Re: [Freesurfer] WM Edits not updating in batch

2015-06-12 Thread Allison Moreau
Hi Matt, Could you upload that subject to our filedrop and I will take a look. https://gate.nmr.mgh.harvard.edu/filedrop2/ -Allison On 06/12/2015 01:04 AM, Matthew Peverill wrote: (I'm working with Kate on this one) The problem is with the white matter surface. The pial surface is usually

Re: [Freesurfer] WM Edits not updating in batch

2015-06-11 Thread Allison Moreau
Hi Kate, I am having trouble viewing the image. Could you send it as an attachment? When you say main surface, are you referring to the pial or white surface? -Allison On 06/11/2015 03:07 PM, McLaughlin, Katie wrote: Hello Freesurfer Experts, I'm trying to troubleshoot a problem where the ma

[Freesurfer] WM Edits not updating in batch

2015-06-11 Thread McLaughlin, Katie
Hello Freesurfer Experts, I'm trying to troubleshoot a problem where the main surface in our brains is not adjusting following white matter edits using Freesurfer 5.3. To be clear, the procedure here is: 1) Make edits to wm.mgz 2) Run recon-all -3T -mprage -autorecon2-wm -autorecon3 Following