Re: [Freesurfer] Question on using thalseg_1.1.h5

2024-04-08 Thread Tregidgo, Henry
External Email - Use Caution Hi Georgios, This isn’t an error that I’ve personally come across before. Would you mind answering a few questions and we’ll see if we can get this running for you. 1. Can I ask which operating system you are running FreeSurfer on? 2. Have you

Re: [Freesurfer] recon-all exits with errors

2024-04-08 Thread Huang, Yujing
It looks like mris_fix_topology for lh hemisphere core dumped. This is from your recon-all.log: “ An extra large defect has been detected... This often happens because cerebellum or dura has not been removed from wm.mgz. This may cause recon-all to run very slowly or crash. if so, see https://su

Re: [Freesurfer] Easyreg > cortical parcels missing after SynthSeg with --parc option ?

2024-04-08 Thread Hoffmann, Malte,PhD
Hi Edward, What did you run exactly, and could you share the image before and after? Thanks, Malte From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of r04458...@ntu.edu.tw Sent: Sunday, April 7, 2024 05:36 To: 'Freesurfer support list' Subject:

Re: [Freesurfer] recon-all exits with errors

2024-04-08 Thread William Graves
External Email - Use Caution That worked beautifully. Thank you Yujing! Best, Will On Apr 8, 2024, at 8:58 AM, Huang, Yujing wrote: It looks like mris_fix_topology for lh hemisphere core dumped. This is from your recon-all.log: “ An extra large defect has been detected... Thi