diff --git a/docs/data.md b/docs/data.md index c5b55fba..3471729a 100644 --- a/docs/data.md +++ b/docs/data.md @@ -67,28 +67,31 @@ for team in teams: collection.rectify() # Rectified versions are created ``` +> [! TIP] +> In the following examples, use `narps_results` or `python narps_open/data/results` indifferently to launch the command line tool. + ```bash # From the command line -$ python narps_open/data/results -h -usage: results [-h] (-t TEAMS [TEAMS ...] | -a) [-r] +narps_results -h + usage: results [-h] (-t TEAMS [TEAMS ...] | -a) [-r] -Get Neurovault collection of results from NARPS teams. + Get Neurovault collection of results from NARPS teams. -options: - -h, --help show this help message and exit - -t TEAMS [TEAMS ...], --teams TEAMS [TEAMS ...] - a list of team IDs - -a, --all download results from all teams - -r, --rectify rectify the results + options: + -h, --help show this help message and exit + -t TEAMS [TEAMS ...], --teams TEAMS [TEAMS ...] + a list of team IDs + -a, --all download results from all teams + -r, --rectify rectify the results # Either download all collections -python narps_open/utils/results -a +narps_results -a # Or select the ones you need -python narps_open/utils/results -t 2T6S C88N L1A8 +narps_results -t 2T6S C88N L1A8 # Download and rectify the collections -python narps_open/utils/results -r -t 2T6S C88N L1A8 +narps_results -r -t 2T6S C88N L1A8 ``` The collections are also available [here](https://zenodo.org/record/3528329/) as one release on Zenodo that you can download. diff --git a/docs/description.md b/docs/description.md index ac17f588..1723f64f 100644 --- a/docs/description.md +++ b/docs/description.md @@ -12,8 +12,11 @@ The class `TeamDescription` of module `narps_open.data.description` acts as a pa You can use the command-line tool as so. Option `-t` is for the team id, option `-d` allows to print only one of the sub parts of the description among : `general`, `exclusions`, `preprocessing`, `analysis`, `categorized_for_analysis`, `derived`, and `comments`. Options `--json` and `--md` allow to choose the export format you prefer between JSON and Markdown. +> [! TIP] +> In the following examples, use `narps_description` or `python narps_open/data/description` indifferently to launch the command line tool. + ```bash -python narps_open/data/description -h +narps_description -h # usage: __init__.py [-h] -t TEAM [-d {general,exclusions,preprocessing,analysis,categorized_for_analysis,derived,comments}] # # Get description of a NARPS pipeline. @@ -26,7 +29,7 @@ python narps_open/data/description -h # --json output team description as JSON # --md output team description as Markdown -python narps_open/data/description -t 2T6S --json +narps_description -t 2T6S --json # { # "general.teamID": "2T6S", # "general.NV_collection_link": "https://neurovault.org/collections/4881/", @@ -41,7 +44,7 @@ python narps_open/data/description -t 2T6S --json # "preprocessing.preprocessing_order": "We used the provided preprocessed data by fMRIPprep 1.1.4 (Esteban, Markiewicz, et al. (2018); Esteban, Blair, et al. (2018); RRID:SCR_016216), which is based on Nipype 1.1.1 (Gorgolewski et al. (2011); Gorgolewski et al. (2018); RRID:SCR_002502) and we additionally conducted a spatial smoothing using the provided preprocessed data set and SPM12. Here, we attach the preprocessing steps described in the provided data set. \nAnatomical data preprocessing\nThe T1-weighted (T1w) image was corrected for intensity non-uniformity (INU) using N4BiasFieldCorrection (Tustison et al. 2010, ANTs 2.2.0), and used as T1w-reference throughout the workflow. The T1w-reference was then skull-stripped using antsBrainExtraction.sh (ANTs 2.2.0), using OASIS as target template. Brain surfaces we # ... -python narps_open/data/description -t 2T6S -d general --json +narps_description -t 2T6S -d general --json # { # "teamID": "2T6S", # "NV_collection_link": "https://neurovault.org/collections/4881/", @@ -53,7 +56,7 @@ python narps_open/data/description -t 2T6S -d general --json # "general_comments": "NA" # } -python narps_open/data/description -t 2T6S --md +narps_description -t 2T6S --md # # NARPS team description : 2T6S # ## General # * `teamID` : 2T6S diff --git a/docs/running.md b/docs/running.md index eb614eef..edf94171 100644 --- a/docs/running.md +++ b/docs/running.md @@ -2,10 +2,13 @@ ## Using the runner application -The `narps_open.runner` module allows to run pipelines from the command line : +The `narps_open.runner` module allows to run pipelines from the command line. + +> [! TIP] +> In the following examples, use `narps_open_runner` or `python narps_open/runner.py` indifferently to launch the command line tool. ```bash -python narps_open/runner.py -h +narps_open_runner -h usage: runner.py [-h] -t TEAM (-r RANDOM | -s SUBJECTS [SUBJECTS ...]) [-g | -f] Run the pipelines from NARPS. @@ -19,13 +22,14 @@ python narps_open/runner.py -h -f, --first run the first levels only (preprocessing + subjects + runs) -c, --check check pipeline outputs (runner is not launched) -python narps_open/runner.py -t 2T6S -s 001 006 020 100 -python narps_open/runner.py -t 2T6S -r 4 -python narps_open/runner.py -t 2T6S -r 4 -f -python narps_open/runner.py -t 2T6S -r 4 -f -c # Check the output files without launching the runner +narps_open_runner -t 2T6S -s 001 006 020 100 +narps_open_runner -t 2T6S -r 4 +narps_open_runner -t 2T6S -r 4 -f +narps_open_runner -t 2T6S -r 4 -f -c # Check the output files without launching the runner ``` -In this usecase, the paths where to store the outputs and to the dataset are picked by the runner from the [configuration](docs/configuration.md). +> [! NOTE] +> In this usecase, the paths where to store the outputs and to the dataset are picked by the runner from the [configuration](docs/configuration.md). ## Using the `PipelineRunner` object diff --git a/docs/status.md b/docs/status.md index 28492390..8ffc7beb 100644 --- a/docs/status.md +++ b/docs/status.md @@ -46,8 +46,11 @@ report.markdown() # Returns a string containing the markdown You can also use the command-line tool as so. +> [! TIP] +> In the following examples, use `narps_open_status` or `python narps_open/utils/status.py` indifferently to launch the command line tool. + ```bash -python narps_open/utils/status -h +narps_open_status -h # usage: status.py [-h] [--json | --md] # # Get a work progress status report for pipelines. @@ -57,7 +60,7 @@ python narps_open/utils/status -h # --json output the report as JSON # --md output the report as Markdown -python narps_open/utils/status --json +narps_open_status --json # { # "08MQ": { # "softwares": "FSL", @@ -83,7 +86,7 @@ python narps_open/utils/status --json # }, # ... -python narps_open/utils/status --md +narps_open_status --md # ... # | team_id | status | main software | fmriprep used ? | related issues | related pull requests | excluded from NARPS analysis | reproducibility | # | --- |:---:| --- | --- | --- | --- | --- | --- |