Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30067 discussions

mri_fdr questions
by Finn, Quentin 02 Aug '23

02 Aug '23

External Email - Use Caution Freesurfer experts, I have a surface overlay that represents -log_10(p) for a statistical test that I ran using tools other than mri_glmfit. Does mri_fdr still give accurate fdr thresholds, or does it require some of the additional files generated by mri_glmfit ? thank you! Houston Methodist. Leading Medicine. U.S. News & World Report has named Houston Methodist Hospital the Best Hospital in Texas* for 12 years in a row and recognized us on the Honor Roll seven times. For more than 100 years, we have provided patients with the best — and safest — clinical care, advanced technology and patient experience. That is our promise of leading medicine. *In a two-way tie houstonmethodist.org twitter.com/MethodistHosp facebook.com/HoustonMethodist ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Password request for virtual machine installation
by 深水阳光 02 Aug '23

02 Aug '23

External Email - Use Caution Dear technical personnel: Greeting,  I want to obtain the password so that I can extract the virtual machine file 'FS_7_2_0_ubuntu_18_04_06.ova.zip' Thanks for your time! 深水阳光 hdfghdjghdg(a)foxmail.com  

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Freeview update for FS v6.0.0 on MacOS
by Ha Manh Luu 01 Aug '23

01 Aug '23

External Email - Use Caution Hello FreeSurfer Developers, I have installed FreeSurfer v6.0.0 in my MacOS 12.6.7 but I got Freeview crashed due to PETSC error (which has been fixed in FreeSurfer v7.1.1). For the consistency with my previous work, I do not want to upgrade to Freesurfer V7.x in my MAC. I updated the latest freeview from this website: https://secure-web.cisco.com/1GU54Krzar0viM1rYGXBq6dM7Sopf4ca6PYKueDS2-Ie8D… freesurfer-macOS-darwin_x86_64-dev-freeview.tar.gz 2023-07-29 08:52 37M After updating the Freeview, it works for me but whenever I load a pial surface, I got this error message: error: mincRead(): error reading volume from file /Applications/freesurfer/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc I'm not sure this is serious or just relating to the rendering. Could anyone tell me how to fix this? 1) Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 2) Platform: MacOS Darwin 12.6.7 3) freeview: mincRead(): error reading volume from file /Applications/freesurfer/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc 4) FreeSurferColorLUT.txt: see attached Thanks, Ha

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mris_preproc error: cannot allocate memory
by MANSSOUR Wassima 01 Aug '23

01 Aug '23

External Email - Use Caution Hello FreeSurfer Developers, I'm conducting the Surface Based Group Analysis explained on the tutoriel (https://secure-web.cisco.com/1_YynvwS-dkAnt9HfkAib_JfSy9UZxarfHbzK2t54zb7qC…) but I keep getting the error: "Cannot allocate memory" while running the mris_preproc command. I'm using the data of 355 subjects stored on an external hard drive, and a pc of 23G RAM, but it stops at the 334 subject. I've already tried with a windows and mac of 16G RAM and got the error, so moved to the other one but still getting the same issue. Does anyone have any thoughts on how to trouble-shoot this? or any other alternative solution to run the mris_preproc on all the subjects? FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 Platforme: Debian 3.16.7 Thank you for your help, -- Wassima MANSSOUR Master Student at INSEA Rabat M2SI - Information Systems & Intelligent Systems IMRB intern-France wmanssour(a)insea.ac.ma<mailto:wmanssour@insea.ac.ma> wassima.manssour(a)u-pec.fr<mailto:wassima.manssour@u-pec.fr>

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FreeSurfer Pass Code request
by Lewis, Jeramy 01 Aug '23

01 Aug '23

External Email - Use Caution Greetings, I am a postdoc researcher at Washington University School of Medicine in MR imaging and I'm in the process of installing FreeSurfer. I've reached the point where I need a pass code in order to complete the process. I'm installing on a Windows 10 PC utilizing virtual machine Ubuntu. Any assistance is greatly appreciated, [cid:354939e4-69d8-4702-a37f-63865ecb8c58] Jeramy Lewis, PhD Mallinckrodt Institute of Radiology Washington University School of Medicine 4525 Scott Ave, Room 3224 G St. Louis, MO 63110 mobile: 720-885-2044 e-mail: jeramy(a)wustl.edu<https://secure-web.cisco.com/1WGU-kNnE_nPRi0BEIYhcyX3DsBTEe952B3lsHQ44v8CKN…> ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Open research assistant position at Ohio State University
by Osher, David E. 01 Aug '23

01 Aug '23

External Email - Use Caution The Cognition and Brain Circuitry Laboratory at the Ohio State University is recruiting a research assistant. Primary duties include: conducting neuroscience research on the functional and structural architecture of the human brain, and its role in cognition; programming, running, and analyzing behavioral and brain-imaging experiments using functional magnetic resonance imaging (fMRI), diffusion weighted imaging (DWI), functional connectivity, and behavioral assessments; scoring and coding data; performing statistical analyses using programs such as, MATLAB, Python, and shell scripting; recruiting research participants; maintaining participant databases; developing outreach letters. The position is available for one year with the possibility of extension based on satisfactory performance and availability of funds. Required qualifications include: Bachelor's degree in psychology, neuroscience, cognitive science, computer science, data science, engineering, physics, or math; conduct of social science research is required; experience in a social science research capacity. Highly desired: strong mathematical, statistical, and coding skills (e.g., MATLAB, Python, shell scripting); strong interpersonal skills for interacting with a diverse group of people; strong organizational skills. This position is an excellent opportunity for individuals considering future graduate studies in cognitive and computational neuroscience (every one of our research assistants has successfully been admitted into doctoral programs!). We are seeking an aspiring, self-motivated researcher with strong coding/programming skills who is excited about the brain, cognitive neuroscience, and/or clinical disorders and demonstrates evidence of a serious interest in a career in the field. If you are interested in being considered for this position, please apply online at https://secure-web.cisco.com/1w5xNz1auriZm4kg1U9EtUe0L6lVm2ZwBphpkQCXxqGqpg… and submit a current CV and names of three references. If you have questions about the position or the lab, please contact Dr. David Osher at osher.6(a)osu.edu The Ohio State University is an equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation or identity, national origin, disability status, or protected veteran status. _____________________________________ David E. Osher, Ph.D. Assistant Professor of Psychology The Ohio State University davidosher.com<https://secure-web.cisco.com/1_NpgHtrxMaHWVU2jXBgnwwyBjoLFRWnvVowP4st8hUmPl…>

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MP2RAGE recon-all
by Renew Andrade 01 Aug '23

01 Aug '23

External Email - Use Caution Dear Freesurfer experts: I am having trouble processing with recon-all the file I obtain with presurfer from an MP2RAGE. I don’t know if you have any experience with this. The data I obtained from this https://secure-web.cisco.com/1DoAeFvUHnYto_t5xoLbWcFtbuOwQtmlS1ENoWBmeeHffD… Then I use subject “fsm08un”. I run presurfer as in https://secure-web.cisco.com/1avsRdF8F2mgWmm0OUulJTd3eZF6z9U3j9ezKhlvZi12HC… Then I run recon-all -all -i MPRAGEised_stripped.nii.gz -s fsm08un_MPRAGEised -openmp 8 . . . ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=130,y=125, z=130, r=124102 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1447023003 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1862269955 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -230683617 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1409286624 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 943723776 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 943755195 mri_watershed Error: GLOBAL region of the brain empty ! Darwin Renes-MacBook-Air.local 22.5.0 Darwin Kernel Version 22.5.0: Thu Jun 8 22:22:19 PDT 2023; root:xnu-8796.121.3~7/RELEASE_ARM64_T8103 arm64 recon-all -s fsm08un_MPRAGEised exited with ERRORS at Tue Aug 1 15:40:57 CEST 2023 For more details, see the log file /Applications/freesurfer/7.3.2/subjects/fsm08un_MPRAGEised/scripts/recon-all.log To report a problem, see http://secure-web.cisco.com/1t6IHvg5_DeUlvFUHchBUPV_vqGqDEzbhHz1e6IOApGryD_… If you need the recon-all.log I can send it. Best, Rene Andrade.

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Grey Matter Under Segmentation
by Fatima Abboud 01 Aug '23

01 Aug '23

External Email - Use Caution Hello, I have run FreeSurfer v7.1.1 on the CBRAIN platform and I'm performing QC on the output using the information at the following page: https://secure-web.cisco.com/1oUroAUDs4KHQ2Dm_LBBIXd9QC0wayhlpqddWcLfLv3VRD… It seems though that for almost all of my output, a large portion of the grey matter is not being segmented (please see attached example). I'm not sure if there is a solution to this or if the images will just need to be manually edited to fix this under segmentation. I would greatly appreciate any help or insight. Thank you for your time and help, Fatima

2 1

Longitudinal base error
by Bernis SÜTÇÜBAŞI 01 Aug '23

01 Aug '23

External Email - Use Caution Hello FreeSurfer experts, I'm attempting to follow the longitudinal pipeline, as described on the longitudinal processing tutorial (https://secure-web.cisco.com/1vfvhhwIW62eUqagABMhB_WTdPL428NuWWIuhlLA1wrade…) while creating a within-subject template, I get the following error when I run this command: recon-all -base Subj03_template -tp /Users/bernis/Calismalar/results/Subj03/Subj03_TO/Subj03_TO.nii -tp /Users/bernis/Calismalar/results/Subj03/Subj03_TS/Subj03_TS.nii -all error: mghRead(/Users/bernis/Calismalar/results/Subj03_TS.nii/mri/rawavg.mgz, -1): could not open file Does anyone have any idea how I can resolve this problem? 1) FreeSurfer version: v7.2.0 2) Platform: MacOS Big Sur release 11.6.7 3) recon-all.log: see attached Best regards, [https://secure-web.cisco.com/1FcV40hswwSeEl9bym6WfCPck8eyt1yR9LF87hH45tP9co…]<https://secure-web.cisco.com/1gg-VeXoq9W6DUMYRFkUMcIADYHC7qN0RuiQhEnLA0K-N7…> Bernis Sütçübaşı Assist. Prof. Faculty of Humanities and Social Sciences/Department of Psychology Kerem Aydınlar Kampüsü Kayışdağı Cad. 32 Ataşehir 34752 İstanbul Tel 0 216 500 36 05

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Registration open: FSL Course 2023 - Sept 11th-22nd
by Rezvan Farahibozorg 01 Aug '23

01 Aug '23

External Email - Use Caution Dear all, Registration is now open for FSL Course 2023, which will be held fully online, 11th - 22nd September 2023. You can find details and registration info here: https://secure-web.cisco.com/1cIeIiYp0f3jnyTe1eIgI6q513zNQxlZqiN1b6AYIFmgLg… To strike a balance between broad accessibility and the benefits of in-person interaction, the FSL Course intends to follow an approximately alternating pattern of fully in-person and fully online courses. The only option to attend the course in 2023 will be this online course. Both new and existing users of FSL are welcome on the course, as it aims to cover both basic and more advanced features of FSL! The course covers the theory and practice of functional, structural, diffusion and resting state brain image analysis, with recorded lectures and live practical sessions where attendees learn how to carry out analysis for themselves on real data, with access to experienced tutors available throughout each session. In order to accommodate different time zones, there will be two parallel courses repeating the same content. Each session will consist of a self-paced practical, with guidance available from our expert tutors via Zoom (or equivalent), and all FSL software and course data pre-installed and ready to go on a cloud-enabled virtual desktop. All lectures will be pre-recorded and available as video podcasts, and speakers will be available for questions and discussions. You would need your own computer/laptop/tablet that can do video conferencing and host the remote desktop client, as well as a reasonable internet connection that is good enough for video conferencing. If your institute is at a low/middle income country, you will also be able to request a discount, as instructed on the registration page. We hope to see you at the course! The FSL Course team

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