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.manzo...@gmail.com> wrote: > Thanks a lot! > > > On Fri, Jul 12, 2013 at 4:15 PM, Bruce Fischl > <fis...@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 <tianye...@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 >>> <fis...@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 >>> <gr...@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 >>> <gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@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:freesur...@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 >>> gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@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:freesur...@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 >>> gr...@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/**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. >>> >>> >>> >>> >>> -- >>> Best regards, >>> Amirhossein Manzouri >>> >>> >>> >>> >>> > > > -- > Best regards, > Amirhossein Manzouri > > > > -- Best regards, Amirhossein Manzouri
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