diff --git a/INSTALL.md b/INSTALL.md index 28936287..d65be467 100644 --- a/INSTALL.md +++ b/INSTALL.md @@ -30,13 +30,17 @@ Now that you cloned the repository using Datalad, you are able to get the data : # Move inside the root directory of the repository. cd narps_open_pipelines -# Select the data you want to download. Here is an example to get data of the first 4 subjects. +# Select the data you want to download. Here is an example to get data of subjects sub-001, sub-002, sub-003 and sub-004. datalad get data/original/ds001734/sub-00[1-4] -J 12 datalad get data/original/ds001734/derivatives/fmriprep/sub-00[1-4] -J 12 + +# Here is an example to get original results data from team 08MQ +datalad get data/results/orig/4953_08MQ/* -J 12 ``` -> [!NOTE] +> [!NOTE] > For further information and alternatives on how to get the data, see the corresponding documentation page [docs/data.md](docs/data.md). +> Also visit this page to get the whole dataset. ## 4 - Set up the environment @@ -101,11 +105,12 @@ Finally, you are able to use the scripts of the project : * `narps_open_status`: get status information about the development process of the pipelines ```bash -# Run the pipeline for team 2T6S, with 40 subjects -narps_open_runner -t 2T6S -n 40 +# Run the pipeline for team 2T6S, with subjects sub-001, sub-002, sub-003 and sub-004 +narps_open_runner -t 2T6S -s 1 2 3 4 # Run the pipeline for team 08MQ, compare results with original ones, # and produces a report with correlation values. +# WARNING : this will run the pipeline on more than the 4 first subjects narps_open_tester -t 08MQ # Compute the correlation values between results of 2T6S reproduction on 60 subjects with original ones @@ -115,8 +120,8 @@ narps_open_correlations -t 2T6S -n 60 # Get the description of team C88N in markdown formatting narps_description -t C88N --md -# Download the results from all teams -narps_results -a +# Download the results from team 2T6S +narps_results -t 2T6S # Get the pipeline work status information in json formatting narps_open_status --json @@ -126,7 +131,6 @@ narps_open_status --json > For further information about these command line tools, read the corresponding documentation pages. > * `narps_open_runner` : [docs/running.md](docs/running.md) > * `narps_open_tester` : [docs/testing.md](docs/testing.md#command-line-tool) -> * `narps_open_correlations` : [docs/correlation.md](docs/correlation.md#command-line-tool) > * `narps_description` : [docs/description.md](docs/description.md) > * `narps_results` : [docs/data.md](docs/data.md#results-from-narps-teams) > * `narps_open_status` : [docs/status.md](docs/status.md)