Freesurfer

freesurfer@nmr.mgh.harvard.edu

24 participants
30076 discussions

instalation
by refaat el-said 07 Jun '22

07 Jun '22

External Email - Use Caution Good eveningI downloaded Freesurfer 7.2.0 release in Ubuntu 18.04.06: FS_7_2_0_Ubuntu_18_04_06.ova.7zCan you please send me the password to open the zip file?Refaat

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vertex ID in the contralateral hemisphere
by Marina Fernández 07 Jun '22

07 Jun '22

External Email - Use Caution Dear experts, I would like to know the corresponding vertex in the contralateral hemisphere of a given vertex. Do you have a function that allows me to know it? Thank you very much in advance. Best regards, Marina

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VM Image Passcode
by Victoria Jones 07 Jun '22

07 Jun '22

External Email - Use Caution Hello, I've downloaded the VM image (FS_7_2_0_ubuntu_18_04_06.ova.7z) and need the passcode to expand it. Thank you! Best, Victoria -- *Victoria Jones* *(she/her or they/them)* Doctoral Candidate Department of Chemical Engineering & Materials Science University of Minnesota 717-926-7312

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Custom LUT
by Benjamin Deck 07 Jun '22

07 Jun '22

External Email - Use Caution Responding re: Douglas Greve How exactly did you create the LUT? Eg, in windows using notepad? I'm thinking that there might be some hidden characters in there as the color is wrong. I did notice that your first entry had a value of 5 in the last column; usually this is 0 (not sure what it is for). What happens if you switch the LUT to the default? Do you get reasonable colors (even if the names are wrong)? Reply: I used a custom python script that creates a LUT for each subject. Then I ran dos2unix to ensure the line endings were appropriate. If I load the default FS LUT only 2 ROIs are being labeled. Does this mean that I have an issue with my mri_concat call? Which is: mri_concat --sum --f vols.txt --o sub_vols.mgz Thanks, Ben -- *Benjamin L. Deck* *Doctoral Student* *Applied Cognitive and Brain Sciences* *Department of Psychological and Brain Sciences* *Drexel University* <https://secure-web.cisco.com/1orR-DWFSm7AzAYYcqvCSHmblQoGORO7YzkKJqo0iTu7-y…> Virus-free. http://secure-web.cisco.com/1y12Z5EuR0Thcv3zHQ2WDObPbPtIi3GheXNDJxePf3Sumjp… <https://secure-web.cisco.com/1Q_PewrE8ioL4nGaDXS3HygbqgAIyt7ilGvMJtVbT_Yof-…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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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

1 0

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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