Paul Wighton pwighton

[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)

Description of the platform/product:

name and version of the software: FreeSurfer 6.0
free?: yes
commercial?: no
open source?: yes
what DICOM library do you use?: DCMQI to write DICOM-SEG
Description of the relevant features of the platform: Freesurfer's subcortical segmentation results can be converted to DICOM-SEG using fs-aseg.json that has been kindly provided by Emily Lindemer.
are both single and multiple segments supported?: Yes, however Freesurfer's subcortical segmentation process assumes a mutually exclusive label set.
do you support both BINARY and FRACTIONAL segmentation types? BINARY only.
do you support compressed objects? I beleive itkimage2

	#!/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()

	FROM amazonlinux:latest

	# root does everything for now
	# ---------------------------------------------------------------------
	USER root

	# For freesurfer
	# ---------------------------------------------------------------------
	# So that we can run `yum -y install git-lfs`
	RUN curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.rpm.sh \| bash