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Updated for new test dataset and combined additional resources into r…
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…unning the software
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@Gab-D-G
Gab-D-G committed Sep 21, 2023
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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:

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Expand All @@ -40,28 +40,31 @@ Mandatory BIDS specifications are:
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<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>
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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.

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