Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

Ask for help
by 楚佳悦 16 Jul '23

16 Jul '23

External Email - Use Caution Dear freesurfer: I don't want to receive external emails from freesurfer. Please help me cancel it! Thank you very much! Best wishes, Jiayue

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Re: [Freesurfer] Password 7zip Ubuntu VM
by m tl 16 Jul '23

16 Jul '23

External Email - Use Caution Hello I hope this email finds you well. I am reaching out to inquire about obtaining the password for the 7zip file associated with the FreeSurfer VirtualBox VM Image. I recently downloaded the image from your website and encountered difficulty accessing its contents due to the password protection. I would be grateful if you could provide me with the necessary password or any instructions on how to obtain it. If there are any additional requirements or steps involved in the process, please let me know, and I will gladly comply with them. Thank you very much for your time and consideration. I look forward to your prompt response and to continuing my research using FreeSurfer. Best regards, Martin

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Freesurfer virtual machine zip password
by José 15 Jul '23

15 Jul '23

External Email - Use Caution Dear Freesurfer mailing list, I just downloaded the ubuntu virtual machine from the freesurfer wiki site, to run freesurfer in windows. However, when unzipping the file I'm asked for a password. Could you please provide me with the password so I can set up the VM and get started with freesurfer? Thanks in advance. Best regards, José Silva

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Freesurfer installation issue
by Ramesh Babu 15 Jul '23

15 Jul '23

External Email - Use Caution Dear Expert, I am trying to install Freesurfer-7.2 .deb package. I had this package earlier, and after formatting my system now, I am trying to install Freesurfer again. But I am facing the following issues. 'freesurfer_7.2.0_amd64.deb' is not a Debian format archive dpkg: error processing archive freesurfer_7.2.0_amd64.deb (--install): dpkg-deb --control subprocess returned error exit status 2 Errors were encountered while processing: freesurfer_7.2.0_amd64.deb Kindly request you to provide a solution to solve this issue. Thanks in advance Ramesh

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Partnership Proposal for Freesurfer Expert Training with Universitas Indonesia
by Pukovisa Prawiroharjo 15 Jul '23

15 Jul '23

External Email - Use Caution Dear Freesurfer Team, Greetings. My name is dr. Pukovisa Prawiroharjo, Sp.S(K), PhD. I am a lecturer and researcher at the Department of Neurology Faculty of Medicine Universitas Indonesia (UI) in Indonesia. I am pleased to inform you that we have been awarded a grant from the UI Incubate program. This program is aimed at promoting growth in university startups that focus on innovative solutions. Our project revolves around the concept of a "Brain Analysis Consultation Service." Our primary goal is to democratize access to predictive analytics for neurodegenerative diseases, making such advanced techniques more available to the general public. The business model is to build a clinic for brain analysis using Freesurfer as a core element of our service. The data given by the MRI will be used to analyze and predict neurodegenerative diseases from our patients. The service we aim to offer will allow patients to consult with us about their Freesurfer results for our team to analyze. Through this, we hope to give them a clearer understanding of their condition, helping predict the trajectory of their neurodegenerative disease more accurately. With this in mind, we would like to invite your team to conduct an expert class on Freesurfer for us. This class will surely boost our understanding of the software and improve the efficiency and effectiveness of our work. We sincerely hope this proposal interests you and aligns with your mission to further knowledge and research in neuroscience. If so, we would be delighted to discuss this further and provide you with any more details you may need. Thank you for considering our proposal. We look forward to the potential of working together for a common goal. Best regards, *Pukovisa Prawiroharjo, M.D., Sp.N, Subsp. NGD (K), PhD* Neurobehavior Consultant, Neurology Specialist Neurology Department, Faculty of Medicine, Universitas Indonesia Chair of Bioethics Cluster IMERI UI Chair of International Policy Div, Board of Development Med Services IDI

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(no subject)
by Pukovisa Prawiroharjo 15 Jul '23

15 Jul '23

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Longitudinal pipeline for FreeSurfer (v7.3.2)
by Jackson Lee 13 Jul '23

13 Jul '23

External Email - Use Caution Hi there, I am hoping to process some longitudinal data using the longitudinal recon-all pipeline available in FreeSurfer: https://secure-web.cisco.com/1Y9uqixBqGC2B0XHSMg2zr4QS96oUVSkkZcMdhRqdEkVD1… Will this pipeline work for FreeSurfer v7.3.2? I cannot see any resources to suggest this is the case. Additionally, I am hoping to conduct some longitudinal analysis using the hippocampal subfield pipeline: https://secure-web.cisco.com/1ILqdmv74otr5LeRS7UQz83p5UDddkh5pv-Luvs5PHnW-6… Would the best course of action be to run recon-all with the longitudinal pipeline first (assuming it is applicable for freeSurfer v7.3.2) and then use the longitudinal command for post-hoc subfield analysis?: segmentHA_T1_long.sh <baseID> [SUBJECTS_DIR] Thank you, Jack

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Basal Ganglia in brain.mgz denoted as WM
by AmirHussein Abdolalizadeh 13 Jul '23

13 Jul '23

External Email - Use Caution Hi Freesurfer users/experts, I accidentally noticed a bizarre behavior -in my opinion- in the FreeSurfer 7.3.2 in which there were large regions of the basal ganglia changed to the WM value (value = 110). Both the original T1 and the brain.mgz screenshots are attached. I haven't tried it with the latest FreeSurfer versions but it seems quite odd. Any comments are appreciated. Best, Amir

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How to segment the visual cortex?
by 周乐晴 13 Jul '23

13 Jul '23

External Email - Use Caution Dear Sir, I can find Visual_v3_d cortex area in FreeSurferColorLUT.txt. but I was confused that where I can find the result file of the visual cortex, or it needs more process?                                                                         Sincerely                                                                        Rosie Zhou  

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Pass code
by yuanyuelunar 13 Jul '23

13 Jul '23

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