Hi, I'm a freesurfer newbie. I was wondering what constitutes a good grey-white matter segmentation and a good pial surface outline? I've been trying to follow the exercise from the website with respect to the manual intervention, using my own data as an experience, but I don't know how best to decide what is good or bad. Are there any more detailed documentation with respect to troubleshooting? Pardon my ignorance. Thanks!
Hi HweeLing,
sorry, there's not much that we can tell you. Basically the only thing you can do is to visually assess whether the pial surface representation follows what you believe is the true pial surface. I think the wiki has examples of good pial surfaces. If not, we can put some up.
cheers, Bruce
On Tue, 25 Apr 2006, Lee HL wrote:
Hi, I'm a freesurfer newbie. I was wondering what constitutes a good grey-white matter segmentation and a good pial surface outline? I've been trying to follow the exercise from the website with respect to the manual intervention, using my own data as an experience, but I don't know how best to decide what is good or bad. Are there any more detailed documentation with respect to troubleshooting? Pardon my ignorance. Thanks!
Hi Bruce, Thanks for the reply. Specifically, I was not satisfied with the pial outline near the hippocampus region at the coronal section. Part of the hippocampus was "excluded" - outside of the pial outline. How should I edit to include the total hippocampal region? I hope this sounds clear to you. Best regards, HweeLing
On 4/25/06 4:17 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi HweeLing,
sorry, there's not much that we can tell you. Basically the only thing you can do is to visually assess whether the pial surface representation follows what you believe is the true pial surface. I think the wiki has examples of good pial surfaces. If not, we can put some up.
cheers, Bruce
On Tue, 25 Apr 2006, Lee HL wrote:
Hi, I'm a freesurfer newbie. I was wondering what constitutes a good grey-white matter segmentation and a good pial surface outline? I've been trying to follow the exercise from the website with respect to the manual intervention, using my own data as an experience, but I don't know how best to decide what is good or bad. Are there any more detailed documentation with respect to troubleshooting? Pardon my ignorance. Thanks!
Hi HweeLing,
no, the surfaces aren't meant for analyzing the hippocampus, as it's not neocortical and the assumptions of laminar structure will fail there. The aseg.mgz file will have an explicit representation of the hippocampus.
cheers, Bruce
On Tue, 25 Apr 2006, Lee HL wrote:
Hi Bruce, Thanks for the reply. Specifically, I was not satisfied with the pial outline near the hippocampus region at the coronal section. Part of the hippocampus was "excluded" - outside of the pial outline. How should I edit to include the total hippocampal region? I hope this sounds clear to you. Best regards, HweeLing
On 4/25/06 4:17 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi HweeLing,
sorry, there's not much that we can tell you. Basically the only thing you can do is to visually assess whether the pial surface representation follows what you believe is the true pial surface. I think the wiki has examples of good pial surfaces. If not, we can put some up.
cheers, Bruce
On Tue, 25 Apr 2006, Lee HL wrote:
Hi, I'm a freesurfer newbie. I was wondering what constitutes a good grey-white matter segmentation and a good pial surface outline? I've been trying to follow the exercise from the website with respect to the manual intervention, using my own data as an experience, but I don't know how best to decide what is good or bad. Are there any more detailed documentation with respect to troubleshooting? Pardon my ignorance. Thanks!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
On this page there is a link to a snapshot of different quality scans:
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferBeginnersGuide
On Tue, 2006-04-25 at 16:38 +0100, Lee HL wrote:
Hi Bruce, Thanks for the reply. Specifically, I was not satisfied with the pial outline near the hippocampus region at the coronal section. Part of the hippocampus was "excluded" - outside of the pial outline. How should I edit to include the total hippocampal region? I hope this sounds clear to you. Best regards, HweeLing
On 4/25/06 4:17 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi HweeLing,
sorry, there's not much that we can tell you. Basically the only thing you can do is to visually assess whether the pial surface representation follows what you believe is the true pial surface. I think the wiki has examples of good pial surfaces. If not, we can put some up.
cheers, Bruce
On Tue, 25 Apr 2006, Lee HL wrote:
Hi, I'm a freesurfer newbie. I was wondering what constitutes a good grey-white matter segmentation and a good pial surface outline? I've been trying to follow the exercise from the website with respect to the manual intervention, using my own data as an experience, but I don't know how best to decide what is good or bad. Are there any more detailed documentation with respect to troubleshooting? Pardon my ignorance. Thanks!
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Lee HL -
Nick Schmansky