Hi Ani, Thanks for looking into this for me. I'm actually out of town right now, so cannot access the subject in front of me.
Yes, it is. As I am trying to generate the stats on intensity over an ROI, I am hoping to be able to generate good surfaces. To me, the aseg looks pretty good. The brain matter around the stroke area is recognized, but is not in the surfaces. I only edited the brainmask.mgz. I unfortunately cannot tell you the exact slices that I edited until I am back, but I tried to recon edit and add in voxels in the stroke area. I did not notice major problems with the surface including dura or skull, so I did not really remove voxels. I'm not sure if how I did it is correct, but I tried to follow the wiki page on pial surface edits. The command I used to try to regenerate the surface was: recon-all -subjid <SUBJECT> -autorecon2-pial Thanks, Sabrina > On Jun 1, 2016, at 4:39 PM, Ani Varjabedian <a...@nmr.mgh.harvard.edu> wrote: > > Hello Sabrina, > > I have received the subject and am looking at it now. > I've attached a screenshot that is similar to the one you sent. At [158, 115, > 124] I see a hole in the aseg, wm mask, so it makes sense that the brainmask > does not cross over the area. Is this the area you wish to include? I just > want to make sure I'm looking at the correct region. > > What have you done so far to edit? I know you mentioned brainmask editing, > but what specifically did you do? > > Thank you, > Ani > > >> On 05/25/2016 08:47 AM, Ani Varjabedian wrote: >> Hi Sabrina, >> >> Could you upload the whole subject folder to the FTP or to our filedrop? >> https://gate.nmr.mgh.harvard.edu/filedrop2/ >> I can play around with the data a bit to see if we can improve surfaces. If >> that doesn't work then we can discuss other options for how to get the >> information you need. >> >> Thanks! >> >> -Ani >> >>> On 05/23/2016 05:47 PM, Sabrina Yu wrote: >>> Thank you for your explanation. Would it be possible to find a workaround? >>> I want to generate stats on intensity over an ROI for these stroke >>> subjects. For the brain matter not included in the surface, can I create a >>> volume label file in freeview instead of trying to edit the surfaces? >>> >>> Thank you, >>> Sabrina >>> ________________________________________ >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl >>> <fis...@nmr.mgh.harvard.edu> >>> Sent: Monday, May 23, 2016 12:30:30 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] Brainmask edit error >>> >>> because it violates too many of our assumptions about the topology and >>> geometry of the brain. >>> >>> cheers >>> Bruce >>> On Mon, 23 May 2016, Sabrina Yu >>> wrote: >>> >>>> Hi Bruce, >>>> >>>> Thank you for your reply. I've uploaded the .mgz and surfaces using FTP to >>>> FreeSurfer. Why is it that it may not be possible to get good surfaces >>>> with extensive strokes? >>>> >>>> Thank you, >>>> Sabrina >>>> ________________________________________ >>>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>>> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl >>>> <fis...@nmr.mgh.harvard.edu> >>>> Sent: Thursday, May 19, 2016 11:24:51 AM >>>> To: Freesurfer support list >>>> Subject: Re: [Freesurfer] Brainmask edit error >>>> >>>> Hi Sabrina >>>> >>>> it's tough to tell from just the 2 slices. If you upload the subject one >>>> of us will take a look, but it may not be possible to get good surfaces >>>> with that extensive a stroke >>>> >>>> cheers >>>> Bruce >>>> On Wed, 18 May 2016, Sabrina Yu wrote: >>>> >>>>> Hello, >>>>> >>>>> >>>>> I'm having problems with regenerating the surfaces for stroke cases after >>>>> editing the brainmask.mgz file. In the aseg.mgz file, the brain matter >>>>> around lesion area is correctly classified as brain matter. In the pial >>>>> surface, this brain matter is not included. >>>>> >>>>> >>>>> I've tried to edit the brainmask.mgz file to include this region, but >>>>> when I >>>>> run: recon-all -subjid <SUBJECT> -autorecon2-pial, the surfaces generated >>>>> are not changed at all. >>>>> >>>>> >>>>> I have attached some images to this email. I'm new to Freesurfer, so any >>>>> help would be greatly appreciated. >>>>> >>>>> >>>>> Thank you. >>>>> >>>>> >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> _______________________________________________ >>> 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. >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <SUBJECT01.png> > _______________________________________________ > 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.
_______________________________________________ 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.
