Thank you very much Bruce. I do appreciate. Best, Paul
On Sun, Sep 3, 2017 at 2:30 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > yes, I think so. It may not work for the GM ones at the moment, but should > at least be fixable > > On Sun, 3 Sep 2017, miracle ozzoude wrote: > > Hello Bruce, >> Thank you very much. To reiterate our discussion, I should use Left/Right >> non-WM-hypointensities for >> GM lesions and Left/Right-WM-hypointensities for WM lesions when editing >> the aseg.presurf.mgz. >> Correct? >> >> Best, >> Paul >> >> On Sun, Sep 3, 2017 at 1:52 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> wrote: >> nope, I would use Left-non-WM-hypointensities and >> Right-non-WM-hypointensities >> >> On Sun, 3 Sep 2017, miracle ozzoude wrote: >> >> Hello Bruce, >> Thank you. I looked at the LookUpTable.txt for GM and I >> couldn't find any. I >> only found labels for >> Right Lesion, Left lesion, WM lesions (wmsa and other_wmsa). >> What does wmsa >> mean and which of these >> should I use as GM lesion? >> >> Best, >> Paul >> >> On Sun, Sep 3, 2017 at 12:45 PM, Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> >> wrote: >> Hi Paul >> >> GM ones are harder and I'm not sure we have a working >> procedure for >> them yet. I think we >> have separate labels for wm and gm lesions - try using >> them when you >> edit the aseg. >> >> cheers >> Bruce >> On Sun, 3 Sep 2017, miracle ozzoude wrote: >> >> Hello Bruce, >> >> Thank you very much. I'm guessing I should follow >> the tutorial >> for editing >> aseg; or is there a different tutorial on how to >> edit and label >> WM lesions >> on aseg? One last question, what if it's a >> combination of WM and >> GM lesions >> like cortical stroke that extended into the WM? >> Should I use the >> same >> procedure? >> >> Best, >> Paul >> >> Sent from my BlackBerry 10 smartphone. >> Original Message >> From: Bruce Fischl >> Sent: Sunday, September 3, 2017 11:47 AM >> To: Freesurfer support list >> Reply To: Freesurfer support list >> Subject: Re: [Freesurfer] Freesurfer with infarct >> patients >> >> Hi Paul >> >> if they are WM lesions I think you should edit >> the aseg and >> label them as >> such, then run from there forward. It should >> propagate the >> lesions from >> aseg to wm.mgz, so you shouldn't have to do both >> Bruce >> >> >> On Sun, 3 Sep 2017, miracle ozzoude wrote: >> >> Hello Bruce, >> I am interested in this thread because I >> have encountered >> similar problems with my stroke patients. >> How do I solve it? Should I only edit the >> aseg and assign >> a >> label called "Lesion" in the FS >> LookUpTable? or Should I edit both the >> wm.mgz and aseg.mgz >> files? If the former, How do I achieve >> it? My goal is to make sure that WH and GM >> surfaces are >> traced >> properly. Any help will be >> appreciated. Thank you. >> >> Best, >> Paul >> >> On Wed, Jun 21, 2017 at 12:45 PM, Bruce >> Fischl >> <fis...@nmr.mgh.harvard.edu> wrote: >> Hi Mariana >> >> yes, control points would mess everything >> up. It looks >> like the >> rest of the surface was >> generated pretty accurately though - do you >> need to >> correct >> anything? >> >> cheers >> Bruce >> >> On Wed, 21 Jun 2017, Budge, Mariana wrote: >> >> >> Hi Freesurfer experts, >> >> >> >> I am running FS on a patient with a chronic >> right >> occipital lobe >> infarct as >> part of a larger study. The program does >> not recognize the >> area >> around the >> lesion as brain matter, and I am wondering >> how best to >> treat >> this situation. >> I am worried that adding Control Points >> will incorrectly >> label >> the region as >> white matter. I am attaching some pictures >> of slices where >> this >> is apparent. >> Thank you so much for your help! >> >> >> Best, >> >> Mariana >> >> >> >> ______________________________ >> _________________ >> 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.e >> du/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. >> >> >> >> > _______________________________________________ > 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.
