Freesurfer December 2020

freesurfer@nmr.mgh.harvard.edu

97 participants
131 discussions

FS longitudinal editing help {Disarmed}
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 30 Dec '20

30 Dec '20

Hi FS developers, I am following the instructions based on: https://secure-web.cisco.com/1R-_BDytOj92bKEInOUa5egJ0tPFR48r8ux5GKBDt1aqhf… I have run the longitudinal pipeline after meticulously editing the cross sectional scans, but see that after quality checking the base and follow up scans, the scans for the base and the longitudinal have their pial and white lines incorrect, as if I never edited the cross sectional scans. Am I right to observe this? Is it appropriate to register the qc'd brainmask/brain.finalsurfs.manedit.mgz from cross sectional to base/longitudinal, and why isn't this done already? I am using FS6dev. Thanks, Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

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Password Request for VirtualBox Ubuntu
by 藤本花音 30 Dec '20

30 Dec '20

External Email - Use Caution Hello FreeSurfer Developers, I am attempting to start Ubuntu via VirtualBox on Windows 10, but Ubuntu requests a login password for the "Developer" account, while installation guide assumes automatic login. Can I ask for the password or is there any other way to successfully start Ubuntu? For the installation and setup, I followed the Windows VM Install & Setup, using the virtual disk image of the VM Ubuntu_710_clone_2.7z (downloaded on Dec 29, 2020). Thank you very much, Kanon Fujimoto -- -------------------------------------------------------------- 藤本花音 TEL:09081307404 E-mail:fujimotokanon86@gmail.com <fujimotokanon86(a)gmail.com>

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Password Request for VirtualBox Ubuntu {Disarmed}
by 藤本花音 30 Dec '20

30 Dec '20

External Email - Use Caution Hello FreeSurfer Developers, I am attempting to start Ubuntu via VirtualBox on Windows 10, but Ubuntu requests a login password for the "Developer" account, while installation guide assumes automatic login. Can I ask for the password or is there any other way to successfully start Ubuntu? For the installation and setup, I followed the Windows VM Install & Setup ( https://secure-web.cisco.com/1eC_ccs3mJEbb-3rf-v-KzSf9Owg9oJCOMbfLpv8nLlo2Q…) using the virtual disk image of the VM Ubuntu_710_clone_2.7z (downloaded on Dec 29, 2020). Thank you very much, Kanon Fujimoto

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Failed to load surface
by 1248742467 29 Dec '20

29 Dec '20

External Email - Use Caution Hello, Fs I can visualize the lh.white lh.sphere lh.pial and so on. But when I visulized the lh.sulc lh.thickness and  other feature files, the error will be displayed as follows: Failed to load surface. Do you know how to visualize these feature files? Looking forward to your reply

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Post-doc position in cognitive neuroscience of spatial navigation in aging at the University of Florida
by Lussier,Desiree 28 Dec '20

28 Dec '20

External Email - Use Caution Dear all, Now recruiting for a post-doctoral researcher to lead studies on cognitive aging that will use real-time fMRI neurofeedback to affect spatial navigation behavior. Details below and attached: The Spatial Cognition and Navigational Neuroscience (SCANN) and Social-Cognitive and Affective Development Laboratories at the University of Florida are hiring a postdoctoral researcher who will lead behavioral and fMRI experiments related to the cognitive neuroscience of spatial navigation in aging and age-related pathology. The position will be co-supervised by Dr. Steven Weisberg and Dr. Natalie Ebner, in collaboration with Dr. Dawn Bowers, to lead behavioral, fMRI, and real-time fMRI neurofeedback experiments related to spatial navigation strategies in adulthood, healthy aging, and Alzheimer's disease-related pathology. The initial position is a 2-year appointment, with subsequent renewals depending on funding availability. Preferred start date is March 1, 2021, but is negotiable. Salary will be paid at the NIH postdoctoral levels. If interested, please contact Steven Weisberg (stevenweisberg(a)ufl.edu<mailto:stevenweisberg@ufl.edu>) and Natalie Ebner (natalie.ebner(a)ufl.edu<mailto:natalie.ebner@ufl.edu>) by email and include a CV and two letters of recommendation. We will accept applications until the position is filled. Required Qualification: PhD in psychology, neuroscience, computer science, biomedical engineering, or a related field. Preferred Qualifications: (1) Experience with virtual environment design (Unity3D, SteamVR, Vive); (2) Experience with fMRI design and analysis (including FSL, Matlab, or Python tools; knowledge of network neuroscience methods is a plus); (3) Experience with cognitive aging and/or Alzheimer's disease; (4) Experience with real-time fMRI neurofeedback. Sent from Mail<https://secure-web.cisco.com/1wXG0GbusmLSLKxRXs5_Sh0MgoYm0FaLbb4KZjF5sMzF11…> for Windows 10

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Erasing WM
by Elana Sarabin 28 Dec '20

28 Dec '20

External Email - Use Caution Hello, I seem to be having two issues when erasing white matter. My first problem is that when I erase white matter and then run my fixes the voxels will show as being erased but the line that distinguishes between white matter and grey matter doesn't re adjust so it doesn't look like any erasing has been done. The command I use after editing the white matter is recon-all -autorecon2-wm -autorecon3 -s subj_ID . My second issue is sometimes when I go to erase white matter there is nothing to erase. Normally where there is white matter the voxels are pink, however, sometimes despite an area being encompassed by the white matter line, there is no colour underneath to erase. Any suggestions to fix these problems would be greatly appreciated. Kindest Regards, Elana

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monkey atlas D99
by Francesca Strappini 23 Dec '20

23 Dec '20

External Email - Use Caution Dear FreeSurfer experts, I'm trying to use the monkey atlas D99. First, I registered the segmentation atlas to the monkey anatomy through bbregister. Now, I need to resample the segmentation to the functional data and extract the mean value from each functional run using the ROIs contained in the segmentation as masks. I suppose I should mri_segstats but I'm not sure how. Any suggestion? Thank you Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

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Please remove me from the email list
by Rutland, John 23 Dec '20

23 Dec '20

External Email - Use Caution

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Re: [Freesurfer] linkedUbuntu 18 virtual disk image {Disarmed}
by fsbuild 23 Dec '20

23 Dec '20

External Email - Use Caution Hello Amice, The info has been sent to your email address. -R. On Dec 23, 2020, at 07:20, C. Teurlings <amicemaries@gmail..com> wrote:        External Email - Use Caution        Dear All, I have exactly the same question as Miguel, could you sent me the password as well?  Thank you and kind regards, Amice ---------- Forwarded message ---------Van: fsbuild <fsbuild@contbay.com>Date: di 15 dec. 2020 om 00:11Subject: Re: [Freesurfer] password for VirtualBoxTo: <freesurfer(a)nmr.mgh.harvard.edu>Cc: <miguelhornero28@gmail.com>         External Email - Use Caution        Hello Miguel, I am sending the password to your private email. - R.On Dec 14, 2020, at 11:40, Miguel Hornero <miguelhornero28(a)gmail.com> wrote:         External Email - Use Caution         Hi!I wanted to try out FreeSurfer and followed the install guide from the FreeSurfer webpage with the linkedUbuntu 18 virtual disk image (FStutorial_clone_2.7z, downloaded 2020-12-14).However, upon startup of the virtual machine, the Ubuntu installation asks me for my user credentials with a preselected "developer" user (seescreenshot attached). According to the install guide, the virtual machine should just boot up to Desktop without requiring a password.Is there a default password I am supposed to use (I tried leaving the password field blank, "freesurfer", "FreeSurfer", "developer" but none of those worked)Thank you in advance,Miguel_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______… mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThis email has been checked for viruses by Avast antivirus software. MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to bewww.avast.com_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Error
by Weerasekera, Akila 23 Dec '20

23 Dec '20

Hello, I sent a few jobs to launchpad (FreeSurfer segmentation) and they exited with an exit=1, this is the error: "ERROR: Label FG1.mpm.vpnl does not exist in SUBJECTS_DIR fsaverage! The fsaverage link probably points to an older freesurfer version" I switched from Fs 6 to FS 7.1.1, how do I change the fsaverage link? Any help is appreciated. Thank you Akila Weerasekera, PhD | Postdoctoral Research Fellow Pain and Neuroinflammation Imaging Laboratory | Ratai Lab for Clinical Spectroscopy | Harvard Medical School | A. A. Martinos Center for Biomedical Imaging | Massachusetts General Hospital | 149 Thirteenth Street, Room 1101 | Charlestown, MA 02129 Mobile: (781) 820 4501 aweerasekera(a)mgh.harvard.edu <mailto:aweerasekera@mgh.harvard.edu> www.nmr.mgh.harvard.edu<http://www.nmr.mgh.harvard.edu> https://scholar.harvard.edu/loggia

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Freesurfer December 2020