graph TB

%% structural
subgraph structural information
    tone(T1)
    surf(FreeSurfer surfaces)
    setup["mne.setup_source_space()"]
    src(mne.SourceSpaces)
    tone   -->  surf
    surf   -->  setup
    setup  -->  src


    %% bem
    flash(Flash5/30)
    makebem["mne.make_bem_model()<br/>
             mne.make_bem_solution()"]
    flashbem["$ mne flash_bem"]
    bem(Boundary Element Model)
    surf --> makebem
    flash --> flashbem
    flashbem --> bem
    makebem --> bem
end

%% forward
trans("Coregistration between MRI and<br/>sensor coordinate systems<br/>(mne.trans)")
makefwd["mne.make_forward_solution(trans, src, bem, ...)"]
trans --> makefwd
bem --> makefwd
src --> makefwd
makefwd --> fwd


%% labels
surf --> makelab
makelab["$ mris_ca_label"]
fslab("Cortical Labels<br/>(*.annot)")
readlab["mne.read_label()"]
lab(mne.Label)
makelab --> fslab
fslab --> readlab
readlab --> lab


%% importing
acq(Raw data from system)
read["mne.io.read_raw_ctf()<br/>
      mne.io.read_raw_fif()<br/>
      mne.io.read_raw_fieldtrip()<br/>
      mne.io.read_raw_brainvision()<br/>
      etc."]
raw(mne.io.Raw)
acq   -->  read
read  -->  raw


%% preprocessing
prep["raw.filter()<br/>
      raw.resample()<br/>
      raw.set_montage()<br/>
      raw.set_eeg_refererence()<br/>
      raw.drop_channels()<br/>
      mne.prepessing.find_eog_events()<br/>
      mne.prepessing.create_eog_epochs()<br/>
      mne.prepessing.compute_proj_eog()<br/>
      mne.prepessing.maxwell_filter()<br/>
      mne.prepessing.ICA()<br/>
      etc."]
prep  -->  raw
raw   -->  prep


%% events
events["mne.find_events()<br/>
        mne.make_fixed_length_events()"]
evarr("events (numpy.array)")
raw     -->  events
events  -->  evarr


%% epoching
epoching["mne.Epochs(raw, events, ...)"]
epo(mne.Epochs)
raw       -->  epoching
evarr     -->  epoching
epoching  -->  epo


%% epochs from array
arr("data (numpy.array)")
epoarray["mne.EpochsArray(array, ...)"]
arr       -->  epoarray
epoarray  -->  epo


%% evoked
avg["epochs.average()"]
evk(mne.Evoked)
epo  -->  avg
avg  -->  evk


%% covariance
compcov["mne.compute_covariance(epochs, ...)"]
cov(mne.Covariance)
epo      -->  compcov
compcov  -->  cov


%% make inverse
fwd(mne.forward.Forward)
makeinv["mne.minimum_norm.make_inverse_operator(forward, noise_cov, ...)"]
inv(mne.minimum_norm.Inverse)
cov      -->  makeinv
fwd      -->  makeinv
makeinv  -->  inv


%% apply inverse
applyinv["mne.minimum_norm.apply_inverse(evoked, inverse, ...)"]
stc(mne.SourceEstimate)
evk       -->  applyinv
inv       -->  applyinv
applyinv  -->  stc


%% apply inv epochs
applyinvepo["mne.minimum_norm.apply_inverse_epochs(epochs, inverse, ...)"]
epo          --> applyinvepo
inv          -->  applyinvepo
applyinvepo  --> stc


%% restrict stc to label
inlab["source_est.in_label(label, ...)"]
stc(mne.SourceEstimate)
lab --> inlab
stc --> inlab
inlab --> stc


%% convert stc to label
tolab("source_est.to_label()")
stc --> tolab
src --> tolab
tolab --> lab


%% label time course
ltc["mne.extract_label_time_course([stcs], [labels], source_space, ...)"]
ltcarr("Label time courses (list of numpy.arrays)")
lab --> ltc
stc --> ltc
src --> ltc
ltc --> ltcarr


%% connectivity
sconn["mne.connectivity.spectral_connectivity()"]
conn("Spectral connectivity (list of numpy.arrays)")
ltcarr --> sconn
sconn --> conn


%% %% %% %% %%
%% classes  %%
%% %% %% %% %%

%% red: freesurfer objects
classDef source font-weight:bold,fill:#fcc,stroke:#633,stroke-width:4px;
class bem,tone,flash,src,surf,trans,fslab source;

%% Blue: python objects
classDef obj font-weight:bold,fill:#bce,stroke:#225,stroke-width:4px;
class acq,raw,ppraw,epo,evk,cov,inv,arr,fwd,stc,evarr,lab obj;
class ltcarr,conn obj;

%% green: python functions/methods
classDef fxn fill:#cda,stroke:#252;
class read,prep,epoching,events,epoarray,avg,compcov fxn;
class makeinv,applyinv,applyinvepo,setup,makefwd,makebem fxn;
class inlab,tolab,ltc,readlab,sconn fxn;

%% gray: bash programs
classDef console fill:#ddd,stroke:#555;
class flashbem,makelab console