Usage¶
fmridenoise
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
--version
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]
bids_dir
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.
-p PIPELINES [PIPELINES ...], --pipelines PIPELINES [PIPELINES ...]
Name of pipelines used for denoising, can be both
paths to json files with pipeline or name of pipelines
from package.
-d DERIVATIVES, --derivatives DERIVATIVES
Name (or list) of derivatives for which fmridenoise
should be run. By default workflow looks for fmriprep
dataset.
--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
'/tmp/fmridenoise
--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¶
dummy¶
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
saved
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