Re: [Freesurfer] aparc & wm underestimation

2024-03-03 Thread Douglas N. Greve
Can you send pictures of the slices showing the problem? On 3/3/2024 3:18 PM, Stanica, Maria wrote: External Email - Use Caution Hello FS developers, I ran my subjects through skullstripping and recon-all. Everything processed correctly (and exited without errors), except 4 images

Re: [Freesurfer] Freesurfer white matter overestimated

2024-03-03 Thread Douglas N. Greve
Can you include an image with and without the surfaces? Make sure to include slices where you think the white surface extends too far. On 2/28/2024 9:13 AM, Luisa Klahn wrote: External Email - Use Caution Dear Douglas, Please find the nu.mgz screenshot attached. Best, Luisa

Re: [Freesurfer] Is the slice delay of each slice needed for slice time correction with preprocess-sess?

2024-03-03 Thread Douglas N. Greve
Yes, you can use the siemens STC option (ie, -stc siemens) On 2/26/2024 9:02 PM, Maria Hakonen wrote: External Email - Use Caution Dear all, Have I understood correctly that the slice delay of each slice is not needed when performing slice time correction with preprocess-sess? I

[Freesurfer] aparc & wm underestimation

2024-03-03 Thread Stanica, Maria
External Email - Use Caution Hello FS developers, I ran my subjects through skullstripping and recon-all. Everything processed correctly (and exited without errors), except 4 images which have an underestimation in coronal subcortical region. The underestimation is significant