Computing Skills
Schedule of upcoming sessions
The regularly scheduled computing skills series will not be running during the 2018–2019 academic year.
Past sessions
Tue, Nov 14, 2017. Working with NIfTI headers: Resetting the origin and other parameters
In preparing some example data from a public repository, we ran across some issues with coregistration that resulted from origins in the functional and anatomical images being too dissimilar. We'll take a look at two ways to check NIfTI header information about image origin and to modify it for a group of subjects, one using Bash shell scripting and FSL the other using Python and Nibabel.
Tue, Oct 10, 2017. Application containers, and why you should know about them
Bennet has recently been working on creating application containers for some complex pipelines. Putting the software into a container can enable you to run the same version of a pipeline on quite different systems. In this case, a Red Hat machine in Psychology, an Ubuntu virtual machine in the cloud(s), and CentOS on the cluster. Bennet will talk about what containers are, how to make them (or find someone who will), how to use them, and why, if they are the coolest thing since sliced bread, they are sometimes found to be butter-side down on the floor?
Tue, Sep 19, 2017. Linux utilities for data management
We will take a look at some of the standard Linux programs that you may find useful for managing data, both your own and other people's. We will look at how to find files that have certain attributes, including type, age, owner, and permissions. If you get data from a repository, or just from a collaborator, it will most likely be in an archive and possibly compressed; we'll look at the programs to make those and to unpack those and some of the options available beyond the standard ones.
Tue, Jun 06, 2017. Some shell programming in Linux
Python can do a lot of things, but some things are more easily done from the shell (bash). We'll take a look at how some of the things we have already seen in Python can be done in the shell. We'll look at how to use if...then statements to conditionally perform actions and we'll look at the for...do looping mechanism for repeating an operation once for a list of items. We'll also look at shell variables and some of the Unix utilities that are used in common shell scripts.
Tue, Jun 06, 2017. Nipype for real work
We will look at one common preprocessing stream and begin to work on implementing it with Nipype. This will have several purposes: 1) familiarizing people with what is done in preprocessing and why, 2) building familiarity with Nipype as a tool for working with neuroimaging data in Python, and 3) building a reusable basic workflow that can be used as is or modified to preprocess your own study data.
Tue, Feb 21, 2017. We will continue looking at the Nipype
tutorial. We will take a short look at running programs from within
Python, as that will be implicitly used by Nipype, and it's generally
useful. The materials at the
Basic
Python site have been updated, in particular the Step03.md
file and some scripts have been added, which we'll look at.
Tue, Feb 14, 2017. At the Feb 7 meeting, we showed people two possible tracks to take in exploring Python. One is more process oriented and would follow the Nipype introduction to construct a Nipype pipeline. The other would be more analytic and would be based on material used at UC Berkeley. People expressed an interest in being able to dig into the respective web sites to see on their own time what each might get them into. Preference should be sent to michigan-nii@umich.edu.
The two web sites are
Nipype Beginner's Guide
Nipype and Neuroimaging possibly with supplemental material from the official Nipype web site.
functional MRI methods
Psych 214 — functional MRI methods
| Tally of votes as of Feb 11 | |
|---|---|
| Nipype | fMRI methods |
| 6 | 5 |
Past computing talk topics
Multivoxel pattern analysis (MVPA) of fMRI data: Tutorial and examples
Date: Mar 7, 2017
Time: 4:00 PM
Location: 4464 East Hall
Thad Polk from the Psychology department will give a presentation introducting Multivoxel pattern analysis (MVPA) of fMRI data. Basic concepts will be presented along with a demonstration. There will be a code example written for Matlab shown.
Neuroimaging workflows: What works, what flows?
Date: Jan 31, 2017
Time: 4:00 PM
Location: 4464 East Hall
At the Jan 31 meeting of the Computing Skills group, we will use the Askren, et al., paper as a jumping off place to discuss What is a workflow (or pipeline)? Why make them? Processing many subjects at once? How not to process needlessly.
Reading Mary K Askren, et al. Using Make for Reproducible and Parallel Neuroimaging Workflow and Quality-Assurance http://journal.frontiersin.org/article/10.3389/fninf.2016.00002/full
fMRI preprocessing stream and Methods Core scripts
Tue, Jan 17, 2017. Scott and Krisanne from the fMRI Lab and Mike Angstadt from the Methods Core/Psychiatry will go over the preprocessing streams used by the fMRI lab and the Psychiatry Methods Core. What is done, in what order, using which programs will be presented.
Location: East Hall 4464
Time: 4:00 PM