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Merge pull request #318 from CoBrALab/docu_updates
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Docu updates
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@Gab-D-G
Gab-D-G authored Sep 27, 2023
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5 changes: 0 additions & 5 deletions docs/additional.md
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7 changes: 4 additions & 3 deletions docs/installation.md
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Expand Up @@ -10,15 +10,16 @@ However, this does not account for non-python dependencies found in `dependencie
## Container (Singularity/Docker)
For most uses, we recommend instead using a containerized installation with [Singularity](https://singularity.lbl.gov) or [Docker](https://www.docker.com). Containers allow to build entire computing environments, grouping all dependencies required to run the software. This in turn reduces the burden of installing dependencies manually and ensures reproducible behavior of the software. Singularity is generally preferred over Docker since it requires less permission, and can thus be imported from most computing environment (e.g. high performance computing clusters such as Compute Canada.)

A containerized version of RABIES is available on [Docker Hub](https://hub.docker.com/r/gabdesgreg/rabies). After installing Singularity or Docker, the following command will pull and build the container:
A [containerized version](https://github.com/CoBrALab/RABIES/pkgs/container/rabies) of RABIES is available from Github. After installing Singularity or Docker, the following command will pull and build the container:
* Install Singularity .sif file:
```
singularity build rabies.sif docker://gabdesgreg/rabies:tagname
singularity build rabies.sif docker://ghcr.io/cobralab/rabies:latest
```
* Install Docker image:
```
docker pull gabdesgreg/rabies:tagname
docker pull ghcr.io/cobralab/rabies:latest
```
A specific tag version can be selected (instead of `latest`) from the [list online](https://github.com/CoBrALab/RABIES/pkgs/container/rabies). Versions prior to 0.5.0 are found on [Docker Hub](https://hub.docker.com/r/gabdesgreg/rabies).

## Neurodesk
RABIES is also made available on the [Neurodesk platform](https://neurodesk.github.io/), as part of the [built-in tools](https://neurodesk.github.io/applications/) for neuroimaging. The Neurodesk platform allows for an entirely browser-based neuroimaging computing environment, with pre-built neuroimaging tools from the community, and aims at reducing needs for manual development of computing environments and at improving reproducible neuroimaging. More details on Neurodesk here <https://neurodesk.github.io/docs/>.
58 changes: 34 additions & 24 deletions docs/running_the_software.md
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Expand Up @@ -12,15 +12,15 @@ Mandatory BIDS specifications are:
* `run-{run #}` is necessary for functional images if there are multiple scans per session

### Directory structure for an example dataset
* Our [example dataset](http://doi.org/10.5281/zenodo.3937697) has the following BIDS structure:
* Our [example dataset](http://doi.org/10.5281/zenodo.8349029) has the following BIDS structure:

<!DOCTYPE html>
<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<meta name="Author" content="Made by 'tree'">
<meta name="GENERATOR" content="$Version: $ tree v1.7.0 (c) 1996 - 2014 by Steve Baker, Thomas Moore, Francesc Rocher, Florian Sesser, Kyosuke Tokoro $">
<!--
<!--
BODY { font-family : ariel, monospace, sans-serif; }
P { font-weight: normal; font-family : ariel, monospace, sans-serif; color: black; background-color: transparent;}
B { font-weight: normal; color: black; background-color: transparent;}
Expand All @@ -40,28 +40,31 @@ Mandatory BIDS specifications are:
-->
</head>
<body>
<p>
<a href="test_dataset">test_dataset</a><br>
├── <a href="test_dataset/sub-MFC067/">sub-MFC067</a><br>
│   └── <a href="test_dataset/sub-MFC067/ses-1/">ses-1</a><br>
│   &nbsp;&nbsp;&nbsp; ├── <a href="test_dataset/sub-MFC067/ses-1/anat/">anat</a><br>
│   &nbsp;&nbsp;&nbsp; │   └── <a href="test_dataset/sub-MFC067/ses-1/anat/sub-MFC067_ses-1_acq-FLASH_T1w.nii.gz">sub-MFC067_ses-1_acq-FLASH_T1w.nii.gz</a><br>
│   &nbsp;&nbsp;&nbsp; └── <a href="test_dataset/sub-MFC067/ses-1/func/">func</a><br>
│   &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; └── <a href="test_dataset/sub-MFC067/ses-1/func/sub-MFC067_ses-1_task-rest_acq-EPI_run-1_bold.nii.gz">sub-MFC067_ses-1_task-rest_acq-EPI_run-1_bold.nii.gz</a><br>
└── <a href="test_dataset/sub-MFC068/">sub-MFC068</a><br>
&nbsp;&nbsp;&nbsp; └── <a href="test_dataset/sub-MFC068/ses-1/">ses-1</a><br>
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; ├── <a href="test_dataset/sub-MFC068/ses-1/anat/">anat</a><br>
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; │   └── <a href="test_dataset/sub-MFC068/ses-1/anat/sub-MFC068_ses-1_acq-FLASH_T1w.nii.gz">sub-MFC068_ses-1_acq-FLASH_T1w.nii.gz</a><br>
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; └── <a href="test_dataset/sub-MFC068/ses-1/func/">func</a><br>
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; └── <a href="test_dataset/sub-MFC068/ses-1/func/sub-MFC068_ses-1_task-rest_acq-EPI_run-1_bold.nii.gz">sub-MFC068_ses-1_task-rest_acq-EPI_run-1_bold.nii.gz</a><br>
<br><br>
</p>
<p>

8 directories, 4 files
<br><br>
</p>
<hr>
<a href="https://zenodo.org/record/8349029/preview/test_dataset.zip">https://zenodo.org/record/8349029/preview/test_dataset.zip</a><br>
├── <a href="https://zenodo.org/record/8349029/preview/test_dataset.zip/sub-PHG001/">sub-PHG001</a><br>
│ └── <a href="https://zenodo.org/record/8349029/preview/test_dataset.zip/sub-PHG001/ses-3/">ses-3</a><br>
│ &nbsp;&nbsp;&nbsp; ├── <a href="https://zenodo.org/record/8349029/preview/test_dataset.zip/sub-PHG001/ses-3/anat/">anat</a><br>
│ &nbsp;&nbsp;&nbsp; │ ├── <a href="https://zenodo.org/record/8349029/preview/test_dataset.zip/sub-PHG001/ses-3/anat/sub-PHG001_ses-3_acq-RARE_T2w.json">sub-PHG001_ses-3_acq-RARE_T2w.json</a><br>
│ &nbsp;&nbsp;&nbsp; │ └── <a href="https://zenodo.org/record/8349029/preview/test_dataset.zip/sub-PHG001/ses-3/anat/sub-PHG001_ses-3_acq-RARE_T2w.nii.gz">sub-PHG001_ses-3_acq-RARE_T2w.nii.gz</a><br>
│ &nbsp;&nbsp;&nbsp; └── <a href="https://zenodo.org/record/8349029/preview/test_dataset.zip/sub-PHG001/ses-3/func/">func</a><br>
│ &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; ├── <a href="https://zenodo.org/record/8349029/preview/test_dataset.zip/sub-PHG001/ses-3/func/sub-PHG001_ses-3_task-rest_acq-EPI_run-1_bold.json">sub-PHG001_ses-3_task-rest_acq-EPI_run-1_bold.json</a><br>
│ &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; └── <a href="https://zenodo.org/record/8349029/preview/test_dataset.zip/sub-PHG001/ses-3/func/sub-PHG001_ses-3_task-rest_acq-EPI_run-1_bold.nii.gz">sub-PHG001_ses-3_task-rest_acq-EPI_run-1_bold.nii.gz</a><br>
└── <a href="https://zenodo.org/record/8349029/preview/test_dataset.zip/sub-PHG002/">sub-PHG002</a><br>
&nbsp;&nbsp;&nbsp; └── <a href="https://zenodo.org/record/8349029/preview/test_dataset.zip/sub-PHG002/ses-3/">ses-3</a><br>
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; ├── <a href="https://zenodo.org/record/8349029/preview/test_dataset.zip/sub-PHG002/ses-3/anat/">anat</a><br>
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; │ ├── <a href="https://zenodo.org/record/8349029/preview/test_dataset.zip/sub-PHG002/ses-3/anat/sub-PHG002_ses-3_acq-RARE_T2w.json">sub-PHG002_ses-3_acq-RARE_T2w.json</a><br>
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; │ └── <a href="https://zenodo.org/record/8349029/preview/test_dataset.zip/sub-PHG002/ses-3/anat/sub-PHG002_ses-3_acq-RARE_T2w.nii.gz">sub-PHG002_ses-3_acq-RARE_T2w.nii.gz</a><br>
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; └── <a href="https://zenodo.org/record/8349029/preview/test_dataset.zip/sub-PHG002/ses-3/func/">func</a><br>
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; ├── <a href="https://zenodo.org/record/8349029/preview/test_dataset.zip/sub-PHG002/ses-3/func/sub-PHG002_ses-3_task-rest_acq-EPI_run-1_bold.json">sub-PHG002_ses-3_task-rest_acq-EPI_run-1_bold.json</a><br>
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; └── <a href="https://zenodo.org/record/8349029/preview/test_dataset.zip/sub-PHG002/ses-3/func/sub-PHG002_ses-3_task-rest_acq-EPI_run-1_bold.nii.gz">sub-PHG002_ses-3_task-rest_acq-EPI_run-1_bold.nii.gz</a><br>
<br><br>
</p>
<p>

8 directories, 8 files
<br><br>
</p>
<hr>
</body>
</html>

Expand Down Expand Up @@ -183,4 +186,11 @@ gabdesgreg/rabies:tagname -p MultiProc preprocess /input_BIDS/ /preprocess_outpu
The syntax in Docker is very similar to Singularity, except that `-B` is replaced by `-v`, and further parameters may be needed (e.g. `-it`, `--rm`). Note that 'tagname' should be replaced by the proper RABIES version you are using (e.g. 0.4.8).


## Additional Resources

* **Workshop and tutorial for RABIES:**
* [Hands-on tutorial](https://github.com/grandjeanlab/INCF_preclinical/tree/main) on RABIES presented at the INCF Neuroinformatics Assembly 2023 (in the `rabies/` folder of the repository).
* A workshop providing a complete software overview was [recorded and posted online](https://www.youtube.com/watch?v=LZohKlUgycc&t=2766s&ab_channel=DouglasResearchCentre) on February 2023.
* Conversion from Bruker raw to Nifti formats can be handled with [BrkRaw](https://brkraw.github.io/) (consult [associated documentation](https://github.com/CoBrALab/documentation/wiki/bruker2nifti-conversion) from the CoBrALab)
* [CoBrALab recommendations](https://github.com/CoBrALab/documentation/wiki/Running-RABIES-on-niagara) for using compute canada.

2 changes: 1 addition & 1 deletion rabies/__version__.py
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Expand Up @@ -3,6 +3,6 @@
# 88YbdP88 8P 88""" dP__Yb Yb 88"Yb dP__Yb Yb "88 88""
# 88 YY 88 dP 88 dP""""Yb YboodP 88 Yb dP""""Yb YboodP 888888

VERSION = (0, 5, 0)
VERSION = (0, 5, 1)

__version__ = '.'.join(map(str, VERSION))

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