Re: [Marsbar-users] select specific values within nifti image

[Rick H. <r.h...@fc...>]

Dear Matthew,

Thanks for your rapid response!

> I think you could do this by applying a function to the image as you do ROI 
> definition->Build->Image,  such as 'img == 12'.  Does that work?

In the GUI mode that does seem to work, although the output image is not 
strictly binarized: some of the 112 values are now replaced by values between 0 
and 1 (and although most of the 12 values are now 1, some of them are also 
between 0 and 1). Do you have any idea why that is? And second, how to batch 
the application of a function to the image? My code is now as follows:

ROI = maroi_image('image.nii');
saveroi(ROI, 'name_roi.mat');
save_as_image(ROI, 'name.img');

addding: ROI = (ROI==12) doesn't work (i.e. it gives me exactly the same image 
as before, including both voxels with values 12 and 112). Save_as_image
(ROI==12,'name.img') also does not work, that gives me an empty image. Any 
other advice?

Thanks a lot! Rick


Rick Helmich <r.helmich <at> fcdonders.ru.nl> writes:

> 
> Dear Matthew and List,
> 
> I am using MarsBar with SPM5 to build ROIs from a set of input images 
> (segmented subcortical structures, using FSL FIRST). 
> 
> These input (nifti) images contain three different numbers: for instance, 0 
at 
> voxels where there is no subcortical structure, 12 at locations where there 
is 
> subcortical structure, and 112 at the border of that structure. 
> 
> I would like to include only one of these values in my ROI (in this case, 
12), 
> while excluding voxels with the value of 0 or 112. How can I indicate this in 
> the batched version of marsbar?
> 
> Thanks a lot for your help!
> 
> Greetings, Rick
> 
> =========================================
> 
> Rick C.G. Helmich, MD (Ph.D student)
> 
> F.C. Donders Centre for Cognitive Neuroimaging 
> P.O. Box 9101 
> 6500 HB Nijmegen 
> The Netherlands 
> 
> T  00 31 (0)24 36 65077 
> F  00 31 (0)24 36 10989 
> E  rick.helmich <at> fcdonders.ru.nl
> web: www.fcdonders.ru.nl 
> =========================================
> 
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