Dear Freesurfers,
In an effort to figure out why my field sign data is a bunch of blue/red speckles, I looked at the polar and eccentricity maps separately on the surface.
In both maps, I found that the values range from 0 to approximately 65. Does that seem to be OK, and if so, what do these numbers represent in terms of polar angle or eccentricity? Also, it seems that the color ranges in the overlay cannot show any values above 4; is there a way to visualize larger ranges (such as 0 to 65)?
Thank you very much. Michelle
Hi Michelle, I don't think you are looking at the angle. The eccen angle should go from 0-2pi. The polar angle should go from -pi to +pi. What is you visualization command-line? You can change the color scale from the View->Configure->Overlay window. doug
Michelle Umali wrote:
Dear Freesurfers,
In an effort to figure out why my field sign data is a bunch of blue/red speckles, I looked at the polar and eccentricity maps separately on the surface.
In both maps, I found that the values range from 0 to approximately 65. Does that seem to be OK, and if so, what do these numbers represent in terms of polar angle or eccentricity? Also, it seems that the color ranges in the overlay cannot show any values above 4; is there a way to visualize larger ranges (such as 0 to 65)?
Thank you very much. Michelle
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug, You're right it was the wrong map, and now the angles make sense.
But when I look at the correct images, the eccen and polar maps are very, very speckled. So, in the relevant visual areas, there are hardly any 0 values, so I would expect a more contiguous color pattern.
Is there any way to improve the visualization?
Here is the command I used: tksurfer-sess -a rtopy.self.lh -s sj17 -map angle
Thanks. Michelle
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
Hi Michelle, I don't think you are looking at the angle. The eccen angle should go from 0-2pi. The polar angle should go from -pi to +pi. What is you visualization command-line? You can change the color scale from the View->Configure->Overlay window. doug
Michelle Umali wrote:
Dear Freesurfers,
In an effort to figure out why my field sign data is a bunch of blue/red speckles, I looked at the polar and eccentricity maps separately on the surface.
In both maps, I found that the values range from 0 to approximately 65. Does that seem to be OK, and if so, what do these numbers represent in terms of polar angle or eccentricity? Also, it seems that the color ranges in the overlay cannot show any values above 4; is there a way to visualize larger ranges (such as 0 to 65)?
Thank you very much. Michelle
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
Look at the significance maps to make sure they look reasonable. Just run
tksurfer-sess -a rtopy.self.lh -s sj17
doug
Michelle Umali wrote:
Hi Doug, You're right it was the wrong map, and now the angles make sense.
But when I look at the correct images, the eccen and polar maps are very, very speckled. So, in the relevant visual areas, there are hardly any 0 values, so I would expect a more contiguous color pattern.
Is there any way to improve the visualization?
Here is the command I used: tksurfer-sess -a rtopy.self.lh -s sj17 -map angle
Thanks. Michelle
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
Hi Michelle, I don't think you are looking at the angle. The eccen angle should go from 0-2pi. The polar angle should go from -pi to +pi. What is you visualization command-line? You can change the color scale from the View->Configure->Overlay window. doug
Michelle Umali wrote:
Dear Freesurfers,
In an effort to figure out why my field sign data is a bunch of blue/red speckles, I looked at the polar and eccentricity maps separately on the surface.
In both maps, I found that the values range from 0 to approximately 65. Does that seem to be OK, and if so, what do these numbers represent in terms of polar angle or eccentricity? Also, it seems that the color ranges in the overlay cannot show any values above 4; is there a way to visualize larger ranges (such as 0 to 65)?
Thank you very much. Michelle
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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@nmr.mgh.harvard.edu
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Douglas N Greve -
Michelle Umali