(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
>>>>>>
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>>>>>>
>>>>>>
>>>>>>
>>>>>
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