Hi Amir
I'm not sure I understand the question. You need to acquire them on each subject them same way you acquire your MPRAGE/T1-weighted image. Andre van der Kouwe (ccd) has some sequences you can use on his website if you want guidance on parameters and such.
cheers Bruce
On Fri, 12 Jul 2013, amirhossein manzouri wrote:
Dear Bruce, Would you please explain how and where to acquire FLAIR or T2 images to solve the problem? BR/Amir
On Thu, Jul 11, 2013 at 9:47 PM, ye tian tianye730@gmail.com wrote: Dear Bruce and Doug, Thank you very much!
PS: I searched through my data folder and didn't find T2 images. There goes all my afternoon!
Ye
On Thu, Jul 11, 2013 at 1:29 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: the fix is to acquire a FLAIR or T2 image. What you are seing is the tentorium of the cerebellum which is very difficult to distinguish from cortical gray matter on a T1-weighted image. If you don't have either of those datasets you probably will need to do manual editing Bruce
On Thu, 11 Jul 2013, ye tian wrote: Sorry! The attachments are really showing the same structure, but in different views. I have at least a hundred slices which include it. Since the pial surface is not extending into cerebellum, should I just edit brainmask.mgz? Is there a quicker fix to the problem than manual editing? Thank you very much! Sincerely, Ye On Thu, Jul 11, 2013 at 12:30 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote: what do you mean by the structure in the circle? The circles are pretty big and have a lot of WM and GM in them. On 07/11/2013 12:55 PM, ye tian wrote: Dear Doug, Thank you very much! Are you basically saying that the structure in the circle is not part of the cortex? Sincerely, Ye On Thu, Jul 11, 2013 at 11:01 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: yes On 07/11/2013 11:22 AM, ye tian wrote: > Dear Freesurfers, > > Do you think I should delete the extra dura-like structure in the > attached case? > > Thank you very much! > > Sincerely, > Ye > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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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.
-- Best regards, Amirhossein Manzouri