Clarification on ICA_FIX Denoising Sequence in HCP Resting-State fMRI Pipeline
Younghyun Oh
Dear HCP Users,
I am writing to inquire about the specific steps involved in the denoising process of resting-state fMRI data in the HCP pipeline, particularly regarding the use of ICA_FIX and the timing of CIFTI file creation.
Could you please clarify the following:
- Is denoising with ICA_FIX applied before converting minimally processed NIFTI files into CIFTI format, or is it performed directly on CIFTI files?
Thank you for your assistance.
Best regards,
Glasser, Matt
ICA is performed on the volume NIFTI file (because many artifacts are not limited to CIFTI graymatter). CIFTI ICA component spatial maps are generated by regressing the component timeseries into the CIFTI timeseries. Both datasets are cleaned via nonaggressive regression of the artifact components in the same way.
Matt.
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Younghyun Oh
Thank you, Matt, for the clarification.
To ensure I've understood correctly, the ICA-FIX processed CIFTI data (for instance, _Atlas_hp2000_clean.dtseries.nii) is created by applying ICA-FIX to clean the NIFTI file, followed by its projection onto the CIFTI format, without undergoing any additional cleaning steps once in CIFTI format.
Glasser, Matt
Actually, it is exactly as I described it in my prior mail. FIX is a component classification step. Currently that uses only the volume information, but we have a new “reclean” process that uses both volume and CIFTI information. The results of that and temporal ICA cleanup will be made available in the future.