diff --git a/docs/additional.md b/docs/additional.md
deleted file mode 100644
index 7c573a1..0000000
--- a/docs/additional.md
+++ /dev/null
@@ -1,5 +0,0 @@
-# Additional Resources
-
-* A workshop providing a complete software overview was recorded and posted online: https://www.youtube.com/watch?v=LZohKlUgycc&t=2766s&ab_channel=DouglasResearchCentre
-* 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 for using compute canada: https://github.com/CoBrALab/documentation/wiki/Running-RABIES-on-niagara
diff --git a/docs/installation.md b/docs/installation.md
index 7990cdf..5a5ae90 100644
--- a/docs/installation.md
+++ b/docs/installation.md
@@ -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 .
\ No newline at end of file
diff --git a/docs/running_the_software.md b/docs/running_the_software.md
index 54c6bd4..0880f98 100644
--- a/docs/running_the_software.md
+++ b/docs/running_the_software.md
@@ -12,7 +12,7 @@ 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:
@@ -20,7 +20,7 @@ Mandatory BIDS specifications are:
-
-
- test_dataset
- ├── sub-MFC067
- │ └── ses-1
- │ ├── anat
- │ │ └── sub-MFC067_ses-1_acq-FLASH_T1w.nii.gz
- │ └── func
- │ └── sub-MFC067_ses-1_task-rest_acq-EPI_run-1_bold.nii.gz
- └── sub-MFC068
- └── ses-1
- ├── anat
- │ └── sub-MFC068_ses-1_acq-FLASH_T1w.nii.gz
- └── func
- └── sub-MFC068_ses-1_task-rest_acq-EPI_run-1_bold.nii.gz
-
-
-
-
-8 directories, 4 files
-
-
-
+ 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.nii.gz
+ │ └── func
+ │ ├── sub-PHG001_ses-3_task-rest_acq-EPI_run-1_bold.json
+ │ └── sub-PHG001_ses-3_task-rest_acq-EPI_run-1_bold.nii.gz
+ └── sub-PHG002
+ └── ses-3
+ ├── anat
+ │ ├── sub-PHG002_ses-3_acq-RARE_T2w.json
+ │ └── sub-PHG002_ses-3_acq-RARE_T2w.nii.gz
+ └── func
+ ├── sub-PHG002_ses-3_task-rest_acq-EPI_run-1_bold.json
+ └── sub-PHG002_ses-3_task-rest_acq-EPI_run-1_bold.nii.gz
+
+
+
+
+8 directories, 8 files
+
+
+