From 24a270ad686eb363fc72c417f6adfa9a73184a4e Mon Sep 17 00:00:00 2001 From: Gab-D-G Date: Thu, 21 Sep 2023 14:29:45 -0400 Subject: [PATCH 1/3] switching to version 0.5.1 --- rabies/__version__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/rabies/__version__.py b/rabies/__version__.py index ad08bdc..e244663 100644 --- a/rabies/__version__.py +++ b/rabies/__version__.py @@ -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)) From 179cb52153ca11c30ed42196a7299a85adaa5859 Mon Sep 17 00:00:00 2001 From: Gab-D-G Date: Thu, 21 Sep 2023 16:16:55 -0400 Subject: [PATCH 2/3] Updated for new test dataset and combined additional resources into running the software --- docs/additional.md | 5 ---- docs/running_the_software.md | 58 +++++++++++++++++++++--------------- 2 files changed, 34 insertions(+), 29 deletions(-) delete mode 100644 docs/additional.md 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/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 +

+

+
@@ -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. From d4a540bdc0968c3992f806622718f38b33b1b2e5 Mon Sep 17 00:00:00 2001 From: Gab-D-G Date: Mon, 25 Sep 2023 18:27:26 -0400 Subject: [PATCH 3/3] container build instructions were updated for Github containers. --- docs/installation.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) 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