When downloading a project from Flywheel, you will receive a tar file. After extracting that tar file, you will have a directory in the form of Project->Subject->Session->Acquisition Flywheel hierarchy.
All of the DICOM files will be in an archive file as they were in Flywheel, e.g. `<filename>.dcm.zip`. If you want to upload this project back to Flywheel, there is no need to unzip the DICOM files. You can login to the CLI and use the `fw import folder` command to import the extracted archive back into Flywheel.
Example:
fw import {unzipped_project_level_directory}However, if you have a need to use the DICOM files in a directory, you'll likely need to unzip them all. Here's some Linux/MacOS commands you can use to do this quickly.
This unzips all `*dcm.zip` files in and below the current directory:
find . -name "*.dcm.zip" -execdir unzip {} \;After those have been unzipped, you can then delete the zip files with:
find . -name "*.dcm.zip" -delete