Re: [Freesurfer] QXcb connection error 170 (was Freeview: missing voxels in reconstructed surfaces)

External Email - Use Caution These errors can happen when the remote machine is running Windows or Linux, but it’s a known issue with some X servers that run on Windows. When the X windows (graphics/windowing) software trying to remotely display images (which is not freeview)

Re: [Freesurfer] matlab 2019b and brainstem substructures analysis

External Email - Use Caution Hello Jung, You can try either matlab R2014b or R2019b with the commands below. You should have already set FREESURFER_HOME in your Environment to point to where it is installed …. I will list a default location here for a linux install but what you

Re: [Freesurfer] 7.2.0 CentOS7 and Ubuntu 18.04

External Email - Use Caution Hello Jim, We do post this caveat on the download page, Important Note:When processing a group of subjects for your study, it is essential to process all your subjects with the same version of FreeSurfer, on the same OS platform and vendor, and for

Re: [Freesurfer] Don't find libquadmath.so.0

External Email - Use Caution The freesurfer .deb installer file will try to install any missing system library and/or program dependencies. If you are running on Ubuntu 21, then you could try the Ubuntu 20 installer which you can download

Re: [Freesurfer] Thalamic segmentation error

Dear Alan, How did you install the runtime? Did you follow the instructions in the wiki? Cheers, /Eugenio Juan Eugenio Iglesias www.jeiglesias.com On Oct 18, 2022, at 2:37 PM, Alan Francis mailto:alandarkene...@gmail.com>> wrote: External Email - Use

[Freesurfer] Thalamic segmentation error

External Email - Use Caution Hi Eugenio - Hope all is well. I am running FS 7.2. I have installed the MATLAB Runtime 2014b. However when I run the thalamic segmentation routine I get this error. Please help. Thanks, Alan copernicus:~/IMAGING> segmentThalamicNuclei.sh 973770

[Freesurfer] Resmoothing subjects that have already been standardised to fsaverage space

External Email - Use Caution Hi I have a query about resmoothing subjects after they have already been standardised to fsaverage space. We were thinking of using the normal steps for smoothing as specified below mri_surf2surf --hemi lh \ --s fsaverage \ --sval

Re: [Freesurfer] Freeview: missing voxels in reconstructed surfaces

This appears to be a rendering artifact that happens sometimes with remote display. Are you viewing remotely from a Windows machine? Ruopeng On Oct 18, 2022, at 9:45 AM, Sarah Lavelle mailto:lavel...@tcd.ie>> wrote: External Email - Use Caution Dear Freesurfer, I have an issue when

Re: [Freesurfer] [External]Re: Getting recon-all stats from SynthSeg 2.0 segmentations

External Email - Use Caution Hi Douglas, Thanks for your response. I have a few follow-up questions > If you want recon-all type stats, you can run synthseg storing the output in > subject/mri, then look at the recon-all.log file 1. Should the recon-all.log file be generated

[Freesurfer] 7.2.0 CentOS7 and Ubuntu 18.04

External Email - Use Caution We've made system software upgrades recently and of some our data was run using the FS 7.2.0 CentOS 7 build but on Ubuntu 18.04 servers. The outputs look good and there no output errors. Should these data be rerun? Jim

[Freesurfer] mris_make_surfaces error: MRISedges(): too many faces

External Email - Use Caution Hey FreeSurfer Devs! I’m trying to do a surface reconstruction on a rodent-sized animal (tree shrew). I have a good segmentation of the white matter and have been able to generate reasonable looking orig / smoothwm surfaces. I’m running into an

[Freesurfer] Don't find libquadmath.so.0

External Email - Use Caution I am reinstalling Freesurfer on an offline system. Run Ubuntu 21.10 and has installed Freesurfer 7.3.2 from a tar-ball and have installed tcsh. However, the run stopes with: libquadmath.so.0 cannot open shared library : No such file. How do I solve

[Freesurfer] Freesurfer Virtual Box 7zip file password

External Email - Use Caution Hello everyone, I downloaded the Virtual Box image provided for windows computers. But was unable to extract the 7zip file. I read that I needed to send an e mail to this group. Can anybody help? Cheers. -- Şiyar BAHADIR, MD. Neurosurgery Resident