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Slight changes in the installation documentation
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bclenet committed Nov 21, 2024
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18 changes: 11 additions & 7 deletions INSTALL.md
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Expand Up @@ -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

Expand Down Expand Up @@ -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
Expand All @@ -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
Expand All @@ -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)

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