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, _andre...@sapo.pt wrote: > (sorry, here it is for the list again) > > > > ----- Mensagem encaminhada de Bruce Fischl <fis...@nmr.mgh.harvard.edu> ----- > Data: Mon, 23 Apr 2012 15:30:17 -0400 (EDT) > De: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Assunto: Re: [Freesurfer] Load Brodmann surface area into inflated surface > Para: _andre...@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, _andre...@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 <fis...@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, >>> _andre...@sapo.pt wrote: >>> >>>> (forgot to do answer all, here it goes for the list too) >>>> >>>> >>>> Citando _andre...@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 <fis...@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, _andre...@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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
