Hi all,
I am currently using MRIQC to check imaging data quality. I find there is one option to include despike in MRIQC. Does it mean imaging data after MRIQC are “despiked”. I am suggested to not run despike before head motion estimation, which is included in fMRIPrep. So I wonder, does it matter that I put despike in MRIQC, then run fMRIPrep (it seems despike cannot be done in fMRIPrep) for pre-processing, and use confounds in generated tsv files for further data analysis? Any suggestion or help is welcome! Thanks in advance!
Best,
Shengjie
MRIQC should not be used for preprocessing, only for quality assessment. As regards fMRIPrep, it is a longstanding feature request (https://github.com/poldracklab/fmriprep/issues/699). Contributions are welcome 
Hi Esteban,
Many thanks for your being prompt in responding! I ran MRIQC with/without despike option on the same group of data yesterday and yes, MRIQC won’t modify original data. As for despike itself, sorry I am not an expert on this issue so I am afraid I cannot help much. Since now this feature is not included in fMRIPrep, if I really want to apply it, what is your suggestion? Should I run despike (currently I plan to use 3dDespike from AFNI) after fMRIPrep?
Best,
Shengjie
Hi @Shengjie_Xu,
I think adding 3dDespike from AFNI as is will not be a good idea - you might be reintroducing artifacts later in regression as you would be establishing a “modular” pipeline (see https://www.biorxiv.org/content/10.1101/407676v1).
You could, though, generate one more regressor based on the RMS difference between signal before and after 3dDespike. @rastko should correct me if this is a bit crazy. If it is not, we should consider this for fMRIPrep.
Cheers,
Oscar