Franz Liem (franziskus.liem@uzh.ch)
BIDS Apps are portable neuroimaging pipelines that understand BIDS datasets. They facilitate executing standard neuroimaging pipelines, like FreeSurfer, fmriprep, cpac, mriqc..., for processing structural and functional MRI data. BIDS Apps run on all three major operating systems with no need for a complex setup and configuration and very little user input.
For more background see Gorgolewski et al. (2017).
For a list of available BIDS Apps see here.
After a brief introduction to BIDS Apps and Docker software containers, participants will run the MRIQC software on their laptops, to judge the quality of MRI data.
The tutorial is open to everyone with basic experience with MRI data. No prior experience with command line tools, docker, BIDS Apps or MRIQC is required.
- Laptop with Docker installed (see guides for mac, windows, linux)
- if possible, already download (pull) the docker container we will be
using:
- open a terminal window/command line
- paste the following command:
docker pull poldracklab/mriqc:0.10.4 - press enter and wait for the download to be finished
- download the this BIDS-formatted example data set (430 MB)
- optionally, bring your own BIDS-formatted MRI data (T1w and/or functional), for instance, the result of the Introduction to BIDS tutorial)
will be posted here.