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Add File organization and DICOM to NIfTI conversion sections #3

Merged
merged 49 commits into from
Sep 5, 2024
Merged

Add File organization and DICOM to NIfTI conversion sections #3

merged 49 commits into from
Sep 5, 2024

Commits on Aug 16, 2024

  1. Add 'Data structure' section

    @valosekj
    valosekj committed Aug 16, 2024
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  2. Add note that only the sourcedata directory is required

    @valosekj
    valosekj committed Aug 16, 2024
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Commits on Aug 20, 2024

  1. Add participants.tsv example

    @valosekj
    valosekj committed Aug 20, 2024
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  2. Fix subject naming

    @valosekj
    valosekj committed Aug 20, 2024
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  3. Update comments

    @valosekj
    valosekj committed Aug 20, 2024
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  4. Add 'data_processed' and 'bids' folders

    @valosekj
    valosekj committed Aug 20, 2024
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Commits on Aug 22, 2024

  1. Store the first version of the script. This version interactively pro… 

    …mpts the user to provide paths to the nifti images.
    @valosekj
    valosekj committed Aug 22, 2024
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  2. Add '-bids-folder' input arg; check whether the BIDS folder already e… 

    …xists, if so, warn the user and exit
    @valosekj
    valosekj committed Aug 22, 2024
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  3. Remove unused import; improve arg help

    @valosekj
    valosekj committed Aug 22, 2024
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  4. Add prints

    @valosekj
    valosekj committed Aug 22, 2024
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  5. t2_path --> path_t2w

    @valosekj
    valosekj committed Aug 22, 2024
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  6. dwi_path --> path_dwi

    @valosekj
    valosekj committed Aug 22, 2024
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  7. Refactor the script to allow selecting the images for further process… 

    …ing from the list of images
    @valosekj
    valosekj committed Aug 22, 2024
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  8. Update description

    @valosekj
    valosekj committed Aug 22, 2024
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  9. Update docstring

    @valosekj
    valosekj committed Aug 22, 2024
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  10. Update docstrings

    @valosekj
    valosekj committed Aug 22, 2024
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  11. Use os.path.expanduser

    @valosekj
    valosekj committed Aug 22, 2024
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  12. Allow to specify the contrasts to process using an input arg

    @valosekj
    valosekj committed Aug 22, 2024
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  13. Add dcm2niix requirement

    @valosekj
    valosekj committed Aug 22, 2024
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  14. Add example of the input and output file structure

    @valosekj
    valosekj committed Aug 22, 2024
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  15. Add TODOs

    @valosekj
    valosekj committed Aug 22, 2024
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  16. Add '-debug' flag to keep the temp folder (output of dcm2niix)

    @valosekj
    valosekj committed Aug 22, 2024
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  17. Move print into copy_files_to_bids_folder

    @valosekj
    valosekj committed Aug 22, 2024
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Commits on Aug 23, 2024

  1. Fix -contrasts to properly accept several contrasts

    @valosekj
    valosekj committed Aug 23, 2024
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  2. Add 'File organization' subsection

    @valosekj
    valosekj committed Aug 23, 2024
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  3. Add '3.2 DICOM to NIfTI conversion' subsection

    @valosekj
    valosekj committed Aug 23, 2024
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  4. Update TOC

    @valosekj
    valosekj committed Aug 23, 2024
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  5. Briefly describe the dependencies

    @valosekj
    valosekj committed Aug 23, 2024
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  6. typos

    @valosekj
    valosekj committed Aug 23, 2024
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Commits on Aug 27, 2024

  1. typo

    @valosekj
    valosekj committed Aug 27, 2024
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  2. update dimensions and pixel_size formatting

    @valosekj
    valosekj committed Aug 27, 2024
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  3. include also series description for dcm2niix

    @valosekj
    valosekj committed Aug 27, 2024
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  4. update df printing

    @valosekj
    valosekj committed Aug 27, 2024
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  5. use logging instead of print statements

    @valosekj
    valosekj committed Aug 27, 2024
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  6. Sort nii files based on the series number (the last number in the fil… 

    …e name before the .nii.gz extension)
    @valosekj
    valosekj committed Aug 27, 2024
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  7. Switch from 'logging.eror' to 'logging.info("Warning: ...'

    @valosekj
    valosekj committed Aug 27, 2024
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  8. Include "Error" into logging.error print

    @valosekj
    valosekj committed Aug 27, 2024
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  9. Explicitly tell users the rows number to select from

    @valosekj
    valosekj committed Aug 27, 2024
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  10. Check if there are any NIfTI files in the folder, if not, print error… 

    … message and exit
    @valosekj
    valosekj committed Aug 27, 2024
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  11. Write a new entry to the participant.tsv 

     - add new args for sex and age
    @valosekj
    valosekj committed Aug 27, 2024
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Commits on Aug 28, 2024

  1. Add '2.3 Downloading this repository' section

    @valosekj
    valosekj committed Aug 28, 2024
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  2. Update script path

    @valosekj
    valosekj committed Aug 28, 2024
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Commits on Sep 4, 2024

  1. Add -contrasts arg to the example usage

    @valosekj
    valosekj committed Sep 4, 2024
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  2. Add example usage

    @valosekj
    valosekj committed Sep 4, 2024
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  3. Update README.md

    @jcohenadad
    jcohenadad authored Sep 4, 2024
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Commits on Sep 5, 2024

  1. Simplify TOC 

    - add 'Getting Started'
- move 'Dependencies' and 'Installation' under 'Getting Started'
    @valosekj
    valosekj committed Sep 5, 2024
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  2. Move printing

    @valosekj
    valosekj committed Sep 5, 2024
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  3. Use 'formatter_class=argparse.RawTextHelpFormatter'

    @valosekj
    valosekj committed Sep 5, 2024
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  4. Add an example on how to distinguish between two images of the same c… 

    …ontrast with different orientation, e.g.

'acq-axial_T2w' and 'acq-sag_T2w'
    @valosekj
    valosekj committed Sep 5, 2024
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