---------- Forwarded message ---------- From: miracooloz@gmail.com Date: Fri, Dec 2, 2016 at 5:42 PM Subject: Edit to wm.seg.mgz. To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Hello Freesurfer, I replaced wm.seg.mgz from freesurfer with white matter +lesion (called it wm.seg.mgz before replacing) from lesion explorer. Do I run recon-all -autorecon2-wm -autorecon3 -s fsdir ( I know -autorecon2 -wm is used when you make edits to wm.mgz) or should I just run recon-all -autorecon2 -autorecon3-s fsdir? Also, how do I know this change I made was incorporated in FS? Thank you. Best, Paul
Sent from my BlackBerry 10 smartphone.
Hi Paul
you should run autorecon2-wm -autorecon3 so you don't have to rerun the whole aseg stuff. I think that thiw will work as we will see that wm.seg.mgz is different than wm.auto.mgz, but perhaps one of our recon-all experts can commment as I've lost track of the various wm*.mgz files we now generate
cheers Bruce
On Mon, 5 Dec 2016, miracle ozzoude wrote:
---------- Forwarded message ---------- From: miracooloz@gmail.com Date: Fri, Dec 2, 2016 at 5:42 PM Subject: Edit to wm.seg.mgz. To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Hello Freesurfer, I replaced wm.seg.mgz from freesurfer with white matter +lesion (called it wm.seg.mgz before replacing) from lesion explorer. Do I run recon-all -autorecon2-wm -autorecon3 -s fsdir ( I know -autorecon2 -wm is used when you make edits to wm.mgz) or should I just run recon-all -autorecon2 -autorecon3-s fsdir? Also, how do I know this change I made was incorporated in FS? Thank you. Best, Paul
Sent from my BlackBerry 10 smartphone.
Thanks bruce. Any comments from other will also be helpful. Also, other wm.*.mgz that were generated besides wm.seg.mgz include: wm.asegedit.mgz, wm.mgz, and wm.parc.mgz. Best, Paul
On Mon, Dec 5, 2016 at 2:22 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Paul
you should run autorecon2-wm -autorecon3 so you don't have to rerun the whole aseg stuff. I think that thiw will work as we will see that wm.seg.mgz is different than wm.auto.mgz, but perhaps one of our recon-all experts can commment as I've lost track of the various wm*.mgz files we now generate
cheers Bruce
On Mon, 5 Dec 2016, miracle ozzoude wrote:
---------- Forwarded message ---------- From: miracooloz@gmail.com Date: Fri, Dec 2, 2016 at 5:42 PM Subject: Edit to wm.seg.mgz. To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Hello Freesurfer, I replaced wm.seg.mgz from freesurfer with white matter +lesion (called it wm.seg.mgz before replacing) from lesion explorer. Do I run recon-all -autorecon2-wm -autorecon3 -s fsdir ( I know -autorecon2 -wm is used when you make edits to wm.mgz) or should I just run recon-all -autorecon2 -autorecon3-s fsdir? Also, how do I know this change I made was incorporated in FS? Thank you. Best, Paul
Sent from my BlackBerry 10 smartphone.
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