[caret-users] ROI Surface Area Calculation

donna at brainvis.wustl.edu donna at brainvis.wustl.edu
Wed Feb 19 10:06:42 CST 2014


I would use "Statistical Report" rather than "Statistical Paint Report" in
this context.  The paint report is intended to report the overlap an ROI
has with various paint/parcels in your paint file.  For example, you have
a metric/fMRI map that you threshold at some value.  You load the PALS
composite paint file, and this feature generates a report like this:

Paint Column 5 Brodmann - BOTH (from colin RIGHT) - PALS-B12
     Paint Name                                          Area    Percent
Area         COG - X         COG - Y         COG - Z        Latitude 
     Longitude
     ???                                                1.696         
62.459          30.575          24.488          -0.628         
25.086         -27.769
     Brodmann.37                                        1.019         
37.541          54.389         -55.346          -0.369          
8.147        -134.914


Paint Column 6 OrbitoFrontal BOTH - PALS-B12 (from case Fb LEFT)
     Paint Name                                          Area    Percent
Area         COG - X         COG - Y         COG - Z        Latitude 
     Longitude
     ???                                                1.019         
37.541          54.389         -55.346          -0.369          
8.147        -134.914
     OngurEtAl_03_47s                                   0.823         
30.330          29.538          22.406          -8.068         
14.020         -28.795
     OngurEtAl_03_Ial                                   0.872         
32.129          31.611          26.570           6.812         
36.153         -26.744

Here, you really want just the ROI surface area, which the Statistical
Report will give you right at the top.  Still use paint as the selection
source, but select Statistical Report instead of Statistical Paint Report.

You can make the Statistical Paint Report give you the right thing, but it
is less straightforward and more error prone.

David will correct me if I'm wrong, but I would cite this paper:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3288593/

Make sure you specify the caret version number you used.

> Hi everyone,
> We use Caret to calculate roi surface area in our paper:
> Brief steps includes:
> 1.Draw border on the ¡°veryinflated¡±  brain , which was saved as paint
> file;
> 2.Then perform a  series of ¡°Region of Interest opreations¡­¡± under
> ¡°Surface¡± including:
> a)Surface: midthickness
> b)Topology£ºclosed
> c)Selection Source: paint
> d)Selcetion logic: normal
> e)After selecting nodes, ¡°Paint statics ¡± with surface correction was
> used to report paint area.
>
>
> Here, I have three questions:
> 1)Is it correct to calculate area?
> 2)Can the paint area represent the surface area?
> 3)Which paper should be cited?
>
>
> Thanks!
>
>
> Zhuangming Shen
>
>
>
>
>
>
>
> _______________________________________________
> caret-users mailing list
> caret-users at brainvis.wustl.edu
> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>




More information about the caret-users mailing list