Tutorial : Workflows¶
This section presents several tutorials on how to setup and use pipelines. Make sure that you have the requirements satisfied and go through the steps required for the analysis tutorials.
Essential reading¶
Beginner’s guide¶
By Michael Notter. Available here
Example workflows¶
Requirements¶
All tutorials
- Release 0.4 of nipype and it’s dependencies have been installed
Analysis tutorials
- FSL, FreeSurfer, Camino, ConnectomeViewer and MATLAB are available and callable from the command line
- SPM 5/8 is installed and callable in matlab
- Space: 3-10 GB
Checklist for analysis tutorials¶
For the analysis tutorials, we will be using a slightly modified version of the FBIRN Phase I travelling data set.
Step 0¶
Download and extract the Pipeline tutorial data (429MB).
(checksum: 56ed4b7e0aac5627d1724e9c10cd26a7)
Step 1.¶
Ensure that all programs are available by calling bet
, matlab
and then which spm
within matlab to ensure you have spm5/8 in your
matlab path.
Step 2.¶
You can now run the tutorial by typing python tutorial_script.py
within the nipype-tutorial directory. This will run a full first level
analysis on two subjects following by a 1-sample t-test on their first
level results. The next section goes through each section of the
tutorial script and describes what it is doing.