clpipe uses fMRIprep via the clpipe preprocess command to perform minimal preprocessing on functional MRI data.
clpipe preprocess creates one batch job per subject. If you find that you are running out of memory, increase the [FMRIPrepOptions][FMRIPrepMemoryUsage] option in the configuration file.
To submit your dataset for preprocessing, use the following command:
clpipe.config.options.FMRIPrepOptions
clpipe.cli:fmriprep_process_cli
*************** Quality Control Reports***************
fMRIprep produces detailed html reports for each subject, allowing users to visually inspect registration, normalization and confound plots. However, these reports do not have the images directly embedded in them, which means that directly downloading them from the HPC will not result in a usable report. There are two options:
- Open the html reports directly on the HPC, using some sort of interactive web browser.
- Download the reports and the images in the correct directory structure.
clpipe has a convenience function to organize and prepare a zip archive containing the reports and images, for quick download onto a personal computer.
This command uses the working directory previously specified to copy the reports and images to, then creates a zip archive containing them. This command is not a batch command, and can take a little time creating the archive, so be aware.
Once the archive is created, it can be downloaded and unzipped to a personal computer. The reports should correctly load images once opened.
clpipe.cli:get_fmriprep_reports_cli