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Update installation documentation #47

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Aug 28, 2024
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Update installation documentation #47

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4edc4a9
Update installation instructions.
tsalo Aug 28, 2024
1592c8a
Create config.yml
tsalo Aug 28, 2024
df864ea
Update installation.rst
tsalo Aug 28, 2024
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5 changes: 5 additions & 0 deletions .github/ISSUE_TEMPLATE/config.yml
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blank_issues_enabled: true
contact_links:
- name: Questions
url: https://neurostars.org/tag/fmripost-aroma
about: For general questions, please search Neurostars for existing posts before starting a new one.
8 changes: 3 additions & 5 deletions README.md
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# fmripost-aroma

[![Docker Image](https://img.shields.io/badge/docker-nipreps/fmripost--aroma-brightgreen.svg?logo=docker&style=flat)](https://hub.docker.com/r/nipreps/fmripost-aroma/tags/)
[![PyPI - Version](https://img.shields.io/pypi/v/fmripost-aroma.svg)](https://pypi.org/project/fmripost-aroma)
[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/fmripost-aroma.svg)](https://pypi.org/project/fmripost-aroma)

fMRIPost-AROMA is a BIDS App for running ICA-AROMA on a preprocessed
fMRI dataset.
It is intended to replace the built-in workflow in fMRIPrep 23.0 and earlier,
but accepts any BIDS derivatives dataset where BOLD images have been resampled
to MNI152NLin6Asym.

***This is currently a placeholder. The workflow still needs to be copied here
and packaged.***
to MNI152NLin6Asym at 2 mm3 resolution.

-----

Expand All @@ -22,7 +20,7 @@ and packaged.***
## Installation

```console
pip install fmripost-aroma
docker pull nipreps/fmripost-aroma:unstable
```

## License
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21 changes: 2 additions & 19 deletions docs/installation.rst
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Expand Up @@ -5,26 +5,9 @@ Installation
------------
*fMRIPost-AROMA* should be installed using container technologies.

The ``fmripost-aroma`` command-line adheres to the `BIDS-Apps recommendations
for the user interface <usage.html#execution-and-the-bids-format>`__.
Therefore, the command-line has the following structure::
.. code-block:: bash
docker pull nipreps/fmripost-aroma:unstable

$ fmripost-aroma <input_bids_path> -d <derivatives_path> <analysis_level> <named_options>

The ``fmripost-aroma`` command-line options are documented in the :ref:`usage`
section.

The command-line will be composed of a preamble to configure the
container execution followed by the ``fmripost-aroma`` command-line options
as if you were running it on a *bare-metal* installation.
The command-line structure above is then modified as follows::

$ <container_command_and_options> <container_image> \
<input_bids_path> <derivatives_path> <analysis_level> <fmriprep_named_options>

Therefore, once specified the container options and the image to be run
the command line is the same as for the *bare-metal* installation but dropping
the ``fmripost-aroma`` executable name.

Containerized execution (Docker and Singularity)
================================================
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