Hi Ani, Thanks so much for your explanation, it makes sense that the brain is too deformed for one continuous surface. If we are not able to find a workaround that creates a continuous surface, can I create a separate surface just for the stroke region? And generate average voxel intensity for that region?
Thanks, Sabrina > On Jun 2, 2016, at 6:21 PM, Ani Varjabedian <a...@nmr.mgh.harvard.edu> wrote: > > Hi Sabrina, > > Usually we don't add voxels in the brainmask. We usually add to the wm.mgz > which pushes the white surf out and ultimately the pial surf out (because it > grows from the white). > If the area around the stroke on both sides looks good but there is a hole in > the middle where there is no information or labels, then the surfaces will > not connect all the way around it. They treat it like two separate pieces. > Does this make sense? I'll try to play around with some different things > (like adding to the wm.mgz) and see if I can get the surfaces to be > continuous around this region. > > Like Bruce said, it might end up being that the brain is too different from > what freesurfer assumes a brain to look like, but I will try some work > arounds and get back to you. > > Thank you, > Ani > >> On 06/02/2016 08:18 AM, Sabrina Yu wrote: >> 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 > > _______________________________________________ > 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.
