[Freesurfer] segmentation problem

Hello, I'm having some issues with the cortex as seen in the attached picture. I know in the more medial regions I can add control points to the white matter to help the pial line extend further out. However, laterally, I'm not sure how to include that cortex that is left out. Any help would

[Freesurfer] co-regtistering a single subject to fsaverage space

Dear FreeSurfer Community... what is the best approach to co-register a single subject to fsaverage space and for the results to have identical number of vertices and faces as fsaverage??? will it work by specifying a single subject in the make_average_surface command?? in other words is the

[Freesurfer] Alternative Standard Brain

Hi there, Is there a "simple" way to plug in and use your own standard brain instead of the mni in the recon-all process? I am using the new 4.0 version. Thanks in advance! Rachel Rachel Marie Dick Research Assistant/Coordinator Brain Research and Imaging Neurosciences De

[Freesurfer] High Resolution Standard Brain

Hello, I have T1 images at 0.8 x 0.8 x 0.8...Is there a high resolution (0.5-0.8) standard brain that I can co-register my images to in place of Freesurfer's? Also, does anyone know of a standard child/adolescent brain that is in use? Thanks in advance, Rachel Rachel Marie Dick Re

[Freesurfer] Orientation

Hello all, I have been using Freesurfer for quite some time. However, I have run into a problem. I am using a properly oriented input image (just like all others I have used before), but when I go to look at the brainmask.mgz after autorecon1, the image is flipped on the y axis. I have used