Command Line Interface

cuBNM command line interface

usage: cubnm [-h] {optimize,grid} ...

Positional Arguments

cmd: Possible choices: optimize, grid

Sub-commands

optimize

Optimize parameters using evolutionary algorithms

cubnm optimize [-h] -m {rWW,rWWEx,Kuramoto} -p PARAMS --duration DURATION --TR
               TR --sc SC [--sc_dist SC_DIST] [-d OUT_DIR] --emp_fc_tril
               EMP_FC_TRIL --emp_fcd_tril EMP_FCD_TRIL [--rand_seed RAND_SEED]
               [--noise_segment_length NOISE_SEGMENT_LENGTH] [--no_ext_out]
               [--states_ts] [--states_sampling STATES_SAMPLING]
               [--bw_params {friston2003,heinzle2016-3T}]
               [--bold_remove_s BOLD_REMOVE_S] [--window_size WINDOW_SIZE]
               [--window_step WINDOW_STEP] [--inc_interhemispheric]
               [--fcd_keep_edges] [--gof_terms GOF_TERMS] [--force_cpu]
               [--force_gpu] [--serial_nodes] [-v]
               [--progress_interval PROGRESS_INTERVAL] [--no_print_args]
               [-o OPTIMIZER] [--optimizer_seed OPTIMIZER_SEED]
               [--n_iter N_ITER] [--popsize POPSIZE]
               [--het_params HET_PARAMS [HET_PARAMS ...]] [--maps MAPS]
               [--maps_coef_range MAPS_COEF_RANGE]
               [--node_grouping NODE_GROUPING] [--multiobj]

Named Arguments

-m, --model

Possible choices: rWW, rWWEx, Kuramoto

Model (required)

-p, --params

Parameters in custom format inside quotation marks (required). Format: “<param_name>=<start>[:<end>[:<step>]],…”

--duration

Duration of the simulation (required)

--TR

Repetition time (required)

--sc

Structural connectivity .txt file or “example” (required)

--sc_dist

Structural connectivity distribution .txt file or “example”

-d, --out_dir

Output directory

Default: 'same'

--emp_fc_tril

Functional connectivity lower triangle .txt file or “example”

--emp_fcd_tril

Functional connectivity dynamics lower triangle .txt file or “example”

--rand_seed

Simulation noise seed

Default: 410

--noise_segment_length

Noise segment length (seconds)

Default: 30

--no_ext_out

Do not return model state variables

Default: False

--states_ts

Return model states timeseries

Default: False

--states_sampling

Sampling rate of model state variables

--bw_params

Possible choices: friston2003, heinzle2016-3T

Balloon Windkessel parameters

Default: 'friston2003'

--bold_remove_s

Remove initial n seconds of the simulation from BOLD and average of state variables

Default: 30

--window_size

FCD window size

Default: 10

--window_step

FCD window step

Default: 2

--inc_interhemispheric

Include interhemispheric connections in cost

Default: False

--fcd_keep_edges

Keep edge windows from FCD calculations

Default: False

--gof_terms

Goodness of fit terms (comma separated in quotation marks) e.g. “+fc_corr,-fcd_ks”.

Default: ['+fc_corr', '-fc_diff', '-fcd_ks']

--force_cpu

Force CPU

Default: False

--force_gpu

Force GPU

Default: False

--serial_nodes

Only applicable to GPUs; Uses one thread per simulation and do calculation of nodes serially; Experimental

Default: False

-v, --sim_verbose

Show simulation progress

Default: False

--progress_interval

Interval of progress updates (in msec). Only used if sim_verbose is True

Default: 500

--no_print_args

Do not print command line arguments table

Default: False

-o, --optimizer

Optimizer type

--optimizer_seed

Optimizer random seed

Default: 0

--n_iter

Optimizer max iterations

Default: 80

--popsize

Optimizer population size

Default: 24

--het_params

List of heterogeneous regional parameters (space separated)

--maps

Path to heterogeneity maps or “example”

--maps_coef_range

Coefficient range for maps. Options: “auto”, “min:max” (same for all maps), “min1:max1,min2:max2,…” (different for each map)

Default: auto

--node_grouping

Path to node grouping array or special values: node, sym

--multiobj

Instead of combining the objectives into a single objective function (via summation) defines each objective separately. This must not be used with single-objective optimizers

Default: False

grid

Grid search

cubnm grid [-h] -m {rWW,rWWEx,Kuramoto} -p PARAMS --duration DURATION --TR TR
           --sc SC [--sc_dist SC_DIST] [-d OUT_DIR] --emp_fc_tril EMP_FC_TRIL
           --emp_fcd_tril EMP_FCD_TRIL [--rand_seed RAND_SEED]
           [--noise_segment_length NOISE_SEGMENT_LENGTH] [--no_ext_out]
           [--states_ts] [--states_sampling STATES_SAMPLING]
           [--bw_params {friston2003,heinzle2016-3T}]
           [--bold_remove_s BOLD_REMOVE_S] [--window_size WINDOW_SIZE]
           [--window_step WINDOW_STEP] [--inc_interhemispheric]
           [--fcd_keep_edges] [--gof_terms GOF_TERMS] [--force_cpu]
           [--force_gpu] [--serial_nodes] [-v]
           [--progress_interval PROGRESS_INTERVAL] [--no_print_args]

Named Arguments

-m, --model

Possible choices: rWW, rWWEx, Kuramoto

Model (required)

-p, --params

Parameters in custom format inside quotation marks (required). Format: “<param_name>=<start>[:<end>[:<step>]],…”

--duration

Duration of the simulation (required)

--TR

Repetition time (required)

--sc

Structural connectivity .txt file or “example” (required)

--sc_dist

Structural connectivity distribution .txt file or “example”

-d, --out_dir

Output directory

Default: 'same'

--emp_fc_tril

Functional connectivity lower triangle .txt file or “example”

--emp_fcd_tril

Functional connectivity dynamics lower triangle .txt file or “example”

--rand_seed

Simulation noise seed

Default: 410

--noise_segment_length

Noise segment length (seconds)

Default: 30

--no_ext_out

Do not return model state variables

Default: False

--states_ts

Return model states timeseries

Default: False

--states_sampling

Sampling rate of model state variables

--bw_params

Possible choices: friston2003, heinzle2016-3T

Balloon Windkessel parameters

Default: 'friston2003'

--bold_remove_s

Remove initial n seconds of the simulation from BOLD and average of state variables

Default: 30

--window_size

FCD window size

Default: 10

--window_step

FCD window step

Default: 2

--inc_interhemispheric

Include interhemispheric connections in cost

Default: False

--fcd_keep_edges

Keep edge windows from FCD calculations

Default: False

--gof_terms

Goodness of fit terms (comma separated in quotation marks) e.g. “+fc_corr,-fcd_ks”.

Default: ['+fc_corr', '-fc_diff', '-fcd_ks']

--force_cpu

Force CPU

Default: False

--force_gpu

Force GPU

Default: False

--serial_nodes

Only applicable to GPUs; Uses one thread per simulation and do calculation of nodes serially; Experimental

Default: False

-v, --sim_verbose

Show simulation progress

Default: False

--progress_interval

Interval of progress updates (in msec). Only used if sim_verbose is True

Default: 500

--no_print_args

Do not print command line arguments table

Default: False