help > Default number of dimensions for White matter and CSF Denoising confounds in batch scripts?
Jun 24, 2022  07:06 PM | Karl Lerud
Default number of dimensions for White matter and CSF Denoising confounds in batch scripts?
In my batch scripts, I usually specify denoising confounds like this:

BATCH.Denoising.confounds.names={'White Matter' 'CSF' 'realignment' 'scrubbing'};

But I noticed that when I open those projects in the GUI, in the Denoising tab, it says (16P) by White matter and CSF, which is the same as specifying Inf number of components/dimensions right? After looking around, 5 seems to be a much more common number for White matter and CSF confounds, and I think it defaults to 5 if you make the whole project in the GUI, is that right?

I believe I figured out how to specify this in the script:

BATCH.Denoising.confounds.names={'White Matter' 'CSF' 'realignment' 'scrubbing'};
BATCH.Denoising.confounds.dimensions={5 5 Inf Inf};

When I do this, it seems to only utilize 5 dimensions for White matter and CSF, which is what I intended. And the results are very different after only changing this aspect of the analysis, generally with many Fisher correlations going up. I wanted to check:

1) Is 5 a good number to stay with for this, and/or how would one choose this number,
2) Is defaulting to 16/Inf expected behavior for a batch script without specifying the number of dimensions, and
3) Am I specifying this correctly in my script with that line?

Thanks, best,

Karl

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TitleAuthorDate
Default number of dimensions for White matter and CSF Denoising confounds in batch scripts?
Karl Lerud Jun 24, 2022
Christopher Hyatt Jan 14, 2025
Christopher Hyatt Jan 14, 2025
Karl Lerud Jul 15, 2022