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] [--dt DT] [--bw_dt BW_DT]
               [-d OUT_DIR] [--emp_fc_tril EMP_FC_TRIL]
               [--emp_fcd_tril EMP_FCD_TRIL] [--emp_bold EMP_BOLD] [--no_fc]
               [--no_fcd] [--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] [--exc_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”

--dt

Neuronal model integration step (msec)

Default: '0.1'

--bw_dt

Balloon-Windkessel model integration step (msec)

Default: '1.0'

-d, --out_dir

Output directory

Default: 'same'

--emp_fc_tril

Functional connectivity lower triangle as space-separated .txt file or “example”

--emp_fcd_tril

Functional connectivity dynamics lower triangle as space-separated .txt file or “example”

--emp_bold

Cleaned and parcellated BOLD signal as space-separated .txt file or “example” BOLD signal should be in the shape (nodes, volumes). Motion outliers should either be excluded (not recommended as it disrupts the temporal structure) or replaced with zeros. If provided emp_fc_tril and emp_fcd_tril will be ignored.

--no_fc

Do not calculate simulated/empirical FC

Default: False

--no_fcd

Do not calculate simulated/empirical FCD

Default: False

--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 FC/FCD calculations and average of state variables

Default: 30

--window_size

FCD window size

Default: 10

--window_step

FCD window step

Default: 2

--exc_interhemispheric

Exclude interhemispheric connections in FC/FCD calculations

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', '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] [--dt DT] [--bw_dt BW_DT] [-d OUT_DIR]
           [--emp_fc_tril EMP_FC_TRIL] [--emp_fcd_tril EMP_FCD_TRIL]
           [--emp_bold EMP_BOLD] [--no_fc] [--no_fcd] [--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] [--exc_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”

--dt

Neuronal model integration step (msec)

Default: '0.1'

--bw_dt

Balloon-Windkessel model integration step (msec)

Default: '1.0'

-d, --out_dir

Output directory

Default: 'same'

--emp_fc_tril

Functional connectivity lower triangle as space-separated .txt file or “example”

--emp_fcd_tril

Functional connectivity dynamics lower triangle as space-separated .txt file or “example”

--emp_bold

--no_fc

Do not calculate simulated/empirical FC

Default: False

--no_fcd

Do not calculate simulated/empirical FCD

Default: False

--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 FC/FCD calculations and average of state variables

Default: 30

--window_size

FCD window size

Default: 10

--window_step

FCD window step

Default: 2

--exc_interhemispheric

Exclude interhemispheric connections in FC/FCD calculations

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', '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