Displaying Neuroimaging Data
00. FreeView, FSLview: displaying and exploring brain images in both volumetric and surface spaces
Image Preprocessing (Diagram)
01. lfcd_01_anatpreproc: preprocessing anatomical images including denoising, brain extraction, stage1 of recon-all.
Notes: there is a document on fixing a bad skull strip
02. lfcd_01_anatsurfrecon: segment anatomical images into wm, csf, gm and generate the cortical surface (stages 2 and 3 of recon-all).
03. lfcd_01_anatcheck_surf: check the quality of surface reconstruction on anatomical images.
Notes: there is a set of QAtools
from Freesurfer release, which also helps.
04. lfcd_01_funcpreproc: preprocessing functional images including common steps needed for all RfMRI computation.
05. lfcd_01_dtipreproc: preprocessing diffusion images including common steps needed for all DTI-based computation.
06. lfcd_02_anatregister: register anatomical images to MNI152 standard template (FNIRT).
07. lfcd_02_anatcheck_fnirt: check the quality of FNIRT on anatomical images.
08. lfcd_02_funcregister: register functional images to MNI152 standard template (FNIRT).
09. lfcd_02_funcregister_surf: generate surface masks and carry out boundary-based co-registration (bbregister).
10. lfcd_02_funccheck_fnirt: check the quality of FNIRT on functional images.
11. lfcd_02_funccheck_bbregister: check the quality of bbregister on functional images.
12. lfcd_03_funcsegment: segment functional images into wm, csf, gm.
13. lfcd_04_funcnuisance: remove nuisance signals from head motion, global brain (option), wm, csf (3dDeconvolve).
14. lfcd_05_funcpreproc_final: remaining functional preprocessing steps.
R-fMRI Metrics Computation
15. lfcd_06_singlesubjectRSFC: seed-based resting-state functional connectivity (3dfim+).
16. lfcd_06_singlesubjectICA: independent component analysis (melodic).
17. lfcd_06_singlesubjectReHo: regional homogeneity (Zang's seminal paper).
18. lfcd_06_singlesubjectALFF: amplitude of low-frequency fluctuations (Zang's seminal paper).
19. lfcd_06_singlesubjectVMHC: voxel-mirrored homotopic connectivity (Zuo2010).
20. lfcd_06_singlesubjectVNCM: voxel-wise network centrality map (matlab: Zuo2012).
21. lfcd_06_singlesubjectRAICAR: Ranking and averaging independent component analysis by reproducibility (Yang2008, matlab codes, please read README for howto).
22 lfcd_06_singlesubjectRSFC_surf: seed-based resting-state functional connectivity on surface (matlab).
23. lfcd_06_singlesubjectICA_surf: independent component analysis on surface (matlab).
24. lfcd_06_singlesubjectReHo_surf: regional homogeneity on surface (matlab).
25. lfcd_06_singlesubjectALFF_surf: amplitude of low-frequency fluctuations on surface (matlab).
26. lfcd_06_singlesubjectVMHC_surf: voxel-mirrored homotopic connectivity on surface (matlab).
27. lfcd_06_singlesubjectVNCM_surf: voxel-wise network centrality map on surface (matlab).
Preparation for Group-level Analyses
28. lfcd_07_grp_mask: generate group masks for both volumeric and surface functional images.
29. lfcd_07_grp_meanbold: generate group mean bold image.
30. lfcd_07_grp_meanstruct: generate group mean T1 image.
31. lfcd_07_grp_4dmaps: generate 4D stacked functional images for final group analysis.
32. lfcd_07_grp_RAICAR: Generalised ranking and averaging independent component analysis by reproducibility (Yang2012, matlab codes, please read README for howto).
Notes: Group level analyses in FSL, Freesurfer, AFNI.
Looking for Small Graphs ??
Here are the small graphs (or connectome matrices) from more than 1000 subjects of KFC project. Enjoy exploring them :)