fsleyes and the fsl python ecosystem
play

FSLeyes and the FSL Python ecosystem Paul McCarthy Brainhack - PowerPoint PPT Presentation

Feb 21, 2023 •341 likes •474 views

FSLeyes and the FSL Python ecosystem Paul McCarthy Brainhack Warwick 2nd-3rd March 2017 Current state of FSL Language Use Virtually all numerical C++ processing/analysis GUIs and processing pipelines Tcl/Tk (FEAT) Bash/sh Smaller

  1. FSLeyes and the FSL Python ecosystem Paul McCarthy Brainhack Warwick 2nd-3rd March 2017

  2. Current state of FSL Language Use Virtually all numerical C++ processing/analysis GUIs and processing pipelines Tcl/Tk (FEAT) Bash/sh Smaller pipelines Python More complex pipelines Matlab/Octave FIX, PALM, FSLNets R FIX GPU / multithreaded code CUDA / OpenMP (EDDY, BEDPOSTX, etc) Summary courtesy of Matthew Webster/Mark Jenkinson

  3. Tcl/Tk

  4. Tcl/Tk Python

  5. Future state of FSL Language Use Virtually all numerical C++ processing/analysis GUIs and processing pipelines Python Tcl/Tk (FEAT) Bash/sh Smaller pipelines Python More complex pipelines Matlab/Octave FIX, PALM, FSLNets R FIX GPU / multithreaded code CUDA / OpenMP (EDDY, BEDPOSTX, etc)

  6. Future state of FSL Language Use Virtually all numerical Python C++ processing/analysis GUIs and processing pipelines Python Tcl/Tk (FEAT) Python Bash/sh Smaller pipelines Python More complex pipelines Python Matlab/Octave FIX, PALM, FSLNets Python R FIX GPU / multithreaded code Python CUDA / OpenMP (EDDY, BEDPOSTX, etc) My secret goal

  7. Future state of FSL Language Use Virtually all numerical Python/C++ processing/analysis GUIs and processing pipelines Python Tcl/Tk (FEAT) Python/bash/sh Smaller pipelines Python More complex pipelines Python/Matlab/Octave FIX, PALM, FSLNets Python/R FIX GPU / multithreaded code CUDA / OpenMP (EDDY, BEDPOSTX, etc) More realistic goal

  8. The FSLPython environment • Future versions of FSL will come bundled with a Miniconda Python 3 environment • FSL tools written in Python will be executed with this environment • Includes all of your favourite Python libraries ( numpy , scipy , matplotlib , nibabel , etc)

  9. Other changes in FSL • Finally migrating from CVS to git • FSL 5.0.10 coming very soon! • FSLeyes • FSLPython • MSM (Multi-modal surface-based registration) • MIST (multi-modal subcortical segmentation) • BIANCA (white-matter hyperintensity classification) • FSL 6 coming later this year • Newmat replaced by armadillo • Other big internal changes

  10. FSLeyes Pronounced “fossilise" • FSL’s new image viewer (to replace FSLView) 
 • Written in Python (built on wxPython, PyOpenGL, numpy, matplotlib, nibabel, and more) 
 • Currently Python 2 (due to wxPython), but is easily ported to Python 3 
 • Does everything that FSLView could do, except for 3D - will be added in a future version

  11. FSLeyes demo Options! • General NIFTI visualisation • NIFTI image editing • FEAT mode • MELODIC/Melview mode • Atlases • Adjusting NIFTI transforms (a.k.a. “Nudge”) • Diffusion visualisation • Surface visualisation • Off-screen rendering • Python shell

  12. Questions/links builds available for • Get a pre-release copy of FSLeyes from: 
 • OSX • CentOS 6 https://users.fmrib.ox.ac.uk/~paulmc/FSLeyes/ 
 • CentOS 7 • Ubuntu 16.04) • FSLeyes user guide available at: 
 https://users.fmrib.ox.ac.uk/~paulmc/fsleyes_userdoc/ 
 • FSL mailing list: http://www.jiscmail.ac.uk/lists/fsl.html 
 • Email me! pauldmccarthy@gmail.com

  13. Thanks!

Download Presentation
Download Policy: The content available on the website is offered to you 'AS IS' for your personal information and use only. It cannot be commercialized, licensed, or distributed on other websites without prior consent from the author. To download a presentation, simply click this link. If you encounter any difficulties during the download process, it's possible that the publisher has removed the file from their server.

Recommend

Python But Python is already great!!! Readability Massive ecosystem Libraries,

Python But Python is already great!!! Readability Massive ecosystem Libraries,

Writing Good Python But Python is already great!!! Readability Massive ecosystem Libraries, Frameworks and Tools Vibrant community Many other things 2 Writing Good Python Hello! I am Prashant Currently a

425 views • 26 slides
iPython Data Analytics in Python 1 / 13 The SciPy Stack SciPy is a Python-based ecosystem of

iPython Data Analytics in Python 1 / 13 The SciPy Stack SciPy is a Python-based ecosystem of

iPython Data Analytics in Python 1 / 13 The SciPy Stack SciPy is a Python-based ecosystem of libraries and tools for scientific computing and data analytics iPython Jupyter notebooks Numpy Pandas Matplotlib iPython is the

608 views • 13 slides
The Python Ecosystem for Data Science: A Guided Tour PyData Warsaw 2017 | at the Copernicus

The Python Ecosystem for Data Science: A Guided Tour PyData Warsaw 2017 | at the Copernicus

The Python Ecosystem for Data Science: A Guided Tour PyData Warsaw 2017 | at the Copernicus Science Centre | 19-20 October 2017 Christian Staudt | Independent Data Scientist Source: Stephan Kolassa @ Stackexchange

648 views • 47 slides
Python Tidbits Python created by that guy ---> Python is named after Monty Pythons

Python Tidbits Python created by that guy ---> Python is named after Monty Pythons

Python Tidbits Python created by that guy ---> Python is named after Monty Pythons Flying Circus 1991 Python 0.9.0 Released 2008 Python 2.6 / 3.0rc2 Current Python 2.7.1 / 3.2 *7 th most popular language

753 views • 37 slides
Why we will use microPython Rapid prototyping with microPython devices Marco Zennaro, ICTP

Why we will use microPython Rapid prototyping with microPython devices Marco Zennaro, ICTP

Why we will use microPython Rapid prototyping with microPython devices Marco Zennaro, ICTP January 21, 2019 Why micropython? python 1 python 2 python ecosystem 3 micropython MicroPython is a lean and fast implementation of the Python 3

981 views • 79 slides
Why we will use microPython Rapid prototyping with microPython devices Marco Zennaro, ICTP

Why we will use microPython Rapid prototyping with microPython devices Marco Zennaro, ICTP

Why we will use microPython Rapid prototyping with microPython devices Marco Zennaro, ICTP January 22, 2019 Why micropython? python 1 python 2 python ecosystem 3 micropython MicroPython is a lean and fast implementation of the Python 3

1.4k views • 80 slides
1 Parallelism in Python The Problem with Shared State Python provides two mechanisms for

1 Parallelism in Python The Problem with Shared State Python provides two mechanisms for

Python Example of a MapReduce Application The mapper and reducer are both self contained Python programs Read from standard input and write to standard output ! Mapper Tell Unix: this is Python #!/usr/bin/env python3 The emit function

464 views • 3 slides
Getting Started with Python The Python Interpreter A piece of software that executes

Getting Started with Python The Python Interpreter A piece of software that executes

Object-Oriented Programming in Python Goldwasser and Letscher Chapter 2 Getting Started with Python The Python Interpreter A piece of software that executes commands for the Python language Start the interpreter by typing python at a

862 views • 27 slides
Why we will use microPython Rapid prototyping with microPython devices Marco Zennaro, ICTP May

Why we will use microPython Rapid prototyping with microPython devices Marco Zennaro, ICTP May

Why we will use microPython Rapid prototyping with microPython devices Marco Zennaro, ICTP May 2, 2018 Why micropython? python 1 python ecosystem 2 micropython MicroPython is a lean and fast implementation of the Python 3 programming

1.13k views • 89 slides
An introduction to Python Andreas Bjerre-Nielsen Agenda 1. Python: what it is; why and how we

An introduction to Python Andreas Bjerre-Nielsen Agenda 1. Python: what it is; why and how we

An introduction to Python Andreas Bjerre-Nielsen Agenda 1. Python: what it is; why and how we learn it 2. Python scripts and Jupyter 3. Fundamental data types 4. Basic Python procedures: operators, functions, methods etc. 5. Conditional

978 views • 66 slides
We already know Java. Why learn Python? Using Python to Implement Algorithms Python has far less

We already know Java. Why learn Python? Using Python to Implement Algorithms Python has far less

We already know Java. Why learn Python? Using Python to Implement Algorithms Python has far less overhead than Java for the programmer. Tyler Moore Python is closer to psuedo-code on the English-pseudocode-code spectrum than Java or C/C++, but

615 views • 9 slides
Dask extending Python data tools for parallel and distributed computing Joris Van den Bossche -

Dask extending Python data tools for parallel and distributed computing Joris Van den Bossche -

Dask extending Python data tools for parallel and distributed computing Joris Van den Bossche - FOSDEM 2017 1 / 29 Python's scientific/data tools ecosystem ## Thanks to Jake VanderPlas for the figure 2 / 29 3 / 29 3 / 29 Provides

466 views • 31 slides
First Tool: Python! Introduction to python programming Gholamhossein Tavasoli @ ZNU First Tool:

First Tool: Python! Introduction to python programming Gholamhossein Tavasoli @ ZNU First Tool:

First Tool: Python! Introduction to python programming Gholamhossein Tavasoli @ ZNU First Tool: Python! Python Programming Language Python Programming Language Created in 1991 by Guido van Rossum Python Cro ross Platform Pro rogramming

662 views • 62 slides
5 Ecosystem Services in Practice: Market-Based Ecosystem Services - From Theory to Application

5 Ecosystem Services in Practice: Market-Based Ecosystem Services - From Theory to Application

Se minar 5 Ecosystem Services in Practice: Market-Based Ecosystem Services - From Theory to Application Speaker Adam Davis Dave Batker Dr. Ben Guillon Ricardo Bayon 2011 ECOSYSTEM SERVICES SEMINAR SERIES Ecosystem Services Seminar

745 views • 35 slides
Ecosystem Services Assessment Multifunctionality Valuation of Ecosystem services Methods and

Ecosystem Services Assessment Multifunctionality Valuation of Ecosystem services Methods and

Ecosystem Services Assessment Multifunctionality Valuation of Ecosystem services Methods and basis for Suitable for ecosystem services decisions: Monetary terms that we have good knowledge of and is (WTP-studies, cost-benefit

617 views • 4 slides
Py Python Strings Python strings are immuatable: s = abc s[2] = d s = abd

Py Python Strings Python strings are immuatable: s = abc s[2] = d s = abd

2/25/20 CS 224 Introduction to Python Spring 2020 Class #14: Strings Py Python Strings Python strings are immuatable: s = abc s[2] = d s = abd These dont change the string abc s = s[:-1] + d they

444 views • 19 slides
THE FIRST STEP TO BECOME FAMILIAR WITH NETWORK SIMULATOR (NS) Neda Mohammadizadeh Cooperative

THE FIRST STEP TO BECOME FAMILIAR WITH NETWORK SIMULATOR (NS) Neda Mohammadizadeh Cooperative

THE FIRST STEP TO BECOME FAMILIAR WITH NETWORK SIMULATOR (NS) Neda Mohammadizadeh Cooperative sub-group BBCR group Feb 2012 2 References http://nsnam.isi.edu/nsnam/index.php/User_Information http://nile.wpi.edu/NS/

772 views • 48 slides
NetFPGA Summer Course Presented by: Noa Zilberman Yury Audzevich Technion August 2 August

NetFPGA Summer Course Presented by: Noa Zilberman Yury Audzevich Technion August 2 August

NetFPGA Summer Course Presented by: Noa Zilberman Yury Audzevich Technion August 2 August 6, 2015 http://NetFPGA.org Summer Course Technion, Haifa, IL 2015 1 DESIGNING CORES Summer Course Technion, Haifa, IL 2015 2 Outline What

651 views • 51 slides
The age of orchestration From Docker basics to cluster management NICOLA PAOLUCCI DEVELOPER

The age of orchestration From Docker basics to cluster management NICOLA PAOLUCCI DEVELOPER

The age of orchestration From Docker basics to cluster management NICOLA PAOLUCCI DEVELOPER INSTIGATOR ATLASSIAN @DURDN Three minute Docker intro? Time me and ring a bell if I am over it. Just kidding Ill be over by a bit

504 views • 38 slides
Future Plans for NOAAs Microwave Integrated Retrieval System Kevin Garre* 1 , Christopher

Future Plans for NOAAs Microwave Integrated Retrieval System Kevin Garre* 1 , Christopher

Future Plans for NOAAs Microwave Integrated Retrieval System Kevin Garre* 1 , Christopher Grasso3 1 , Leslie Moy 1 , Flavio Iturbide Sanchez 1 , Wanchun Chen 2 , and SidAhmed Boukabara 3 NASA Sounder Science Team MeeJng Greenbelt, MD

350 views • 13 slides
Presentation contents Wireless multi-hop networks How is the radio signals propagation

Presentation contents Wireless multi-hop networks How is the radio signals propagation

Presentation contents Wireless multi-hop networks How is the radio signals propagation modeled during the simulation ? Node entities in NS2 Emulating radio signals propagation Briefly mobility Mobile nodes in NS2 Mobile node

620 views • 19 slides
Mapping of Ventricular Tachycardia Coronary Artery Disease: Typical patient with scar-related VT

Mapping of Ventricular Tachycardia Coronary Artery Disease: Typical patient with scar-related VT

What Are We Talking About? Mapping of Ventricular Tachycardia Coronary Artery Disease: Typical patient with scar-related VT Does Entrainment Have a Role in the Era Substantial scar burden of Substrate Modification? Decreased

111 views • 8 slides
CS6710 Tool Suite Verilog-XL Synopsys Behavioral Design Compiler Verilog Structural Verilog

CS6710 Tool Suite Verilog-XL Synopsys Behavioral Design Compiler Verilog Structural Verilog

Synthesis and Place & Route Synopsys design compiler Cadence SOC Encounter CS6710 Tool Suite Verilog-XL Synopsys Behavioral Design Compiler Verilog Structural Verilog Cadence Your SOC Library Encounter Circuit Verilog-XL CSI

598 views • 30 slides
Data processing in the BaBar environment: Configuration done through Tcl files Analysis

Data processing in the BaBar environment: Configuration done through Tcl files Analysis

Data processing in the BaBar environment: Configuration done through Tcl files Analysis consists of a root object (path) containing sequences A sequence may contains other sequences or modules Module execution follows the

175 views • 15 slides

More recommend