usage: fmridenoise [-h] [--version] {compare,dummy} ...

positional arguments:
  {compare,dummy}  commands
    compare        compare image files denoising using selected strategies
                   (pipelines) and denoising quality comparision
    dummy          creates dummy copy of existing dataset. Dummy dataset
                   mimics folders and files structure of origin datasetbut
                   only selected files are copied. Debugging tool.

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

Main functionality - compare

Entrypoint for main functionality of the program fmridenoise compare

usage: fmridenoise compare [-h] [-sub SUBJECTS [SUBJECTS ...]]
                           [-ses SESSIONS [SESSIONS ...]]
                           [-t TASKS [TASKS ...]] [-r RUNS [RUNS ...]]
                           [-p PIPELINES [PIPELINES ...]] [-d DERIVATIVES]
                           [--high-pass HIGH_PASS] [--low-pass LOW_PASS]
                           [-w WORKDIR] [--MultiProc] [--profiler PROFILER]
                           [-g] [--graph GRAPH] [--dry]

positional arguments:
  bids_dir              Path do preprocessed BIDS dataset.

optional arguments:
  -h, --help            show this help message and exit
  -sub SUBJECTS [SUBJECTS ...], --subjects SUBJECTS [SUBJECTS ...]
                        List of subjects
  -ses SESSIONS [SESSIONS ...], --sessions SESSIONS [SESSIONS ...]
                        List of session numbers, separated with spaces.
  -t TASKS [TASKS ...], --tasks TASKS [TASKS ...]
                        List of tasks names, separated with spaces.
  -r RUNS [RUNS ...], --runs RUNS [RUNS ...]
                        List of runs names, separated with spaces.
                        Name of pipelines used for denoising, can be both
                        paths to json files with pipeline or name of pipelines
                        from package.
                        Name (or list) of derivatives for which fmridenoise
                        should be run. By default workflow looks for fmriprep
  --high-pass HIGH_PASS
                        High pass filter value, deafult 0.008.
  --low-pass LOW_PASS   Low pass filter value, default 0.08
  -w WORKDIR, --workdir WORKDIR
                        Temporary working directory. Default is
  --MultiProc           Run script on multiple processors, default False
  --profiler PROFILER   Run profiler along workflow execution to estimate
                        resources usage PROFILER is path to output log file.
  -g, --debug           Run fmridenoise in debug mode - richer output, stops
                        on first unchandled exception.
  --graph GRAPH         Create workflow graph at GRAPH path
  --dry                 Perform everything except actually running workflow

Usage guidelines

Although fmridenoise is able to process data without explicit input parameters such as --sub, --ses, --task, --run and (especially) --pipelines we discourage to do that. When any of mentioned parameters are missing they will be selected based on input dataset, which may become problematic if there is missing data in dataset. Our recommendation is to run fmridenoise with all parameters set explicitly.

Other tools


Debugging tool fmridenoise dummy

usage: fmridenoise dummy [-h] [-c COPY [COPY ...]] bids_dir output_directory

positional arguments:
  bids_dir              Data source bids directory.
  output_directory      Directory in which dummy_complete dataset will be

optional arguments:
  -h, --help            show this help message and exit
  -c COPY [COPY ...], --copy COPY [COPY ...]
                        Extensions of files that should be copied instead of
                        creating dummy_complete