[Freesurfer] Using freeview to view (and edit?) talairach registrations

External Email - Use Caution Dear Freesurfer Developers, I'm working with v6.0 on OS Catalina 10.15 and I'm trying to use freeview to check talairach registrations - I've always used tkmedit, so I am running into some issues with the command line for viewing the transform.

Re: [Freesurfer] Recon-all exited with errors

Hi Lily that looks ok I think, although it's hard to tell for sure. The cerebellum shouldn't be included in the surface. Are you sure you have enough ram on your machine? It looked like half of it was in use when you ran recon-all. If you want you can tar and gzip the whole subject dir and

Re: [Freesurfer] FreeSurfer V 7.0 on Centos 8

External Email - Use Caution Is there going to be an "official" Ubuntu build this time around (as in, built and tested in Ubuntu) that isn't the VM? Both the current CentOS and the dev builds continue to have issues (even when compiled from scratch) on my Ubuntu 18.04 servers.

Re: [Freesurfer] Recon-all exited with errors

Hi Dr. Greve, I'm not seeing any glaring issues with inclusion of cerebellum or skull in the surfaces or the mgz. There is a bit of inclusion of the cerebellum in the wm.mgz. However, two things that do seem strange are 1. a portion of the subject's cerebellum is black/missing, 2. in the

Re: [Freesurfer] Recon-all exited with errors

It looks like there might be a very large defect. Try looking at the wm.mgz and brainmask.mgz and the lh.orig.nofix surface to see if there is a large part of skull or cerebellum that is encompassed in the orig.nofix surface On 3/30/2020 11:26 AM, Wang, Lily wrote: Hi All, I have a subject

Re: [Freesurfer] FreeSurfer V 7.0 on Centos 8

External Email - Use Caution Hello Mina, I see from https://www.centosblog.com/centos-eol-dates/ that CentOS 6 will no longer be updated as of 11/2020, and similarly for CentOS 7 in 6/2024. It looks like CentOS 8 was released around September of 2019. While we do not currently

Re: [Freesurfer] Hippocampal Subfield Segmentation Error

HI Alex, Were you pointed to downloading a version of Java when you first tried to run the subfields? If so, did you follow the instructions? Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of "Lab

Re: [Freesurfer] segmentThalamicNuclei.sh - Undefined symbol error, Invalid MEX file

Same as in 2018, I’ll resort to Andrew here :-) Andrew, any ideas? Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of Chester Kang Reply-To: Freesurfer support list Date: Sunday, March 29, 2020 at 18:54 To:

[Freesurfer] FreeSurfer V 7.0 on Centos 8

External Email - Use Caution Greetings FreeSurfer team, I recently upgraded by workstation from Centos 7 to 8.1 as the support for centos 7 will be over soon. I tried installing freesurfer version 7.0 beta 1 but failed due to some unresolved dependencies (tried on a virtual

Re: [Freesurfer] mri_vol2vol

External Email - Use Caution Thanks, but I want to transform my ROI to the average space from my subjects (as created by make_average_subject). How do i get the xfm file to convert my ROI to this average space? /Ben Am Fr., 27. März 2020 um 16:27 Uhr schrieb Douglas N. Greve <

Re: [Freesurfer] libpng12.so.0

External Email - Use Caution I am successfully running FreeView under 18.04 and 19.04, see https://www.xsmd.org/brain/2019/06/19/freeview-libpng12-so-0-missing-under-lubuntu/ Best, Tim > On March 30, 2020 at 10:26 AM Koustav Chatterjee > wrote: > > > External Email

Re: [Freesurfer] libpng12.so.0

External Email - Use Caution You should download lower versions. Ubuntu 16.04.1 LTS. Then only it will work. On Mon, Mar 30, 2020 at 8:01 AM Gonzalo Rojas Costa < gonzalo.rojas.co...@gmail.com> wrote: > External Email - Use Caution > > Hi: > > I tried to use the