Claude

Claude Code is Anthropic’s command-line coding agent. You can run it inside a Neurodesk JupyterHub terminal and authenticate with an Anthropic subscription.

1. Start Claude in a terminal.

claude

2. Trust the folder when prompted.

Claude Code'll be able to read, edit, and execute files here.

Security guide

> 1. Yes, I trust this folder
  2. No, exit

3. Authenticate with your Anthropic subscription.

Follow the login prompt and open the URL Claude prints in a browser.

Caution

Claude outputs a long authentication URL on the terminal. The JupyterHub terminal can wrap this URL across multiple lines, which makes it invalid when pasted. Copy the URL into an editor and remove the line breaks before pasting it into the browser.

4. Give it a task and approve permission requests as it works.

● Good, datalad is installed and there are many neuroimaging tools. Let me create a structured plan and scripts for this analysis.

● Write(analysis_step1_download.sh)
⎿  Wrote 67 lines to analysis_step1_download.sh
   #!/bin/bash
   #
   # Script: analysis_step1_download.sh
   # Purpose: Download ds003999 (Pre-Post rehabilitation fMRI data of post-stroke patients) from OpenNeuro
   # Dataset: https://openneuro.org/datasets/ds003999
   #

   set -e

   echo "..."
   +57 lines (ctrl+o to expand)

● Bash(chmod +x /home/jovyan/claude/analysis_step1_download.sh && /home/jovyan/claude/analysis_step1_download.sh 2>&1)
⎿  [INFO] siblings is 1 (DataLad siblings)
     datalad siblings -d . add openneuro not auto-enabled, enable with
   install(ok): /home/jovyan/claude/data/ds003999 (dataset)
   Getting dataset content (downloading actual files)...
   [INFO] Ensuring presence of Dataset(/home/jovyan/claude/data/ds003999)
   +15 more lines (10s · timeout 3m)
   ctrl+b to run in background

● Downloading dataset… (1m 40s · ↓ 2.7k tokens · thinking)
⎿  Download ds003999 dataset using datalad
   Explore dataset structure and contents
   Preprocess fMRI data with fmriprep
   Run pre vs post intervention analysis