@@ -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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-
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- # # Conceptual design
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-
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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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- 
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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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-
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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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