[Freesurfer] segmenThalamicNuclei.sh exited with ERRORS

External Email - Use Caution Dear All, I was using Linux Ubuntu to perform my analysis. However, they were changed with Linux . a couple of days ago. And while the segmentThalamicNuclei.sh command was running before the change, after the change it didn't run and I got the foll

Re: [Freesurfer] segmenThalamicNuclei.sh exited with ERRORS

External Email - Use Caution Hello Behçet, Are you saying the version of the Ubuntu operating system changed and now when you run the same command you get this error about the missing library ? If so, I would check with your system administrators to see if they have installed th

Re: [Freesurfer] segmenThalamicNuclei.sh exited with ERRORS

External Email - Use Caution Hello, Thank you for your valuable reply. I would ask something before checking it. I forgot to say something, even after the computers change "recon-all" is running, just like it runs before the change, however not the segmentThalamicNuclei.sh command

Re: [Freesurfer] segmenThalamicNuclei.sh exited with ERRORS

External Email - Use Caution Behçet, This message is the key: > error while loading shared libraries: libncurses..so.5: cannot open shared > object file: No such file or directory FreeSurfer is looking for a supporting library that it expects your operating system installation

Re: [Freesurfer] segmenThalamicNuclei.sh exited with ERRORS

External Email - Use Caution Dear Bennet, Thank you very much for your help and suggestion. I tried it but it didn't work by indicating the following error "*drodriguez* (the ID that I use to login the computers)* is not in the sudoers file. This incident will be reported. * I thin

[Freesurfer] neurological view on command line

External Email - Use Caution Is there a flag on the command line to turn on neurological view or do I have to turn it on in the GUI. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listi

Re: [Freesurfer] neurological view on command line

I don’t think there’s a command line option for it. I’ll add it. Ruopeng From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Aaron Tanenbaum Sent: Wednesday, February 15, 2023 11:31:11 AM To: Freesurfer Subject: [Freesurfer] neurological view on command

Re: [Freesurfer] segmenThalamicNuclei.sh exited with ERRORS

External Email - Use Caution You can try and piecemeal install missing libraries as Bennet suggested, however that is no guarantee everything you need will be installed.   Installing the .deb package (as I originally suggested) should install that and anything else needed.  And

[Freesurfer] recon-all does not produce ?h.white files

External Email - Use Caution Hello, When I use the command recon-all -autorecon2-wm -subjid ${tmp_subj} -noaseg -xopts-use I only get ?h.white.K and ?h.white.H files, but not the ?h.white file that I need for mri_vol2surf script (so it exits with error). What am I doing wrong?

Re: [Freesurfer] recon-all does not produce ?h.white files

You can find information about recon-all process here https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all Add '-finalsurfs' to you recon-all command line options. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Faraz Yazdanibanafshedaragh Sent: Wednesday, February 15,

[Freesurfer] quick question about using the -seg-wlo flag

External Email - Use Caution Dear FS experts, If I run recon-all with the -seg-wlo flag to include more white matter in the segmentation, and then remove some stray white matter voxels on the output wm.mgz using recon edit, necessitating another run of recon-all, do I again ne

Re: [Freesurfer] -pctsurfcon --fsvol default

External Email - Use Caution Hello again, I would like to ask one last thing. How can the class averages computed from csdbase.y.ocn.dat not match the gamma.mgh values in the cluster? e.g. How can gamma show +29 in a vertex that is part of the significantly positive cluster in an