[Freesurfer] Freeview mghRead error

External Email - Use Caution Dear Freesurfer Developers, I have recently switched to a Mac for ease of use and have encountered an error upon trying to view output files from a previous data cohort which were processed on a remote computing server and copied to this Mac's local

Re: [Freesurfer] mris_fix_topology taking ages

External Email - Use Caution Dear Douglas and Bruce, my name is Diana, I am encountering the same issue as Ellen with Fix-topology taking too long. Once we make sense of the origin of the issue (for example, I confirmed that my smoothwm.nofix has a lot of holes), do you know if

Re: [Freesurfer] Tracula registration failure

External Email - Use Caution Hello Anastasia, Not sure if you've had a chance to look at my previous message. I've manually gone through the registrations of all the subjects in my dataset now in Freeview. Although the anatomical scans appear to be complete, the dtifit images

Re: [Freesurfer] mris_fix_topology taking ages

External Email - Use Caution thanks Bruce and Douglas, I was able to see the holes by looking at the surface of ?h.smoothwm.nofix and I found the Freesurfer tutorial on how to correct topological defects. However, as the automatic topology fixer runs during recon-all, how do

Re: [Freesurfer] Recon-all error :Segmentation fault (core dumped)

External Email - Use Caution Yeah,you are right! The prolem has been solved after modifying the 'bc' path. Thank you very much! Have a good day :)! -原始邮件- 发件人:"Douglas N. Greve" 发送时间:2021-06-02 05:52:10 (星期三) 收件人: freesurfer@nmr.mgh.harvard.edu 抄送: 主题: Re:

Re: [Freesurfer] mris_fix_topology taking ages

Hi Diana It’s not the number of defects that matters – it is the large ones. The time it takes to correct them is square in the (convex hull of the) number of vertices in the defect. We have a tutorial on our website about how to find them and fix them. I find it easiest to load the

Re: [Freesurfer] recon-all errors

External Email - Use Caution Doug, Thanks. The one thing I thought of - the FLAIR data were hi-res 3D FLAIR which have a pretty long T2 and not great grey/white contrast (it's an MS project, so mostly acquired for quantifying lesion load). Not sure if this would affect the

[Freesurfer] Time courses and Yeo’s boundaries

External Email - Use Caution Hi, I have two questions please: Hi 1. I’d like to extract the time courses of fMRI data from some selected ROIs. How can I do it? For Yeo’s ROI (splitted atlas) is better to

Re: [Freesurfer] 'help: aparcstats2table'

Hello Dr. Zeynep, Are you running those commands in the directory containing that subject? The script needs the file path to the subject, and absolute paths tend to work better than relative paths. If you have specified these are still getting those errors, please send your full terminal