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
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.yang76@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
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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.yang76@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@nmr.mgh.harvard.edu
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Bruce Fischl -
Don Hagler -
Yang Liu