Command-line interface

lyman

usage: lyman [-h] {template,preproc,model,model-fit,model-res} ...

positional arguments:
  {template,preproc,model,model-fit,model-res}
                        processing stage
    template            functional template definition
    preproc             functional preprocessing
    model               fit univariate GLM and estimate contrasts
    model-fit           fit univariate GLM
    model-res           estimate univariate contrasts

optional arguments:
  -h, --help            show this help message and exit

lyman template

usage: lyman template [-h] [-s [id [id ...]]] [-n number] [--graph [<fname>]]
                      [--debug] [--clear-cache] [--no-qc] [--no-exec]

optional arguments:
  -h, --help            show this help message and exit
  -s [id [id ...]], --subject [id [id ...]]
                        subject id(s)
  -n number, --n-procs number
                        size of multiprocessing pool
  --graph [<fname>]     create graph image instead of executing
  --debug               enable nipype debug mode
  --clear-cache         remove existing cache directory before running
  --no-qc               don't connect qc nodes
  --no-exec             define the workflow but do not execute it

lyman preproc

usage: lyman preproc [-h] [-s [id [id ...]]] [--session [sess [sess ...]]]
                     [-e name] [-n number] [--graph [<fname>]] [--debug]
                     [--clear-cache] [--no-qc] [--no-exec]

optional arguments:
  -h, --help            show this help message and exit
  -s [id [id ...]], --subject [id [id ...]]
                        subject id(s)
  --session [sess [sess ...]]
                        scanning session(s) for single subject
  -e name, --experiment name
                        experiment name
  -n number, --n-procs number
                        size of multiprocessing pool
  --graph [<fname>]     create graph image instead of executing
  --debug               enable nipype debug mode
  --clear-cache         remove existing cache directory before running
  --no-qc               don't connect qc nodes
  --no-exec             define the workflow but do not execute it

lyman model

usage: lyman model [-h] [-s [id [id ...]]] [--session [sess [sess ...]]]
                   [-e name] [-m name] [-n number] [--graph [<fname>]]
                   [--debug] [--clear-cache] [--no-qc] [--no-exec]

optional arguments:
  -h, --help            show this help message and exit
  -s [id [id ...]], --subject [id [id ...]]
                        subject id(s)
  --session [sess [sess ...]]
                        scanning session(s) for single subject
  -e name, --experiment name
                        experiment name
  -m name, --model name
                        model name
  -n number, --n-procs number
                        size of multiprocessing pool
  --graph [<fname>]     create graph image instead of executing
  --debug               enable nipype debug mode
  --clear-cache         remove existing cache directory before running
  --no-qc               don't connect qc nodes
  --no-exec             define the workflow but do not execute it

lyman model-fit

usage: lyman model-fit [-h] [-s [id [id ...]]] [--session [sess [sess ...]]]
                       [-e name] [-m name] [-n number] [--graph [<fname>]]
                       [--debug] [--clear-cache] [--no-qc] [--no-exec]

optional arguments:
  -h, --help            show this help message and exit
  -s [id [id ...]], --subject [id [id ...]]
                        subject id(s)
  --session [sess [sess ...]]
                        scanning session(s) for single subject
  -e name, --experiment name
                        experiment name
  -m name, --model name
                        model name
  -n number, --n-procs number
                        size of multiprocessing pool
  --graph [<fname>]     create graph image instead of executing
  --debug               enable nipype debug mode
  --clear-cache         remove existing cache directory before running
  --no-qc               don't connect qc nodes
  --no-exec             define the workflow but do not execute it

lyman model-res

usage: lyman model-res [-h] [-s [id [id ...]]] [-e name] [-m name] [-n number]
                       [--graph [<fname>]] [--debug] [--clear-cache] [--no-qc]
                       [--no-exec]

optional arguments:
  -h, --help            show this help message and exit
  -s [id [id ...]], --subject [id [id ...]]
                        subject id(s)
  -e name, --experiment name
                        experiment name
  -m name, --model name
                        model name
  -n number, --n-procs number
                        size of multiprocessing pool
  --graph [<fname>]     create graph image instead of executing
  --debug               enable nipype debug mode
  --clear-cache         remove existing cache directory before running
  --no-qc               don't connect qc nodes
  --no-exec             define the workflow but do not execute it