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Update README.md
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Arshitha authored Dec 14, 2023
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Expand Up @@ -130,21 +130,7 @@ To visually inspect quality of defacing with [VisualQC](https://raamana.github.i
```bash
sh ${OUTPUT_DIR}/QC_prep/defacing_qc_cmd
```

## Conceptual design

1. Generate a ["primary" scans](#terminology) to [other scans](#terminology) mapping file.
2. Deface primary scans
with [@afni_refacer_run](https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/refacer/refacer_run.html) program
developed by the AFNI Team.
3. To deface remaining scans in the session, register them to the primary scan (using FSL `flirt` command) and then use
the primary scan's defacemask to generate a defaced image (using `fslmaths` command).
4. Visually inspect defaced scans with [VisualQC](https://raamana.github.io/visualqc) deface tool or any other preferred
tool.
5. Correct/fix defaced scans that failed visual inspection. See [here](FILLINTHEBLANK) for more info on types of failures.
![Defacing Pipeline flowchart](images/defacing_pipeline.png)

## Terminology

While describing this process, we frequently use the following terms:
Expand All @@ -158,18 +144,6 @@ While describing this process, we frequently use the following terms:
- **[VisualQC](https://raamana.github.io/visualqc):** A suite of QC tools developed by Pradeep Raamana, PhD (Assistant
Professor at University of Pittsburgh).

## References
1. Theyers AE, Zamyadi M, O'Reilly M, Bartha R, Symons S, MacQueen GM, Hassel S, Lerch JP, Anagnostou E, Lam RW, Frey
BN, Milev R, Müller DJ, Kennedy SH, Scott CJM, Strother SC, and Arnott SR (2021)
[Multisite Comparison of MRI Defacing Software Across Multiple Cohorts](10.3389/fpsyt.2021.617997). Front. Psychiatry
12:617997. doi:10.3389/fpsyt.2021.617997
2. `@afni_refacer_run` is the defacing tool used under the
hood. [AFNI Refacer program](https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/refacer/refacer_run.html).
3. FSL's [FLIRT](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT)
and [`fslmaths`](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Fslutils?highlight=%28fslmaths%29) programs have been used
for registration and masking steps in the workflow.
4. [VisualQC](https://raamana.github.io/visualqc/) utility.

## Acknowledgements

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