Re: [Freesurfer] inflated surface
Dear Bruce, Allison, Thank you for your answer. In tkmedit the surfaces look good. Can this concavity mean that sulci are deeper in this region as compared to neighboring regions? I am not sure I understand how to interpret the inflated surface, therefore I cannot control if it is correct. Best wishes, Tanja. On Fri, Apr 29, 2011 at 8:05 PM, Bruce Fischl wrote: > I agree, sometimes this happens in the inflated surface and I don't think > it's cause for concern > > Bruce > On Fri, 29 Apr 2011, Allison Stevens wrote: > >> When you look at the case in tkmedit, in that same area, do you see an >> error? Looking at your snapshot, it looks like it could be normal. >> >> On Apr 26, 2011, at 8:45 AM, Tetiana Dadakova wrote: >> >>> Dear FreeSurfer list, >>> >>> When I look at inflated surface of my subjects (healthy males and >>> females), almost all of them have a concavity in the posterior part of >>> the brain (the arrow in attached image). >>> It doesn't look correct to me. What can cause this problem? >>> >>> Thank you, >>> Tanja. >>> >>> ___ >>> 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
Re: [Freesurfer] distortion of flat map
for occipital patches you can try running mris_flatten with -complete. This will use the complete distance matrix instead of a random sampling of it cheers Bruce On Fri, 29 Apr 2011, Don Hagler wrote: > > For retinotopy, I find it convenient to use the sphere surface. It does not > require a cut down the middle of V1 and it is flat enough to easily draw > ROIs. Also, in my experience, the patch flattening algorithm often produces > poor results (e.g. large distortions, twisting). > > Date: Thu, 28 Apr 2011 23:03:50 -0400 > From: liu.yan...@gmail.com > To: freesurfer@nmr.mgh.harvard.edu > Subject: [Freesurfer] distortion of flat map > > Hi surfers, > > I am working on generating surface ROIs from the retinotopy surface. > We cut the occipital lobe and draw paths on the flattened map to create > labels. However, I found that there are distortions on the flat map that > cause large errors when drawing these paths. I attached two pictures. The > path_example2_dots.jpg are the dots that I selected to draw a path. > Basically it is the method we use to demarcate the boundaries of visual > areas. > > And the path_example2_line.jpg are the line that is supposed to connect the > dots and to be the correct boundary. > Notice the dots and the line do not overlap! > so when I draw a line on the flat map, Freesurfer actually doesn't draw the > line I want it to be. > > > Has anyone met this problem before? Is there a better solution to create > surface ROIs? Drawing the boundary on inflated surface? > > Yang > > > ___ > 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
Re: [Freesurfer] inflated surface
no, I don't think it means that. It has more to do with the overall shape of the brain I believe, but we've never really investigated it On Sat, 30 Apr 2011, Tetiana Dadakova wrote: > Dear Bruce, Allison, > > Thank you for your answer. > > In tkmedit the surfaces look good. > Can this concavity mean that sulci are deeper in this region as > compared to neighboring regions? I am not sure I understand how to > interpret the inflated surface, therefore I cannot control if it is > correct. > > Best wishes, > Tanja. > > On Fri, Apr 29, 2011 at 8:05 PM, Bruce Fischl > wrote: >> I agree, sometimes this happens in the inflated surface and I don't think >> it's cause for concern >> >> Bruce >> On Fri, 29 Apr 2011, Allison Stevens wrote: >> >>> When you look at the case in tkmedit, in that same area, do you see an >>> error? Looking at your snapshot, it looks like it could be normal. >>> >>> On Apr 26, 2011, at 8:45 AM, Tetiana Dadakova wrote: >>> Dear FreeSurfer list, When I look at inflated surface of my subjects (healthy males and females), almost all of them have a concavity in the posterior part of the brain (the arrow in attached image). It doesn't look correct to me. What can cause this problem? Thank you, Tanja. ___ 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
