README.oldmd

# 


## Global environment setup






## Set MATLAB paths

<code>Set Path - Add with Subfolders ... - Select BrainMRIpipelines folder</code>. This will be automatically configured in <code>bmp_init.sh</code> in the future.


## Workflows

Please go to specific folders for details:

- [Initialisation for BMP](https://github.com/JiyangJiang/BrainMRIpipelines/tree/master/init)
- [Converting to BIDS](https://github.com/JiyangJiang/BrainMRIpipelines/tree/master/BIDS)
- [Structural MRI workflow](https://github.com/JiyangJiang/BrainMRIpipelines/tree/master/sMRI)
- [ASL workflow](https://github.com/JiyangJiang/BrainMRIpipelines/tree/master/ASL)

## Useful readings
- [Siemens scanner slice ordering](https://practicalfmri.blogspot.com/2012/07/siemens-slice-ordering.html)
- [practiCal fMRI: the nuts & bolts](https://practicalfmri.blogspot.com/)
- [U of A: Neuroimaging Core Documentation](https://neuroimaging-core-docs.readthedocs.io/en/latest/index.html)
- [Chris Rordens Neuropsychology Lab Documentation](https://crnl.readthedocs.io/index.html)