Paul Wighton pwighton

FreeBrowse Status Update

2026/03/04

New features since last update

2 URL parameters:
- ?nvd=<url>: Open the niivue document at the specified URL
- ?vol=<url>: Open the volume at the specified URL
Initial support for Surfaces (WIP)
4d volume support
UI element to manipulate label intent code

[Free|Pet]Surfer by Example

Init FreeSurfer env

At the NIH

Connect to Biowulf via NoMachine
Launch a terminal on Biowulf
Run:

Trying to make the atlas for Dorit on Nike

On Nike
With same parameters as original samseg atlas
Using Koens trick stiffnes 1.0 -> 0.1 trick
Using edgeCollapseEncouragmentFactor.txt=1.025 on restart
Using full set of subjects

ssh to nike

singularity run \
  --cleanenv \
  -B /autofs/cluster/gerenuk/pwighton/singularity-images/license.txt:/license.txt \
  -B /autofs/cluster/gerenuk/pwighton/fmriprep-singularity/ds003455:/data \
  --env FS_LICENSE='/license.txt' \
  /autofs/cluster/gerenuk/pwighton/singularity-images/fmriprep-20.2.0rc2.simg \
    /data \
    /data/derivatives2 \
 participant \

An open Source QMS to facilitate translational research

Background: Cmet

CorticoMetrics is working to bring FreeSurfer to the clinic
To be used in the clinic, it needs to be FDA approved as a "Class II medical device"
A Medical device must be developed under a QMS (Quality Management System)
A QMS is a set of business processes and records that must be adhered to
- "Design Review"
"Validation"

FreeSurfer 6.0 Installation Notes

Notes on how to install FreeSurfer 6.0 so that every command used during the course tutorials can be run. This fills in some missing details documented here

Download and install

Follow instructions here to download and install FreeSurfer
Download tutorial data from here and extract
Patch FreeView (scroll to bottom of page)

	#!/bin/bash
	# provision-freeview-gpu.sh
	# Configure a Jetstream2 GPU instance (g3.*, GRID A100X vGPU) for hardware-
	# accelerated FreeView over the Exosphere web desktop (TurboVNC + Guacamole).
	#
	# What it does:
	# 1. Installs VirtualGL — FreeView renders on the vGPU via EGL, VirtualGL
	# reads frames back into the (CPU-driven) VNC X server.
	# 2. Adds freeview/tkmeditfv aliases that route through vglrun. The
	# __EGL_VENDOR_LIBRARY_FILENAMES pin is needed because Mesa's EGL vendor

	#!/usr/bin/env bash
	#
	# Install FreeSurfer 8.2.0 on Ubuntu 24.04
	#
	# Ported from:
	# - https://github.com/pwighton/fs-docker/blob/master/freesurfer/Dockerfile.8.2.0
	# See also:
	# - https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads/rel8notes

	set -euo pipefail

	#!/usr/bin/env python3

	import argparse
	import pydicom

	parser = argparse.ArgumentParser(description='Parse command line options')
	parser.add_argument('input_file')
	args = parser.parse_args()

	dcm = pydicom.dcmread(args.input_file)

	#!/usr/bin/env python3

	import argparse
	import socket
	import traceback

	parser = argparse.ArgumentParser(description="Parse command line options")
	parser.add_argument("port")
	parser.add_argument("outfile")
	args = parser.parse_args()