Freesurfer June 2022

freesurfer@nmr.mgh.harvard.edu

84 participants
123 discussions

aseg and surface edit corrections - grey matter surface fails editing
by Helena Pereira 07 Jun '22

07 Jun '22

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to get the new surface pial from the grey-matter. I note that the grey-matter from the temporal areas is not correctly segmented (a few slices are not identified as grey-matter nor with any label) in the aseg file, which influences the surface pial of the grey matter. To correct this, I manually corrected the aseg file expecting to get the correct surface pials. Nevertheless, after running recon-all make -all, the surface remains the same. I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, I've attached an example of my problem, after recon-all make -all. 1) FreeSurfer version: 7.1.1 2) Operating system info: AlmaLinux 8.5, rhel centos fedora 8.5 Thanks in advance, Best regards, Helena Pereira

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VM password
by fabianhuth1＠web.de 07 Jun '22

07 Jun '22

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passcode needed
by Hoptman, Matthew (NKI) 06 Jun '22

06 Jun '22

External Email - Use Caution Hi all, I would like to install the VM for freesurfer: FS_7_2_0_Ubuntu_18_04_06.ova.7z<https://secure-web.cisco.com/1F_QnhlGU_NWZZsaWFeR_lWlnPeUrHiPZmtwTfu_MTEPxh…> Could I please get the pass code? Thanks, Matt Matthew J. Hoptman, PhD Research Scientist IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. ________________________________ IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who was not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation.

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Freeview XDG_runtime_dir not set
by Manuela Dorado Novoa 06 Jun '22

06 Jun '22

External Email - Use Caution Hi Freesurfer team, I am having issues launching freeview from my linux terminal. My freesurfer works fine but when I call freeview it opens but I can't load images, I get an error message in my terminal that says: "QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-manuela.dorado'" I noticed that a user had the same issue but their post <https://secure-web.cisco.com/1z4DOkMcFIGoBCUnrhUReqHSFBlgKt9O5kHhhPm0fLQ5AD…> did not reflect any reply so I do not know what the solution could be to this. Thank you for your help. MANUELA DORADO NOVOA Research Scientist I Buffalo Learning & Memory Lab Dept. of Physiology & Biophysics

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Re: [Freesurfer] Freeview XDG_runtime_dir not set
by fsbuild 06 Jun '22

06 Jun '22

External Email - Use Caution I've seen XDG_RUNTIME not be set/recognized if you are logged in as root/admin user or prefacing your commands with sudo when you run them logged in as a normal or non-privileged user. It might help for us know what operating system you are on, what version of freesurfer you are running and how freesurfer was installed, e.g., did you use the package installer or the tar archive. - R. On Jun 5, 2022, at 21:29, Manuela Dorado Novoa <manuelad(a)uw.edu> wrote:        External Email - Use Caution        Hi Freesurfer team,I am having issues launching freeview from my linux terminal. My freesurfer works fine but when I call freeview it opens but I can't load images, I get an error message in my terminal that says: "QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-manuela.dorado'"I noticed that a user had the same issue but their post did not reflect any reply so I do not know what the solution could be to this. Thank you for your help.MANUELA DORADO NOVOAResearch Scientist IBuffalo Learning & Memory LabDept. of Physiology & Biophysics_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Password for the archive
by fsbuild 05 Jun '22

05 Jun '22

External Email - Use Caution Sending the info to your email shortly. - R. On Jun 5, 2022, at 16:03, sapere-aude(a)tuta.io wrote:        External Email - Use Caution        Hi,I would like to request the password for the archive "FS_7_2_0_Ubuntu_18_04_06.ova.7z".Regards,Sapere-Aude_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] FreeSurfer Expand Archive Passcode
by fsbuild 05 Jun '22

05 Jun '22

External Email - Use Caution Sending the info to your email shortly. - R. On Jun 5, 2022, at 22:42, Berres, Halle <hberres(a)mcw.edu> wrote:        External Email - Use Caution        Hello FreeSurfer Developers,I am attempting to start Ubuntu via VirtualBox on Windows 10, but a passcode is needed to expand the archive for the FS_7_2_0_Ubuntu_18_04_06.ova.7z file. I was hoping to receive this passcode.I appreciate your time,Halle BerresStudent Research AssistantNeurology DepartmentMedical College of Wisconsinhberres@mcw.edu_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Password
by fsbuild 05 Jun '22

05 Jun '22

External Email - Use Caution Sending the info to your email shortly. - R. On Jun 5, 2022, at 07:26, Dom Martin <dal.gon(a)hotmail.com> wrote:        External Email - Use Caution        Good Evening, Could you please send me the password for the Ubuntu VB file?Cheers_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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FreeSurfer Expand Archive Passcode
by Berres, Halle 05 Jun '22

05 Jun '22

External Email - Use Caution Hello FreeSurfer Developers, I am attempting to start Ubuntu via VirtualBox on Windows 10, but a passcode is needed to expand the archive for the FS_7_2_0_Ubuntu_18_04_06.ova.7z file. I was hoping to receive this passcode. I appreciate your time, Halle Berres Student Research Assistant Neurology Department Medical College of Wisconsin hberres(a)mcw.edu

1 0

Password for the archive "FS_7_2_0_Ubuntu_18_04_06.ova.7z".
by sapere-aude＠tuta.io 05 Jun '22

05 Jun '22

External Email - Use Caution Hi, I would like to request the password for the archive "FS_7_2_0_Ubuntu_18_04_06.ova.7z". Regards, Sapere-Aude

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Freesurfer June 2022