Freesurfer April 2022

freesurfer@nmr.mgh.harvard.edu

97 participants
155 discussions

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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passcode file
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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passcode
by Aya Ben Abdallah 18 Apr '22

18 Apr '22

External Email - Use Caution hi please send me passcode freesurfer

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Re: [Freesurfer] Passcode
by fsbuild 17 Apr '22

17 Apr '22

External Email - Use Caution It was sent about 30 minutes ago.  You might want to check your junk or email filters if you do not see it. - R. On Apr 17, 2022, at 23:06, Jabeur Mouna <jabeurmouna(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.7z Please!Thank you._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer April 2022