SCMP943

Python for MRI analysis
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Courses tagged with "SCMP943"

Get familiar with how one can manipulate and transform neuroimaging data using Python s neuroimaging packages (nibabel, nilearn). Develop an understanding how MRI data is represented in Python and perform some hands-on tasks such as basic manipulation on both structural MR and functional MR. Then we will discuss the steps required to take minimally pre-processed MR data (fmriprep), to clean and workable data through the process of motion cleaning and dimensionality reduction. Finally, we will cover how to perform functional connectivity (FC) analysis to build a resting state connectivity matrix. All analyses will be performed using Jupyter notebooks in the spirit of reproducible and open science.
Teacher: Camh Team
Start date: 21 Jul 2020
End date: 23 Jul 2020
Python is increasingly becoming common-place in the analysis of neuroimaging data. This course will familiarize attendees with how one can manipulate and transform neuroimaging data using Python s neuroimaging packages (nibabel, nilearn). We will begin with first developing an understanding how MRI data is represented in Python and perform some hands-on tasks such as basic manipulation on both structural MR and functional MR. Then we will discuss the steps required to take minimally pre-processed MR data (fmriprep), to clean and workable data through the process of motion cleaning and dimensionality reduction. The final component of the course will involve performing functional connectivity (FC) analysis to build a resting state connectivity matrix. All analyses will be performed using Jupyter notebooks in the spirit of reproducible and open science.
Teacher: SciNet Team
Date: Wed, 26 Jun 2019 - 1:30 pm
This 1 day course will introduce python packages and approaches for medical imaging applications (MRI specifically). We will give an overview of specific command line based tools (freesurfer/FSL) for image analysis introduce how to interface with them using python. Specific python packages will be for nibabel (for MR image i/o), nilearn (for plotting/visualization) and nipype (for pipeline development/parallelization).
Teacher: Camh Team
Date: Mon, 11 Jun 2018 - 1:30 pm
Part of the 2017 Ontario Summer School.
Teacher: SciNet Team
Date: Wed, 26 Jul 2017 - 9:30 am