Question about additional preprocessing for HCP-YA 2025 rfMRI hp2000_clean_rclean_tclean before FC

[tiankui peng]

Hello,

I am using the HCP-Young Adult 2025 Release and plan to compute functional connectivity (FC) from the file:

rfMRI_REST1_RL_hp2000_clean_rclean_tclean.nii.gz

Before computing FC, I would like to confirm whether this output has already undergone:

1. detrending / removal of linear trend,

2. temporal filtering (and if so, what type; e.g., high-pass or band-pass 0.01-0.08hz),

3. spatial smoothing (and if so, the kernel/FWHM).

If any of these steps have not been applied, do you recommend applying them before FC analysis?

Best regards

[Glasser, Matthew]

1. Yes, on a per-run basis before concatenating across runs into ${StudyFolder}/${Subject}/MNINonLinear/Results/rfMRI_REST/rfMRI_REST_Atlas_MSMAll_hp2000_clean_rclean_tclean.dtseries.nii
2. No.  Although you can do this (e.g., with fslmaths), we don’t recommend it.  In HCP data there is measurable BOLD variance up to about 0.5hz.  Tools like Wishart Filtering remove unstructured noise while preserving the structured signal, though see #3.
3. No.  Although you can do this (e.g., with wb_command -cifti-smoothing), we don’t recommend it.  Parcellation (with wb_command -cifti-parcellation and the HCP’s multi-modal parcellation: https://balsa.wustl.edu/file/87B9N) is a better idea.

Matt.

--
You received this message because you are subscribed to the Google Groups "HCP-Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to hcp-users+...@humanconnectome.org.
To view this discussion visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/29b85fd0-e925-45c5-96de-a509573827d3n%40humanconnectome.org.

 

---

The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.