When running ICA-AROMA within fmriprep 1.2.4, BOLDs are automatically resampled. However, I would like to keep resampling to a minimum (and be able to use the brain masks provided by fmriprep). So I thought of manually smoothing my preprocessed BOLDs (MNI) using SUSAN and then removing fmriprep-derived components using fsl_regfilt.
Can anyone direct me to fmriprep’s implementation of SUSAN? Looking at these defaults (https://rdrr.io/cran/fslr/man/susan.html), I am not sure whether fmriprep used the very same ones (except for sigma, obviously)…
Also: Does anyone know why/at which step BOLDs are being resampled in ICA-AROMA?
So fmriprep does not explicitly pass any brightness threshold to the nipype wrapper but must be using some kind of default, right?
Just a quick follow-up question: After resampling of my BOLDs to MNI space, they have a shape of 78 x 93 x 78 x time (MNI152NLin2009cAsym_desc-preproc_bold). When inspecting my BOLDs after running ICA-AROMA, they have a shape of 91 x 109 x 91 x time (MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold). So there must happen some additional resampling within the AROMA workflow in fmriprep. Do you know where and why this happens?
I would like to clarify, on the inputs to the ICA-AROMA pipeline, as I want to do some additional nonaggr denoising on the preprocessed data, but would like to match the data that are fed into ICA-AROMA, and hence match the temporal courses in the melodic mixing matrix.
Is ICA-AROMA applied to preprocessed data (after smoothing) in native space or MNI space? If I want to do additional denoising (using aroma components), then what are steps that I need to follow?
My take on was
Remove non-steady volumes from *space-T1w_desc-preproc_bold
ICA AROMA is applied to the BOLD series in MNI152NLin6Asym (MNI) space.
I do not believe applying the AROMA components from MNI space to “most” other spaces should impact the results significantly (unless the transformation from one space to another is extreme and/or poor).
@dvsmith linked a superthread about different ICA-AROMA conversations, you can see if you find some useful suggestions there too:
I just wanted to follow up on this question. I just wanted further confirmation, is ICA Aroma performed in Native Space or MNI space? It will be important to know as it will affect our post-processing steps.
I took a look at the fMRI prep code, in one place it says:
#. Return classified_motion_ICs and melodic_mix for user to complete
non-aggressive denoising in T1w space
#. Calculate ICA-AROMA-identified noise components
(columns named AROMAAggrCompXX)
But then in another place following that bit of code it says:
Additionally, non-aggressive denoising is performed on the BOLD series
resampled into MNI space.