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Documentation Index

Fetch the complete documentation index at: https://docs.brainworkup.org/llms.txt

Use this file to discover all available pages before exploring further.

This guide walks you through the full workflow: installing the required tools, scaffolding a new report project from a Luria Voice template, filling in patient metadata, and rendering your first PDF. By the end you will have a working PDF evaluation report on your machine.

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Prerequisites

Before you start, make sure you have the following installed:
  • Quarto ≥ 1.4.0 — Typst is bundled with Quarto; no separate Typst install needed.
  • R — with packages dplyr, readr, here, yaml, ggplot2, and systemfonts.
  • cingulate R package — installed from GitHub (see Installation).
Quarto includes a compatible Typst binary. You do not need to install Typst separately unless you are customizing the Typst templates directly.

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Steps

1

Install Quarto

Download and install Quarto from quarto.org. Verify the installation:
quarto --version
You need version 1.4.0 or later. If you see an older version, update before continuing.
2

Scaffold a new report project

Choose the template that matches your evaluation type and run the corresponding command. Quarto will download the extension, copy the template file, and set up the project directory.
quarto use template brainworkup/neurotyp-adult
Quarto will ask you to confirm the template trust and choose a directory name. The scaffolded project contains a template.qmd file and the extension files under _extensions/.
If you already have a Quarto project and want to add a format without overwriting existing files, use quarto add brainworkup/neurotyp-adult instead. See Installation for details.
3

Configure patient metadata

Open template.qmd in your editor. The YAML front matter at the top of the file holds all patient-specific fields. Replace the placeholder values with real data:
---
title: NEUROCOGNITIVE EXAMINATION
patient: Doe
name: Doe, Jane
dob: "1980-01-15"
age: 45
doe: "2025-03-10"
doe2: "2025-03-11"
doe3: "2025-03-12"
date_of_report: last-modified
case_number: "2025-001"
---
FieldDescription
patientPatient surname used in confidential headers
nameFull name in “Last, First” format
dobDate of birth (ISO 8601: YYYY-MM-DD)
ageAge in years at time of evaluation
doe / doe2 / doe3Dates of evaluation sessions
date_of_reportSet to last-modified to auto-stamp, or an explicit date
case_numberYour internal case reference
Pages 2 and later automatically display a CONFIDENTIAL header containing the patient name and evaluation date. This is driven by the patient and doe fields — make sure both are set correctly.
4

Write your report content

Below the front matter, template.qmd contains pre-structured sections for your evaluation. Fill in each section with your clinical content:
  • Neurological Symptom Evaluation (NSE) — presenting concerns and symptom history
  • Behavioral observations — observations from the evaluation sessions
  • Cognitive domain findings — results by domain (attention, memory, language, etc.)
  • SIRF summary — Summary, Impressions, Recommendations, and Findings
  • Clinical recommendations — specific recommendations for the patient
Each section uses standard Quarto Markdown. You can embed R code chunks for score tables and visualizations generated by the cingulate package.
5

Render to PDF

From inside your project directory, run:
quarto render template.qmd
This renders using the default format defined in the template’s front matter. To target a specific format explicitly:
quarto render template.qmd --to neurotyp-adult-typst
Quarto writes the finished PDF to the same directory as your .qmd file. Open it to confirm the layout, typography, and patient metadata are correct.
If fonts like Equity B or IBM Plex Sans are not installed on your system, Typst will fall back to a system font. Install the preferred fonts or configure alternatives in _brand/_brand.yml to match your clinic’s style guide.

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Next steps

Patient metadata reference

Full reference for every supported front matter field across all four templates.

Cognitive domains guide

Structure domain-level findings, embed score tables, and generate visualizations with cingulate.

AI-assisted narratives

Set up a local Ollama backend and use neurotyp-luria for LLM-generated narrative sections.

Customizing output

Adjust brand colors, fonts, margins, and clinic identity in _brand/_brand.yml.
Last modified on May 20, 2026