Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
* Add 'Data structure' section * Add note that only the `sourcedata` directory is required * Add participants.tsv example * Fix subject naming * Update comments * Add 'data_processed' and 'bids' folders * Store the first version of the script. This version interactively prompts the user to provide paths to the nifti images. * Add '-bids-folder' input arg; check whether the BIDS folder already exists, if so, warn the user and exit * Remove unused import; improve arg help * Add prints * t2_path --> path_t2w * dwi_path --> path_dwi * Refactor the script to allow selecting the images for further processing from the list of images * Update description * Update docstring * Update docstrings * Use os.path.expanduser * Allow to specify the contrasts to process using an input arg * Add dcm2niix requirement * Add example of the input and output file structure * Add TODOs * Add '-debug' flag to keep the temp folder (output of dcm2niix) * Move print into `copy_files_to_bids_folder` * Fix `-contrasts` to properly accept several contrasts * Add 'File organization' subsection * Add '3.2 DICOM to NIfTI conversion' subsection * Update TOC * Briefly describe the dependencies * typos * typo * update dimensions and pixel_size formatting * include also series description for dcm2niix * update df printing * use logging instead of print statements * Sort nii files based on the series number (the last number in the file name before the .nii.gz extension) * Switch from 'logging.eror' to 'logging.info("Warning: ...' * Include "Error" into logging.error print * Explicitly tell users the rows number to select from * Check if there are any NIfTI files in the folder, if not, print error message and exit * Write a new entry to the participant.tsv - add new args for sex and age * Add '2.3 Downloading this repository' section * Update script path * Add `-contrasts` arg to the example usage * Add example usage * Update README.md * Simplify TOC - add 'Getting Started' - move 'Dependencies' and 'Installation' under 'Getting Started' * Move printing * Use 'formatter_class=argparse.RawTextHelpFormatter' * Add an example on how to distinguish between two images of the same contrast with different orientation, e.g. 'acq-axial_T2w' and 'acq-sag_T2w' --------- Co-authored-by: Julien Cohen-Adad <[email protected]>
- Loading branch information