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README.md

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@@ -130,21 +130,7 @@ To visually inspect quality of defacing with [VisualQC](https://raamana.github.i
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```bash
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sh ${OUTPUT_DIR}/QC_prep/defacing_qc_cmd
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```
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## Conceptual design
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1. Generate a ["primary" scans](#terminology) to [other scans](#terminology) mapping file.
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2. Deface primary scans
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with [@afni_refacer_run](https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/refacer/refacer_run.html) program
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developed by the AFNI Team.
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3. To deface remaining scans in the session, register them to the primary scan (using FSL `flirt` command) and then use
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the primary scan's defacemask to generate a defaced image (using `fslmaths` command).
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4. Visually inspect defaced scans with [VisualQC](https://raamana.github.io/visualqc) deface tool or any other preferred
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tool.
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5. Correct/fix defaced scans that failed visual inspection. See [here](FILLINTHEBLANK) for more info on types of failures.
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![Defacing Pipeline flowchart](images/defacing_pipeline.png)
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## Terminology
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While describing this process, we frequently use the following terms:
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- **[VisualQC](https://raamana.github.io/visualqc):** A suite of QC tools developed by Pradeep Raamana, PhD (Assistant
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Professor at University of Pittsburgh).
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## References
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1. Theyers AE, Zamyadi M, O'Reilly M, Bartha R, Symons S, MacQueen GM, Hassel S, Lerch JP, Anagnostou E, Lam RW, Frey
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BN, Milev R, Müller DJ, Kennedy SH, Scott CJM, Strother SC, and Arnott SR (2021)
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[Multisite Comparison of MRI Defacing Software Across Multiple Cohorts](10.3389/fpsyt.2021.617997). Front. Psychiatry
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12:617997. doi:10.3389/fpsyt.2021.617997
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2. `@afni_refacer_run` is the defacing tool used under the
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hood. [AFNI Refacer program](https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/refacer/refacer_run.html).
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3. FSL's [FLIRT](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT)
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and [`fslmaths`](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Fslutils?highlight=%28fslmaths%29) programs have been used
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for registration and masking steps in the workflow.
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4. [VisualQC](https://raamana.github.io/visualqc/) utility.
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## Acknowledgements
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