Dear Suvarnalata,

One of the features of rfxplot is that it uncouples voxel selection (via a 2nd level contrast) and image selection for data extraction (via specification of 1st level images, usuallly beta or con). You can define your search volume (voxel selection) with whatever 2nd level contrast you like, it doesn't have to relate to the 1st level images that you select the data from. For insetance, you can select voxels from your rfx contrast of interest and then extract the data from regressors that model something completely different (like movement parameter, not that this would be of great interest, but rfxplot will let you do it). The two steps (voxel selection and dats extraction) can even come from differetnt SPM.mat files.

However, if you dissociate these to steps then your data plot will most likely look different that what you would expect based on your rfx contrast upon which you selected your voxels. You just have to keep this in mind. In that way rfxplot is very flexible, but you kind of have to know what you are doing. It will also let you do things that some people would call "quesrtionable" and that I don't use myself (like searching for individual peaks in an rfx search volume). The responsibility is clearly with the user who should create plots that are meaningful and an accurate reflection of what is going on. Also keep in mind that the goal of this toolbox is to visualize data in a flexible way, NOT to run statistics, which ultimately tell you about the effects in your data. Therefore, the user should crate data plot for publication that reflect the statistics accurately.

If you have further concrete questions you can email me directly, but I won't be able to respond until the end of nest week.

Beat wishes,
Jan

Sent from my iPad



> On Jun 12, 2015, at 11:42, Suvarnalata Xanthate Duggirala <[log in to unmask]> wrote:
>
> Dear SPMers,
> My doubt is regarding the rfx plot toolbox. I am using it to calculate percent signal change (PSC) in my ROIs. My paradigm has four conditions (two active, one low level baseline and one high level baseline) A1, A2, B1, B2. I have defined A1, A2, and B1 explicitly in the GLM (meaning I have three regressors defined).
> Now, for rfxplot one needs to open an unbiased rfx contrast, which in most of the cases is an average contrast. Now, because I want to compare PSC for A1 and A2, I have the following two options-
> 1) [1 1 -2]
> OR
> 2) [1 1 0]
> So, which of the above mentioned contrasts should be used? And what are the pros and cons with respect to each?
> Any help would be highly appreciated!
> Best,
> D S Xanthate