Feedback appreciated: Toshihiko ASO aso.toshihiko@gmail.com / https://www.researchgate.net/profile/Toshihiko_Aso
Pipeline for extraction and removal of the perfusion lag structure within 4D BOLD-fMRI data in HCP-style protocols
BOLD deperfusioning is extracting Einstein (local neurovascular coupling) by removing smooth Marilyn Monroe (perfusion structure), so that the fMRI result becomes sharp and precise.
For Linux/Mac. MATLAB scripts call FSL commands and SPM12 functions.
- Install FSL & MATLAB then evoke MATLAB from the shell.
- niimath from https://github.com/rordenlab/niimath is preferred because fslmaths in FSL6 may not funciton with the option "-subsamp2offc". FSL5 works fine, but no longer actively maintained.
Main script Einsteining_vXX.m calls drLag4DrevXX.m for lag mapping and drDeperf_hcp_seed_niimath.m for deperfusioning.
- Einsteining is a hard working process to pick up Einstein face (neural signal) by (1) extracting perfusion lag structure, a major component of physiological noise for fMRI, and (2) removing it.
- Application before ICA-FIX is recommended (see Aso & Hayashi, ISMRM2022)
- Modify "Fdir" to point to your FSL5 installation.
- For drLag4D scripts, note that tracking range should now be specified in TR, not seconds. Arguments are given in text at present.
For input data BOLD_REST1_AP, BOLD_REST1_PA, BOLD_REST2_AP, BOLD_REST2_PA
output directories will be dep_BOLD_REST1_AP, dep_BOLD_REST1_PA, dep_BOLD_REST2_AP, dep_BOLD_REST2_PA
Einsteining_v02( Sdir, 0.8, 478, 8, 0.2, 1, 8, 1)
- Sdir: Subject directory
- TR = 0.8s
- Number of volumes per run = 375
- MaxLag = 8 -> lag mapping up to -8TR / +8TR
- MinR = 0.2 -> Cross-correlogram peak < 0.2 will not be used
- Fixed = 0 -> Recursive (flexible) LFO instead of Fixed-sLFO algorithm
- Spatial smoothing at 8mm FWHM
- onlyLag = 0 -> Lag mapping + deperfusioning
