Freesurfer October 2020

freesurfer@nmr.mgh.harvard.edu

112 participants
180 discussions

Re: [Freesurfer] Developer login on boot
by fsbuild 15 Oct '20

15 Oct '20

External Email - Use Caution Hell Brandon, Sending you the password shortly. - R. On Oct 15, 2020, at 17:41, Parks,Brandon <b.parks(a)ufl.edu> wrote:        External Email - Use Caution        Hello, On booting up Freesurfer v7.1.0 after following the installation guide, a developer account login is prompted, but I do not see any such login in the documentation. What is the password for this login? Thanks_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Developer login on boot
by Parks,Brandon 15 Oct '20

15 Oct '20

External Email - Use Caution Hello, On booting up Freesurfer v7.1.0 after following the installation guide, a developer account login is prompted, but I do not see any such login in the documentation. What is the password for this login? Thanks

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DTI scan process steps for single and multiple shells
by Zeng, Qi 15 Oct '20

15 Oct '20

External Email - Use Caution Hi Freesurfer experts, Are the steps for processing DTI scan the same for single and multiple shells? for example, both via -prep, -bedp, -path. Thank you so much! Best, Qi

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Openings for Postdoc and PhD positions @UConn Brainlens
by Jieyin Feng 15 Oct '20

15 Oct '20

External Email - Use Caution Hi all, *We have openings for Postdoc and PhD positions @ UConn brainLENS Lab:* https://www.brainlens.org/employment *Fumiko Hoeft MD PhD*, Professor of the Departments of Psychological Sciences, Mathematics, Neuroscience and Psychiatry, and Director of the Brain Imaging Research Center at the University of Connecticut in CT US, is now accepting applications of *up to two postdoctoral fellows* to begin sometime between now and the fall of 2021; and/or *two PhD students* to begin in the fall of 2021. Our bicoastal labs at UCSF and UConn have a strong track-record in interdisciplinary research spanning from theory, multimodal neuroimaging (fMRI, dMRI, TMS, MRS, EEG, etc), genetics, machine learning and network approaches, on topics relevant to reading development, dyslexia and resilience/compensatory mechanisms (see on the website). We are particularly interested in candidates who have a background or interest in behavioral genetics, and/or computational (machine learning / network) approaches that can be applied to neuroimaging data; and/or fetal/neonatal neuroimaging. The positions are fully funded, primarily by NIH grants, and by graduate research assistantships (GRAs). There are opportunities to be involved in federally funded and interdisciplinary graduate and postdoctoral training programs (NSF NRT, NIH T32 ). Interested applicants should contact Prof. Fumiko Hoeft @ brainLENS(a)uconn.edu. Best, Jieyin

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Openings for Postdoc and PhD positions @UConn Brainlens {Disarmed}
by Jieyin Feng 15 Oct '20

15 Oct '20

External Email - Use Caution Hi all, *We have openings for Postdoc and PhD positions @ UConn brainLENS Lab: **https://www.brainlens.org/employment <https://www.brainlens.org/employment>* *Fumiko Hoeft MD PhD*, Professor of the Departments of Psychological Sciences, Mathematics, Neuroscience and Psychiatry ( https://psych.uconn.edu/person/fumiko-hoeft/ <https://urldefense.proofpoint.com/v2/url?u=https-3A__nam10.safelinks.protec…>), and Director of the Brain Imaging Research Center (https://birc.uconn.edu <https://urldefense.proofpoint.com/v2/url?u=https-3A__nam10.safelinks.protec…>) at the University of Connecticut in CT US, is now accepting applications of *up to two postdoctoral fellows* to begin sometime between now and the fall of 2021; and/or *two PhD students* to begin in the fall of 2021. Our bicoastal labs at UCSF and UConn (https://www.brainlens.org <https://urldefense.proofpoint.com/v2/url?u=https-3A__nam10.safelinks.protec…>) have a strong track-record in interdisciplinary research spanning from theory, multimodal neuroimaging (fMRI, dMRI, TMS, MRS, EEG, etc), genetics, machine learning and network approaches, on topics relevant to reading development, dyslexia and resilience/compensatory mechanisms (see on the website). We are particularly interested in candidates who have a background or interest in behavioral genetics, and/or computational (machine learning / network) approaches that can be applied to neuroimaging data; and/or fetal/neonatal neuroimaging. The positions are fully funded, primarily by NIH grants, and by graduate research assistantships (GRAs). There are opportunities to be involved in federally funded and interdisciplinary graduate and postdoctoral training programs (NSF NRT https://slac.uconn.edu <https://urldefense.proofpoint.com/v2/url?u=https-3A__nam10.safelinks.protec…>, NIH T32 https://cncct.research.uconn.edu <https://urldefense.proofpoint.com/v2/url?u=https-3A__nam10.safelinks.protec…>). Interested applicants should contact Prof. Fumiko Hoeft @ brainLENS(a)uconn.edu. Best, Jieyin

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Re: [Freesurfer] tk applications failing to launch on VM (Windows)
by fsbuild 14 Oct '20

14 Oct '20

External Email - Use Caution Hello Chris, I think tksurfer has been deprecated as newer versions of freeview can be used instead.  A search thru the freesurfer support mail list for tksurfer brings up several posts including these, [Instead of tksurfer] you can also use tkmeditfv and tksurferfv. They take the tkmedit/tksurfer arguments but run freeview. Freeview does support surface-based ROI drawing. There is a Path/Custom Fill tool button on the left pane. Once it is checked, you should see a bunch of tool buttons similar to what tksurfer had for ROI drawing.  Are you saying that a new install of the VM on your Mac OS machine did not work, as in the Ubuntu OS did not come up in the VM window?   It would be good to know what version of Mac OS you are running.  I would also try and use the latest version of Virtualbox to run on the Mac.   Many people have Macs where they retain having everything on one partition as the machines come out of the box, i.e., they don’t re-partition the disk into multiple partitions to keep a separate/clean boot partition.  So depending upon the size of the built in drive/SSD and what is already occupying space there, I have seen some people run out of space on that single partition after installing the VM.   I would check that you have ~40G of space free on your boot partition if that is where the VM also lives. - R. On Oct 14, 2020, at 11:05, Mcnorgan, Christopher <cpmcnorg(a)buffalo.edu> wrote:        External Email - Use Caution        Hi,I run Freesurfer remotely on Ubuntu, and locally on my Mac, so I’ve not had this problem personally. Two students are working remotely with PCs and are using the VM installation you folks provided (https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads). Both of the students report that the tk applications (tkmedit and I think also tksurfer) fail to launch. At the command line, they run the command, and nothing really happens.One student provided a bit more information:I don't know if this helps, but I ran tksurfer and actually got an error that read out, ' TCL_init failed: Cannot find a usable init.tcl.  This probably means that Tcl wasn't installed properly.  TK_init failed: invalid command name "tcl_find/library” ‘Unfortunately I could not provide any help at all because when I attempt to run the VM on virtualbox on my mac, following the directions at https://surfer.nmr.mgh.harvard.edu/fswiki//VM_67_macThe OS fails to boot, and I only see a series of messages about recovering a journaled filesystem before the VM halts.Most of their learning has involved the CLI so it hasn’t been a huge impediment, but we’re about to run the GLM, and will require these resources to visualize.Thanks,Chris/*********************************************** Chris McNorgan* Assistant Professor* Department of Psychology* University at Buffalo, * The State University of New York* http://ccnlab.buffalo.edu/* Office: 716.645.0236* Lab: 716.645.0222**********************************************/_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail..nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Password
by fsbuild 14 Oct '20

14 Oct '20

External Email - Use Caution Hello Satya, I will send the password to your email directly. - R. On Oct 14, 2020, at 15:49, Satya Kothapalli <satya.au(a)gmail.com> wrote:        External Email - Use Caution        Hi,  I wanted to try out FreeSurfer and  followed the install guide from https://surfer.nmr..mgh.harvard.edu/fswiki/VM_67_win with the linked Ubuntu18 virtual disk image (FStutorial_clone_2.7z, downloaded 2020-09-10). 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? <image.png> Thank you,Regards,Satya. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Password
by Satya Kothapalli 14 Oct '20

14 Oct '20

External Email - Use Caution Hi, I wanted to try out FreeSurfer and followed the install guide from https://surfer.nmr..mgh.harvard.edu/fswiki/VM_67_win with the linked Ubuntu18 virtual disk image (FStutorial_clone_2.7z, downloaded 2020-09-10). 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? [image: image.png] Thank you, Regards, Satya.

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tk applications failing to launch on VM (Windows)
by Mcnorgan, Christopher 14 Oct '20

14 Oct '20

External Email - Use Caution Hi, I run Freesurfer remotely on Ubuntu, and locally on my Mac, so I’ve not had this problem personally. Two students are working remotely with PCs and are using the VM installation you folks provided (https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads) Both of the students report that the tk applications (tkmedit and I think also tksurfer) fail to launch. At the command line, they run the command, and nothing really happens. One student provided a bit more information: I don't know if this helps, but I ran tksurfer and actually got an error that read out, ' TCL_init failed: Cannot find a usable init.tcl. This probably means that Tcl wasn't installed properly. TK_init failed: invalid command name "tcl_find/library” ‘ Unfortunately I could not provide any help at all because when I attempt to run the VM on virtualbox on my mac, following the directions at https://surfer.nmr.mgh.harvard.edu/fswiki//VM_67_mac The OS fails to boot, and I only see a series of messages about recovering a journaled filesystem before the VM halts. Most of their learning has involved the CLI so it hasn’t been a huge impediment, but we’re about to run the GLM, and will require these resources to visualize. Thanks, Chris /********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/

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Postdoc and PhD positions @ BrainLENS Lab w/ Fumiko Hoeft {Disarmed}
by Jieyin Feng 13 Oct '20

13 Oct '20

External Email - Use Caution Hi All, *We have openings for Postdoc and PhD positions @ UConn brainLENS Lab: **https://www.brainlens.org/employment <https://www.brainlens.org/employment>* *Fumiko Hoeft MD PhD*, Professor of the Departments of Psychological Sciences, Mathematics, Neuroscience and Psychiatry ( https://psych.uconn.edu/person/fumiko-hoeft/ <https://urldefense.proofpoint.com/v2/url?u=https-3A__nam10.safelinks.protec…>), and Director of the Brain Imaging Research Center (https://birc.uconn.edu <https://urldefense.proofpoint.com/v2/url?u=https-3A__nam10.safelinks.protec…>) at the University of Connecticut in CT US, is now accepting applications of *up to two postdoctoral fellows* to begin sometime between now and the fall of 2021; and/or *two PhD students* to begin in the fall of 2021. Our bicoastal labs at UCSF and UConn (https://www.brainlens.org <https://urldefense.proofpoint.com/v2/url?u=https-3A__nam10.safelinks.protec…>) have a strong track-record in interdisciplinary research spanning from theory, multimodal neuroimaging (fMRI, dMRI, TMS, MRS, EEG, etc), genetics, machine learning and network approaches, on topics relevant to reading development, dyslexia and resilience/compensatory mechanisms (see on the website). We are particularly interested in candidates who have a background or interest in behavioral genetics, and/or computational (machine learning / network) approaches that can be applied to neuroimaging data; and/or fetal/neonatal neuroimaging. The positions are fully funded, primarily by NIH grants, and by graduate research assistantships (GRAs). There are opportunities to be involved in federally funded and interdisciplinary graduate and postdoctoral training programs (NSF NRT https://slac.uconn.edu <https://urldefense.proofpoint.com/v2/url?u=https-3A__nam10.safelinks.protec…>, NIH T32 https://cncct.research.uconn.edu <https://urldefense.proofpoint.com/v2/url?u=https-3A__nam10.safelinks.protec…>). Interested applicants should contact Prof. Fumiko Hoeft @ brainLENS(a)uconn.edu. Best, Jieyin

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Freesurfer October 2020