > Strong proficiency and independence with various neuroimaging analysis platforms, multivariate modeling strategies and network connectivity analyses. > Established quantitative and statistical skills, including strong programming skills and comfort with diverse computing environments. Experience with R, Linux, Matlab or Python preferred. > Background in systems/cognitive neuroscience, neuroanatomy and psychological/clinical constructs. > A demonstrated capacity to drive first author publications. > Excellent communication and writing skills, motivated and driven to publish. > Preferred Qualifications: > > Connectomics network analysis and machine learning modeling confer a very significant advantage. > Management/coding of neuroimaging databases (XNAT or others). > > Arpana "Annie" Gupta, Ph.D. > Associate Professor > Director: Neuroimaging Core > G. Oppenheimer Center for Neurobiology of Stress and Resilience > Ingestive Behavior and Obesity Program > UCLA Vatche and Tamar Manoukian Division of Digestive Diseases > David Geffen School of Medicine > UCLA CHS 42-210, 10833 Le Conte Avenue | Los Angeles, CA 90095-7378 > Email: agupta(a)mednet.ucla.edu <mailto:agupta@mednet.ucla.edu> > https://secure-web.cisco.com/1hhsXFQO3_XzW7eqkp7i_t1kyJoD1KGKvCjC_NxMu-HJ2U… <https://secure-web.cisco.com/1hhsXFQO3_XzW7eqkp7i_t1kyJoD1KGKvCjC_NxMu-HJ2U…> > https://secure-web.cisco.com/1hEK-fceY0ve7vGXpNdkOtpqNx7-FslJ199inEtjRniL1s… <https://secure-web.cisco.com/1hEK-fceY0ve7vGXpNdkOtpqNx7-FslJ199inEtjRniL1s…> | Twitter: @AGuptaCNS > > This message (including any attachments) contains confidential > information intended for a specific individual and purpose, and is > protected by law. If you are not the intended recipient, you should > delete this message and any disclosure, copying, or distribution of > this message, or the taking of any action based on it, by you is > strictly prohibited. >

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segmenThalamicNuclei.sh exited with ERRORS
by behçet ayyıldız 22 Feb '23

22 Feb '23

External Email - Use Caution Dear All, I was using Linux Ubuntu to perform my analysis. However, they were changed with Linux ..... a couple of days ago. And while the segmentThalamicNuclei.sh command was running before the change, after the change it didn't run and I got the following message. drodriguez@causal:/data_august/Daniela/Behcet/Freesurfer_pulvinar_OCD$ segmentThalamicNuclei.sh con_HaJa93 Setting ITK threads to 1 #-------------------------------------------- #@# Thalamic Nuclei processing Wed 15 Feb 2023 11:09:10 AM CET ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/sw/freesurfer/7.1.1//MCRv84//runtime/glnxa64:/sw/freesurfer/7.1.1//MCRv84//bin/glnxa64:/sw/freesurfer/7.1.1//MCRv84//sys/os/glnxa64:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64: /sw/freesurfer/7.1.1//bin/SegmentThalamicNuclei: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory 127 Linux causal.brain.mri.tu-muenchen.de 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux Do you guys have any idea how to fix it ? Thanks in advance. -- *Behçet Ayyıldız..*

2 1

How to calculate the mean FA value in the hippocampus
by Lin Cai 22 Feb '23

22 Feb '23

External Email - Use Caution Dear Freesurfer experts, I want to calculate the mean FA value in the hippocampus. Now I have already obtained the FA map for the whole brain in the native space. And I have the aparc+aseg.mgz file after running the recon -all analysis. Does someone know how to use freesurfer functions to obtain the hippocampus mask according to the DK atlas? I want to use this mask to calculate the mean FA value in the hippocampus. Best regards, Lin

2 4

Sulcal depth and Gyrus height
by Giulia Baldassari 22 Feb '23

22 Feb '23

External Email - Use Caution Hi, I want to obtain the gyral height and the sulcal depth for every region of the aparc atlas. I know that in the file lh.sulc the positive values are the depth of the sulcus and the negative one are the height of the gyrus. How can I obtain separately the gyrus height and sulcus depth for the aparc regions? Giulia.

1 0

(no subject)
by Giulia Baldassari 22 Feb '23

22 Feb '23

1 0

quick question about using the -seg-wlo flag
by Harriott, Emily M 21 Feb '23

21 Feb '23

External Email - Use Caution Dear FS experts, If I run recon-all with the -seg-wlo <threshold> flag to include more white matter in the segmentation, and then remove some stray white matter voxels on the output wm.mgz using recon edit, necessitating another run of recon-all, do I again need to include -seg-wlo <threshold> in that next run of recon-all? Any assistance anyone might be able to provide would be greatly appreciated. Thank you so very much! Emily Harriott (doctoral student, Vanderbilt University)

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Password FS_7_2_0_ubuntu_18_04_06.ova
by Luis Antonio Marrufo Franco 20 Feb '23

20 Feb '23

External Email - Use Caution Hello, I would like to request the password for FS_7_2_0_ubuntu_18_04_06.ova.7z in order to install the virtual image and run Freesurfer in Oracle VM. Thanks a lot! Luis Marrufo,Biomedical Engineer at Tecnológico de Monterrey.

1 0

freesurfer installation pass code request
by 심정민 19 Feb '23

19 Feb '23

External Email - Use Caution Hi, I have downloaded the Freesurfer Virtualbox VM images. Would you please send me the pass code? Sincerely,

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