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 :)