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Steps for processing fmri data using fmriprep, Tedana and ANTs

This code was developed by HAM Lab Otago University as a test for our internal data processing pipeline and not intended for external use. Use with caution!

Prerequisites

Note: Be sure to configure docker to be run as a user, this is important to avoid output files being owned by root, which can lead to problems down the track.

Step 1

Configure file paths inside the file step_1_fmri.sh Run script using $ sh step_1_fmri.sh

Step 2

Configure file paths inside the file step_2_fmri.sh Run script using $ sh step_2_fmri.sh

Step 3

Configure file paths inside the file step_3_tedana.py Note: Make sure to activate your virtual enviroment if you are using conda or another Python package manager Run script using $ python step_3_tedana.sh

Step 4

Configure file paths inside the file step_4_ants.sh Run script using $ sh step_4_ants.sh

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HAM Lab's internal data processing pipeline

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