Dear Freesurfers,
Do you think I should delete the extra dura-like structure in the attached case?
Thank you very much!
Sincerely, Ye
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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/
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.
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.
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.**edugreve@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<Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<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> <http://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/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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, YeOn 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/
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.eduwrote:
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, YeOn Thu, Jul 11, 2013 at 11:01 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@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 structurein the > attached case? > > Thank you very much! > > Sincerely, > Ye > > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
>https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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<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> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<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><http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.**harvard.edu Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> The information in this e-mail is intended only for theperson 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/**compliancelinehttp://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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.eduwrote:
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, YeOn Thu, Jul 11, 2013 at 11:01 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@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 structurein the > attached case? > > Thank you very much! > > Sincerely, > Ye > > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
>https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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<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> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<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><http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> The information in this e-mail is intended only for theperson 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/**compliancelinehttp://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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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 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/
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.
-- Best regards, Amirhossein Manzouri
Thanks a lot!
On Fri, Jul 12, 2013 at 4:15 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
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<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<Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer 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<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> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<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> <http://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/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer 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<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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<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/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://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
Dear Bruce, Thanks again for the response. I have FLAIR images for each subject acquired with MPRAGE/T1. I wonder in which way I can use FLAIR images in the analyses of cortical thickness to be able to edit (subtract) only the part of the brain which is missegmented (segmented as gray matter where the structure is tentorium of the cerebellum) and improve segmentation?
On Fri, Jul 12, 2013 at 6:54 PM, amirhossein manzouri < a.h.manzouri@gmail.com> wrote:
Thanks a lot!
On Fri, Jul 12, 2013 at 4:15 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
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<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<Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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<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> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<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> <http://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/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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<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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<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/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://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
-- Best regards, Amirhossein Manzouri
if the FLAIR is reasonably high resolution (no voxel dimension greater than around 1.5mm) then you can use the -flairpial switch to recon-all
cheers Bruce
On Mon, 15 Jul 2013, amirhossein manzouri wrote:
Dear Bruce, Thanks again for the response. I have FLAIR images for each subject acquired with MPRAGE/T1. I wonder in which way I can use FLAIR images in the analyses of cortical thickness to be able to edit (subtract) only the part of the brain which is missegmented (segmented as gray matter where the structure is tentorium of the cerebellum) and improve segmentation?
On Fri, Jul 12, 2013 at 6:54 PM, amirhossein manzouri a.h.manzouri@gmail.com wrote: Thanks a lot!
On Fri, Jul 12, 2013 at 4:15 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: 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/ _______________________________________________ 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. -- Best regards, Amirhossein Manzouri-- Best regards, Amirhossein Manzouri
-- Best regards, Amirhossein Manzouri
freesurfer@nmr.mgh.harvard.edu
-
amirhossein manzouri -
Bruce Fischl -
Douglas N Greve -
ye tian