BIDS_process_depends.txt

Standard Library Modules
os: Interface with the operating system
sys: Access system-specific parameters and functions
argparse: Parser for command-line options, arguments, and sub-commands
logging: Logging facility for Python
subprocess: Spawn new processes, connect to their input/output/error pipes, and obtain their return codes
re: Regular expression operations
json: JSON encoder and decoder
warnings: Issue warning messages and control their disposition
tempfile: Generate temporary files and directories
shutil: High-level file operations
glob: Unix style pathname pattern expansion

Third-Party Modules
numpy: Fundamental package for scientific computing with Python
pandas: Data structures and data analysis tools
matplotlib.pyplot: Plotting and visualization
scipy.io: SciPy Input and Output
pydicom: Read, modify, and write DICOM files with Python

Specific Functionality from Matplotlib
matplotlib.backends.backend_pdf.PdfPages: Create multipage PDFs with matplotlib plots

Collections Module
collections.OrderedDict: Dictionary that remembers the order entries were added

Additional Tools (Mentioned but not Imported)
pydeface: Defacing tool for MRI images
cubids: Tool for organizing neuroimaging data into the BIDS format
dcm2niix: Converts DICOM and PAR/REC files into the NIfTI format

Notes
For the additional tools (pydeface, cubids, dcm2niix), 
make sure they are installed in your environment and accessible from your 
script. These might not be standard Python modules but standalone tools 
or applications.