Hi all, I’m using fmriprep for fmri preprocessing and then using the confounds_regressors.tsv file to regress out CSF + WM signals. A lot of papers have mentioned using 6 acompcor vectors. However, it seems like some people use percentages (at least 75% of variance explained in the acompcor). To ge…

Gotcha. Thanks @Steven ! A quick follow up question. So, if fmriPrep says 122 components explain 50% of my variance, then it would make sense to include all 122 components from the _confounds.tsv file in my physiological regression? Why is it that some people only have 5 or 6 components vs. my 122…

Hi @cchang , [image] cchang: So, if fmriPrep says 122 components explain 50% of my variance, then it would make sense to include all 122 components from the _confounds.tsv file in my physiological regression? If you want to be consistent in regressing out 50% variance, then yes. [image] c…

[image] Steven: Others choose to prioritize keeping temporal degrees of freedom (tDOF) in the GLM the same across subjects, which (assuming the scan lengths are constant) would mean including the same amount of regressors in each model. Especially in shorter scans, removing too many tDOF could l…

Hi @cchang , [image] cchang: As for the tDOF, does this mean that they’re extracting 5 or 6 components from the tCompcor or the aCompcor? aCompcor [image] cchang: This makes a lot of sense. My runs are currently around 10 mins each. What would be considered as a “shorter scan”? Depend…

Neurostars

CSF and WM regression

python, fmriprep

Steven June 12, 2025, 5:25pm 2

fMRIPrep Confounds for GLM

Hello all, I am trying to use some of the confounds generated by fMRIPrep to denoise “task” data within the FSL FEAT GLM, and I am wondering which columns to include as regressors. I’ve followed along with this previous post so far, but wanted to ask for some further instruction/validation of methods. I am planning to include the 6 major motion regressors (x,y,z trans & rot) and some combination of a/c/tCompCor regressors to account for physiological noise, but my question lies in which of th…

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