(forgot to do answer all, here it goes for the list too)
Citando _andreia_@sapo.pt:
Hi Bruce,
The ideia is to show one control subject vs. one patient inflated surface with BA surface (not volume, sorry) to show the difference (reduced surface area in one patient). Loading the relevant labels worked (I have the statistics shown in bar graphs, the images are only for visualizing the difference between controls and patients). When I threshold the labels in the subject's inflated surface they shrink a lot, is this supposed to happen?
The BA are V1, V2 and MT. What is the thresghold for V2?
And is it correct to load ?h.sulc in a gray scale to have the usual cortex representation, or I should do it other way?
And getting back to my previous email:
Another question is, how is the volume of the BA calculated? Is it
from the surface-based stream?
And, which surface area is the on in the output of the BA stats? Is it the pial or wm?
Thanks, Andreia
Citando Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Andreia
sorry, I don't understand. What do you mean when you say you want to " show the resulting Brodmann area (only 3 BA) volume in the inflated surface of my subjects". Do you mean just to show what portion of the surface is in each of 3 Brodmann areas? That you would do by loading the relevant labels, although you will probably want to threshold them differently (e.g. V1 you could threshold at .9 which is 90% and it would have about the surface area of an individual, while MT would need to be closer to .4 or .5). Or do you actually mean the volume of gray matter within each BA? If the latter, it's just 3 numbers/subject, so I would think you would want a scatter plot or something, not a map on the surface.
cheers Bruce
On Mon, 23 Apr 2012, _andreia_@sapo.pt wrote:
Hi all,
I'm sorry if these questions have already been covered here, but I've looked into the archives and still can't do what I need (and since I'm running out of time for this task I decided to post here):
I'm using version 5.0.0.
I want to show the resulting Brodmann area (only 3 BA) volume in the inflated surface of my subjects to show the differences between patients and controls (for visualization purpose only). I've managed to overlay the volume in the curvature menu but this is for the entire cortex and I can't show the values bar. How can I show the volume of only 3 BAs and have the scale bar?
Another question is, how is the volume of the BA calculated? Is it from the surface-based stream?
And, which surface area is the on in the output of the BA stats? Is it the pial or wm?
Thanks in advance, Andreia
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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.
Hi Andreia,
yes, they will always shrink since the label contains every point that could possibly be in the BA, no matter how unlikely. I'll try to find time to automatically threshold the BAs so that they have the average area of the individual examples, but for now V2 is probably around .7 and MT around .4 I think. And yes, I would use ?h.sulc as the background gray scale. The volume of the BAs would be computed using both surfaces, but the surface area can be from either one. I think we use the white by default, but you can use label_area to measure on whatever surface you want.
cheers Bruce
On Mon, 23 Apr 2012, _andreia_@sapo.pt wrote:
(forgot to do answer all, here it goes for the list too)
Citando _andreia_@sapo.pt:
Hi Bruce,
The ideia is to show one control subject vs. one patient inflated surface with BA surface (not volume, sorry) to show the difference (reduced surface area in one patient). Loading the relevant labels worked (I have the statistics shown in bar graphs, the images are only for visualizing the difference between controls and patients). When I threshold the labels in the subject's inflated surface they shrink a lot, is this supposed to happen?
The BA are V1, V2 and MT. What is the thresghold for V2?
And is it correct to load ?h.sulc in a gray scale to have the usual cortex representation, or I should do it other way?
And getting back to my previous email:
Another question is, how is the volume of the BA calculated? Is it
from the surface-based stream?
And, which surface area is the on in the output of the BA stats? Is it the pial or wm?
Thanks, Andreia
Citando Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Andreia
sorry, I don't understand. What do you mean when you say you want to " show the resulting Brodmann area (only 3 BA) volume in the inflated surface of my subjects". Do you mean just to show what portion of the surface is in each of 3 Brodmann areas? That you would do by loading the relevant labels, although you will probably want to threshold them differently (e.g. V1 you could threshold at .9 which is 90% and it would have about the surface area of an individual, while MT would need to be closer to .4 or .5). Or do you actually mean the volume of gray matter within each BA? If the latter, it's just 3 numbers/subject, so I would think you would want a scatter plot or something, not a map on the surface.
cheers Bruce
On Mon, 23 Apr 2012, _andreia_@sapo.pt wrote:
Hi all,
I'm sorry if these questions have already been covered here, but I've looked into the archives and still can't do what I need (and since I'm running out of time for this task I decided to post here):
I'm using version 5.0.0.
I want to show the resulting Brodmann area (only 3 BA) volume in the inflated surface of my subjects to show the differences between patients and controls (for visualization purpose only). I've managed to overlay the volume in the curvature menu but this is for the entire cortex and I can't show the values bar. How can I show the volume of only 3 BAs and have the scale bar?
Another question is, how is the volume of the BA calculated? Is it from the surface-based stream?
And, which surface area is the on in the output of the BA stats? Is it the pial or wm?
Thanks in advance, Andreia
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
-
_andreia_＠sapo.pt -
Bruce Fischl