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.