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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
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
Threaded View
Title | Author | Date |
---|---|---|
Karl Lerud | Jun 24, 2022 | |
Christopher Hyatt | Jan 14, 2025 | |
Christopher Hyatt | Jan 14, 2025 | |
Karl Lerud | Jul 15, 2022 | |