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.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. > >
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