Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

Failed to open FS 7.2 on Virtual Machine
by krystaly 20 Apr '22

20 Apr '22

External Email - Use Caution Dear Freesurfer experts, I would like to ask for your advise on how to fix the issue – failed to open VM. Please see below message for your reference: Failed to open a session for the virtual machine FS_7_2_0_ubuntu_18_04_06. Could not open the medium 'C:\Users\chauc\VirtualBox VMs\FS_7_2_0_ubuntu_18_04_06\Snapshots/{d9705495-47cf-4772-8e41-9473c3807781}.vdi'. VD: error VERR_FILE_NOT_FOUND opening image file 'C:\Users\chauc\VirtualBox VMs\FS_7_2_0_ubuntu_18_04_06\Snapshots/{d9705495-47cf-4772-8e41-9473c3807781}.vdi' (VERR_FILE_NOT_FOUND). Result Code: E_FAIL (0x80004005) Component: MediumWrap Interface: IMedium {ad47ad09-787b-44ab-b343-a082a3f2dfb1} I am currently using Windows 10. Would you please kindly advise? Thanks. Best regards, Krystal

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Re: [Freesurfer] Failed to load MRI error
by HYE JUNG YOUN 20 Apr '22

20 Apr '22

External Email - Use Caution Hi, Thanks for your email. I checked the space: And I also made an empty file as you advised. Is there any specific reason to create this new empty file? Should I move the previous recon-all files to this new folder to successfully view them via freeview? I’ll have to get into the previous subjects_dir to select specific MRI file to view unless I move them or re-do the recon-all process to the newly created empty folder, right? Thank you. H From: fsbuild <fsbuild(a)contbay.com <mailto:fsbuild@contbay.com> > Sent: Tuesday, April 19, 2022 12:40 PM To: freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Cc: hyejung7890(a)amc.seoul.kr <mailto:hyejung7890@amc.seoul.kr> Subject: Re: [Freesurfer] Failed to load MRI error You could try checking some things with these commands, $ cd /Applications/freesurfer/7.2.0 $ df -h . Under the column “Avail” it will list how much free disk space you have available. If you are running out of disk space then maybe deleting files you don’t need from your Downloads folder will free up some disk space. (It’s a good idea to keep at least 10G of free space available on your boot drive for MacOS and many people keep 20G - 30G free). See if you can create a new empty file under that location with, $ touch /Applications/freesurfer/7.2.0/subjects/211025/empty_file Without write permission that will fail, and you will probably need to preface the command with “sudo” for it to work and then authenticate with your password. Once your sudo privileges expire, you won’t be able to write files there until you sudo again. So some users create a new subdirectory for subjects in a location where they always have write permission, like their home subdirectory. For example, $ cd $HOME $ mkdir -p subjects/211025 … copy in whatever files you need to that new location and then … $ export SUBJECTS_DIR=$HOME/subjects/211025 You would need to always set that in your environment to override the default SUBEJCTS_DIR location of /Applications/freesurfer/7.2..0/subjects - R. On Apr 18, 2022, at 20:02, HYE JUNG YOUN <hyejung7890(a)amc.seoul.kr <mailto:hyejung7890@amc.seoul.kr> > wrote: External Email - Use Caution Hi Bruce, Do you mean that I should re-do the recon-all process? I tried to re run freeview but it did not work. And Yes I think the files have been overwritten at some point which I am trying to figure out to avoid making the same mistake in the future. However, the question is I have done the exact same process I always did to view mri files on freeview. I have set and used the same subject directory, used the same code, and etc. Here’s the code I used: <image004.png> Which gives me this: <image005.png> Then, when I check mri folder, notice the selected files have been overwritten (I think) and are shown as 0 byte in size. <image006.png> Can you see where I went wrong to overwrite those files? Thank you for your help. Best, H From: <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> freesurfer-bounces(a)nmr.mgh.harvard.edu < <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of Fischl, Bruce Sent: Monday, April 18, 2022 10:35 PM To: Freesurfer support list < <mailto:freesurfer@nmr.mgh.harvard.edu> freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Failed to load MRI error Is this for a subject that you can’t load the wm.mgz for? It doesn’t show any errors. Is the wm.mgz zero length? I don’t see how those things can both be true unless you overwrote it at some point. If you haven’t manually edited this subject maybe you should just rerun it? From: <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> freesurfer-bounces(a)nmr.mgh.harvard.edu < <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of HYE JUNG YOUN Sent: Monday, April 18, 2022 2:44 AM To: 'Freesurfer support list' < <mailto:freesurfer@nmr.mgh.harvard.edu> freesurfer@nmr.mgh..harvard.edu> Subject: Re: [Freesurfer] Failed to load MRI error External Email - Use Caution Hi Bruce, Please find the attached log file. Thanks. H _______________________________________________ Freesurfer mailing list <mailto:Freesurfer@nmr.mgh.harvard.edu> Freesurfer(a)nmr.mgh.harvard.edu <https://secure-web.cisco.com/1lbYaY5CGlZ9b-xDOPo18Ud8lnTXespGfJOrr-fPro1Abj…> https://secure-web.cisco.com/1lbYaY5CGlZ9b-xDOPo18Ud8lnTXespGfJOrr-fPro1Abj…

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Postdoctoral Research Associate at the Institute of Psychology, University of Muenster (WWU), Germany
by Falko Mecklenbrauck 20 Apr '22

20 Apr '22

External Email - Use Caution Dear all, the Department of Biological Psychology (Institute of Psychology) at the University of Muenster (WWU), Germany (https://secure-web.cisco.com/1RZ-xwuqqr0H1V5QPM6K90JjpfVOkoZ1LEvfjmBpM3Zdv6…) is looking for a *Postdoctoral Research Associate* (/Wissenschaftliche/r Mitarbeiter/in/) *(salary level TV-L E13, 100%)* in the field of Cognitive Neuroscience. The duration of this full-time position is three years, with the possibility of an extension. You are invited to join a collaborative research team working on predictive mechanisms in the human brain and behaviour. We are interested in the classification of different types of surprise, predictions, the statistical and declarative knowledge that supports predictions, and the adaptation and learning processes triggered by prediction errors. We use neuroimaging (fMRI) and electrophysiological (EEG, SCR) techniques on healthy subjects and impaired populations (e.g. Parkinson’s disease, stroke, schizophrenia, Asperger autism). The research group has an EEG laboratory with a shielded booth and systems for acquisition of heartbeat and skin conductance data, behavioural laboratories, a laboratory with neuro-navigated transcranial magnetic stimulation (TMS) and controlled access to a 3T research MRI scanner (Magnetom Prisma, Siemens). A 3D video data acquisition system for analysing body and eye movements of group of individuals is currently under construction. We maintain several active collaborations with neurological and psychiatric departments. *Your tasks:* You will develop and conduct your own research project in line with the methodology and research focus of the group. At the moment, we want to advance two topics in particular: the prediction horizon and the cost-benefit functions of prediction. We value your active involvement in the research projects of our doctoral students, supporting and advancing them through scientific exchange and sharing of methodological expertise. As a full-time employee, you will be required to teach four hours per week during the semester. *Our expectations:* Applicants should hold a graduate degree and a completed PhD in neuroscience/psychology/biology or related fields, have already demonstrated a strong motivation for cognitive neuroscience and/or computational neuroscience, and a promising publication list. We are particularly looking for candidates who have advanced skill using fMRI or EEG and a profound knowledge of statistics and programming. Experience with eye tracking and/or SCR would also be a plus. The University of Muenster is an equal opportunity employer and is committed to increasing the proportion of women academics. Consequently, we actively encourage applications by women. Female candidates with equivalent qualifications and academic achievements will be preferentially considered within the framework of the legal possibilities. The University of Muenster is committed to employing more staff with disabilities. Candidates with recognized severe disabilities who have equivalent qualifications are given preference in hiring decisions. Positions can generally be filled as part-time positions if there are no compelling work-related reasons against doing so. To apply, send your CV, a brief description of research interests, list of publications, and the names of two potential references to Prof. Dr. Ricarda Schubotz, rschubotz(a)uni-muenster.de. *Applications will be considered until 1 June 2022.*

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Re: [Freesurfer] Failed to load MRI error
by fsbuild 18 Apr '22

18 Apr '22

External Email - Use Caution You could try checking some things with these commands, $ cd /Applications/freesurfer/7.2.0 $ df -h . Under the column “Avail” it will list how much free disk space you have available.  If you are running out of disk space then maybe deleting files you don’t need from your Downloads folder will free up some disk space.   (It’s a good idea to keep at least 10G of free space available on your boot drive for MacOS and many people keep 20G - 30G free).. See if you can create a new empty file under that location with, $ touch /Applications/freesurfer/7.2.0/subjects/211025/empty_file Without write permission that will fail, and you will probably need to preface the command with “sudo” for it to work and then authenticate with your password.  Once your sudo privileges expire, you won’t be able to write files there until you sudo again.. So some users create a new subdirectory for subjects in a location where they always have write permission, like their home subdirectory.  For example, $ cd $HOME$ mkdir -p subjects/211025 … copy in whatever files you need to that new location and then … $ export SUBJECTS_DIR=$HOME/subjects/211025 You would need to always set that in your environment to override the default SUBEJCTS_DIR location of /Applications/freesurfer/7.2.0/subjects - R. On Apr 18, 2022, at 20:02, HYE JUNG YOUN <hyejung7890(a)amc.seoul.kr> wrote:        External Email - Use Caution        Hi Bruce,  Do you mean that I should re-do the recon-all process? I tried to re run freeview but it did not work. And Yes I  think the files have been overwritten at some point which I am trying to figure out to avoid making the same mistake in the future.  However, the question is I have done the exact same process I always did to view mri files on freeview. I have set and used the same subject directory, used the same code, and etc. Here’s the code I used:<image004..png>Which gives me this:<image005.png> Then, when I check mri folder, notice the selected files have been overwritten (I think) and are shown as 0 byte in size. <image006.png> Can you see where I went wrong to overwrite those files?  Thank you for your help.  Best, HFrom: freesurfer-bounces@nmr.mgh..harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Fischl, BruceSent: Monday, April 18, 2022 10:35 PMTo: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] Failed to load MRI error Is this for a subject that you can’t load the wm.mgz for? It doesn’t show any errors. Is the wm.mgz zero length? I don’t see how those things can both be true unless you overwrote it at some point. If you haven’t manually edited this subject maybe you should just rerun it? From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of HYE JUNG YOUNSent: Monday, April 18, 2022 2:44 AMTo: 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] Failed to load MRI error         External Email - Use Caution        Hi Bruce, Please find the attached log file.  Thanks.  H_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh..harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Passcode freesurfer
by fsbuild 18 Apr '22

18 Apr '22

External Email - Use Caution Sending the info to your email shortly. - R. On Apr 18, 2022, at 04:57, Aya Ben Abdallah <ayabenabdallah17(a)gmail.com> wrote:        External Email - Use Caution          Hello,Can I get the passcode of the file :  FS_7_2_0_ubuntu_18_04_06.ova.7zPlease!Thank you._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Passcode VM Image
by fsbuild 18 Apr '22

18 Apr '22

External Email - Use Caution Sending the info to your email shortly. - R. On Apr 18, 2022, at 15:50, Paul Ockenfuß <paul.ockenfuss(a)awi.de> wrote:       External Email - Use Caution        Hello everyone,I am looking for the password for the freesurfer VM image: FS_7_2_0_ubuntu_18_04_06.ova.7zThank you in advance!Best,Paul_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Passcode VM Image
by Paul Ockenfuß 18 Apr '22

18 Apr '22

External Email - Use Caution Hello everyone, I am looking for the password for the freesurfer VM image: FS_7_2_0_ubuntu_18_04_06.ova.7z Thank you in advance! Best, Paul

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Data formats review - Surface and surface-sampled data
by Christopher Markiewicz 18 Apr '22

18 Apr '22

External Email - Use Caution Hi all, This Friday, April 22, we at Nipy will be hosting a journal club on surface and surface-sampled data formats. We are focused on current interchange formats and possible future directions, which seems like it might be of interest to the FreeSurfer community. The presenters will include Tim Coalson (GIFTI and CIFTI-2), Eric Larson (MNE STC) and Qianqian Fang (JData and BMesh). The time will be 1pm EDT on Friday, Apr 22. Here's an AreWeMeetingYet<https://secure-web.cisco.com/1Bb8JZGH9ZUzqUW-6PN5G8slaCufeP35r48uFYuHJPveUF…> link that will resolve in your time zone. I've also posted the event to the Nipy meetings calendar<https://secure-web.cisco.com/1v8RXZrNTki2T1L9Tiswk64LBLOwW94VIJqhYW5ON3dYKS…>, where we will also post future meetings of this sort. Both include a Zoom link for the call. For further discussion, we have a discourse: https://secure-web.cisco.com/1zfKDCpus1rwQRLZbhGF2mjBZQNW0AJ6rTWAwMjov1a7V9… Best, -- Christopher J. Markiewicz, PhD Center for Reproducible Neuroscience Stanford University

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pass code for FS_7_2_0_Ubuntu_18_04_06.ova.7z
by Chen ZY 18 Apr '22

18 Apr '22

External Email - Use Caution Dear freeesurfer developer, Can you send me the pass code of FS_7_2_0_Ubuntu_18_04_06.ova.7z? Thanke you very much! ZYC

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Passcode freesurfer
by Aya Ben Abdallah 18 Apr '22

18 Apr '22

External Email - Use Caution Hello, Can I get the passcode of the file : FS_7_2_0_ubuntu_18_04_06.ova.7z Please! Thank you.

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