Dear Bruce and all,
I am trying to fix the scull strip, as it affects ?h.white/?h.pial surfaces. I used -wsthresh with preflooding height of down to 1. It didn't really help much. Therefore, I have two question:
1. Regarding mri_gcut: should I use the default intensity of 110 for white matter mask? How much it is acceptable to change the -T parameter (threshold to value of WM intensity), which default value is 0.36?
2. Regarding manual removing of some voxels: the 'Edit Voxels' tool doesn't seem to work on MacOS. Even though I have a 3-button mouse, when I try click (or click and drag) with any mouse button, nothing happens. What can be wrong?
Thank you, Tetiana.
On Mon, Jan 31, 2011 at 2:00 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Tetiana,
do you mean the bit of skull left over that is misclassified? I wouldn't worry about it unless it causes the ?h.white/?h.pial surfaces to be inaccurate. In general we use the surface-based measures to estimate gray/white morphometry and the aseg for everything else. It is a minor skull strip failure and you could either fix it by manually erasing it from the brainmask.mgz or trying to mess with the watershed/gcut.
cheers Bruce
On Mon, 31 Jan 2011, Tetiana Dadakova wrote:
Dear FreeSurfer users,
I run a <recon-all -all> for one of my subjects. When I check the segmentation, it looks incorrect (see attached picture). What can be the problem? At which step can I change something? Should I do manual correction?
Thank you, Tetiana.
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.