Hello Surfers,
we just finished processing our subjects (recon-all -all) with freesurfer version 5.0. In 16 out of 240 subjects i found severe errors: in about 4 of them the surface looks damaged (see attached screenshot1), in the others the skullstrip didn't work, in one case gnawing away some brain (see attached screenshot2), in the others there's too much skull left, the surface seems ok though (screenshot3).
all of the 16 subjects looked fine with version 4.5. is this a known issue? by the way, recon-all reported no errors on any of them. will keep using v4.5 for now.
thanks, andreas
Andreas, Could you send us one of these subjects so we can take a look? Allison
um, ok, everything (about 250mb) or just the 001.mgz? also, where do i send it? i think the mailing list doesn't like big attachments.
thanks andreas
On Mon, 22 Nov 2010 09:30:23 -0500 (EST) Allison Stevens astevens@nmr.mgh.harvard.edu wrote:
Andreas, Could you send us one of these subjects so we can take a look? Allison
--
On Mon, 22 Nov 2010, Andreas Berger wrote:
Hello Surfers,
we just finished processing our subjects (recon-all -all) with freesurfer version 5.0. In 16 out of 240 subjects i found severe errors: in about 4 of them the surface looks damaged (see attached screenshot1), in the others the skullstrip didn't work, in one case gnawing away some brain (see attached screenshot2), in the others there's too much skull left, the surface seems ok though (screenshot3).
all of the 16 subjects looked fine with version 4.5. is this a known issue? by the way, recon-all reported no errors on any of them. will keep using v4.5 for now.
thanks, andreas
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Hi Andreas,
if the surfaces and aseg are ok when the skull strip left stuff around, that should be fine. Not sure what's going on with the other one.Probably a topology problem. If you upload the subject we'll take a look Bruce
On Mon, 22 Nov 2010, Andreas Berger wrote:
Hello Surfers,
we just finished processing our subjects (recon-all -all) with freesurfer version 5.0. In 16 out of 240 subjects i found severe errors: in about 4 of them the surface looks damaged (see attached screenshot1), in the others the skullstrip didn't work, in one case gnawing away some brain (see attached screenshot2), in the others there's too much skull left, the surface seems ok though (screenshot3).
all of the 16 subjects looked fine with version 4.5. is this a known issue? by the way, recon-all reported no errors on any of them. will keep using v4.5 for now.
thanks, andreas
freesurfer@nmr.mgh.harvard.edu