Dipy Workflow Wrapper
This is a Brainlife wrapper App for various Dipy workflows (dipy_* commands installed as part of Dipy distribution). This single wrapper is exposed through multiple Dipy Apps registered on Brainlife.io. The code then runs different Dipy workflow based on "command" parameter as part of config.json generated by various Brainlife Apps.
Please dipy homepage for more information about Dipy.
Authors
- Serge Koudoro (skoudoro@iu.edu)
- Soichi Hayashi (hayashis@iu.edu)
Project directors
- Franco Pestilli (franpest@indiana.edu)
- Eleftherios Garyfallidis (elef@indiana.edu)
Funding
Running the App
On Brainlife.io
You can see a list of Dipy Apps currently regsitered on Brainlife. Find the App that you'd like to run and click "Execute" tab to specify dataset that you'd like to run the App on.
Running Locally (on your machine)
This repo is a wrapper around various Dipy workflows so that Brainlife can execute them. You can simply run each dipy workflow through various dipy command lines once you install dipy.
dipy_fit_csa dipy_fit_dki dipy_fit_mapmri dipy_mask dipy_nlmeans dipy_track_det
dipy_fit_csd dipy_fit_dti dipy_info dipy_median_otsu dipy_reslice
Dependencies
This App runs on singularity.
Reconstruction information
TODO - please explain what this table shows.
| Method | Single Shell | Multi-Shell | Cartesian |
|---|---|---|---|
| SHORE | x | ||
| MAP-MRI | x | ||
| MAPL | x | ||
| DKI - Standard | x | ||
| DKI - Micro | ? | ? | |
| DTI (SLS, WLS, NNLS) | x | x | |
| CSD | x | ||
| MCSD | x | ||
| SDT | x | ||
| DSI | x | ||
| DSID | x | ||
| GQI - GQI2 | x | x | |
| SFM | x | x | |
| Q-BALL | x | ||
| CSA | x | ||
| Westin CSA | x | ||
| ForeCast | x | ||
| IVIM | x | ||
| ActiveAx | x | ||
| Noddi / NoddiX | x | ||
| Ball & Stick | x | x |