Hi Bruce,
I'm using freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0. I will also be using FS 5.1 paralelly.
Thank you very much!!
Andreia
Citando Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Andreia
I just modified label_area to allow the specification of a threshold (with -t <thresh>) and a surface (with -s <surface name>), and to use white by default. If you let us know what hardware/software platform you are running on we can send you an updated binary
cheers Bruce On Mon, 23 Apr 2012, _andreia_@sapo.pt wrote:
(sorry, here it is for the list again)
----- Mensagem encaminhada de Bruce Fischl fischl@nmr.mgh.harvard.edu ----- Data: Mon, 23 Apr 2012 15:30:17 -0400 (EDT) De: Bruce Fischl fischl@nmr.mgh.harvard.edu Assunto: Re: [Freesurfer] Load Brodmann surface area into inflated surface Para: _andreia_@sapo.pt
Hi Andreia,
can you cc the list so others can answer? I just took a look and label_area is so old that is uses ?h.smoothwm without any ability to change it. I think there are probably other tools around that will do it, but someone else will know. If not I'll fix label_area to be less obstinate.
cheers Bruce
On Mon, 23 Apr 2012, _andreia_@sapo.pt wrote:
Hi Bruce,
Thanks for the help! How do I know from which surface, i.e. pial or wm is the command label_area getting the value? I compared V1 surface area given in the BA.stats and the one I get with the command, and the late is higher (V1 from BA.stats= 2081 and from label_area = 2592.272).
Now, imagine the follwing: I have no differences in cortical thickness (CT) and surface area of this BA but the volume is different (with p values near 0.04...). Also, other BA shows no differences in CT neither in volume, but with differences showing up in the surface area (with lower p value here). Since the values for volume and surface are computed in different ways, can this account for these odd results?
Thanks! Andreia
Citando Bruce Fischl fischl@nmr.mgh.harvard.edu:
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
----- Fim de mensagem reenviada -----
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer