My last email seemed to be too big because of the picture, so I try it without the picture....
Dear FreeSurfers,
after having now completed the automatic Freesurfer reconstruction without error message (with Fressurfer Centos X64 v4.5.0 on a Debian Machine version 5.0.4, see my email from yesterday) I realized that the white and pial surfaces were reconstructed very badly (see tiff attached). Searching within the mailing list, I found a case that might be very symilar to my problem. Unfortunatly the discussion aborts at this entry
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11770.html
without offering a solution. Thus, I wanted to ask if you might have any idea what might have caused this problem and how I could fix it?
Thank you very much in advance!
Kind regards
Cindy ___________________________________________________________ WEB.DE DSL ab 19,99 Euro/Monat. Bis zu 150,- Euro Startguthaben und 50,- Euro Geldprämie inklusive! https://freundschaftswerbung.web.de
I guess you should send to the mailing list your recon-all.log
-- Sent via iPhone iOS4
Em 25/06/2010, às 05:40, Cindy Eckart cindy.eckart@web.de escreveu:
My last email seemed to be too big because of the picture, so I try it without the picture....
Dear FreeSurfers,
after having now completed the automatic Freesurfer reconstruction without error message (with Fressurfer Centos X64 v4.5.0 on a Debian Machine version 5.0.4, see my email from yesterday) I realized that the white and pial surfaces were reconstructed very badly (see tiff attached). Searching within the mailing list, I found a case that might be very symilar to my problem. Unfortunatly the discussion aborts at this entry
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11770.html
without offering a solution. Thus, I wanted to ask if you might have any idea what might have caused this problem and how I could fix it?
Thank you very much in advance!
Kind regards
Cindy ___________________________________________________________ WEB.DE DSL ab 19,99 Euro/Monat. Bis zu 150,- Euro Startguthaben und 50,- Euro Geldprämie inklusive! https://freundschaftswerbung.web.de _______________________________________________ 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 Cindy,
it's hard to say without knowing what the strange surfaces looked like. Were they cut off? That would probably mean the skull stripping, or the topology fixing. Does the wm.mgz look correct? How about the aseg?
cheers Bruce On Fri, 25 Jun 2010, Cindy Eckart wrote:
My last email seemed to be too big because of the picture, so I try it without the picture....
Dear FreeSurfers,
after having now completed the automatic Freesurfer reconstruction without error message (with Fressurfer Centos X64 v4.5.0 on a Debian Machine version 5.0.4, see my email from yesterday) I realized that the white and pial surfaces were reconstructed very badly (see tiff attached). Searching within the mailing list, I found a case that might be very symilar to my problem. Unfortunatly the discussion aborts at this entry
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11770.html
without offering a solution. Thus, I wanted to ask if you might have any idea what might have caused this problem and how I could fix it?
Thank you very much in advance!
Kind regards
Cindy ___________________________________________________________ WEB.DE DSL ab 19,99 Euro/Monat. Bis zu 150,- Euro Startguthaben und 50,- Euro Geldprämie inklusive! https://freundschaftswerbung.web.de
_______________________________________________ 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.
___________________________________________________________ GRATIS f�r alle WEB.DE Nutzer: Die maxdome Movie-FLAT! Jetzt freischalten unter http://movieflat.web.de
can you check the T1.mgz or brain.mgz and see if the gray matter is still okay in it? That is, check to make sure that the intensity normalization didn't make gray matter look like white matter (compare it to the orig.mgz)
On Fri, 25 Jun 2010, Cindy Eckart wrote:
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.
GRATIS für alle WEB.DE Nutzer: Die maxdome Movie-FLAT! Jetzt freischalten unter http://movieflat.web.de
_______________________________________________ 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.
___________________________________________________________ WEB.DE DSL ab 19,99 Euro/Monat. Bis zu 150,- Euro Startguthaben und 50,- Euro Geldpr�mie inklusive! https://freundschaftswerbung.web.de
Hi Cindy,
can you send us the orig.mgz, nu.mgz brain.mgz, wm.mgz and T1.mgz and we'll take a look?
cheers Bruce On Mon, 28 Jun 2010, Cindy Eckart wrote:
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.
WEB.DE DSL ab 19,99 Euro/Monat. Bis zu 150,- Euro Startguthaben und 50,- Euro Geldprämie inklusive! https://freundschaftswerbung.web.de
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Cindy Eckart -
Pedro Paulo de Magalhães Oliveira Junior