Add File organization and DICOM to NIfTI conversion sections

[valosekj]

This PR:

• adds 3.1 File organization and 3.2 DICOM to NIfTI conversion sections to the README
• adds file_loader.py script for the DICOM to NIfTI conversion and to select the images for further analysis. Example script usage: Add File organization and DICOM to NIfTI conversion sections #3 (comment)

Related: #1

[valosekj]

I drafted a script for the DICOM to NIfTI (BIDS) conversion in my latest commits.

The script can be run by:

python ~/code/balgrist-sci/file_loader.py \
-dicom-folder ~/data/experiments/balgrist-sci/source_data/dir_20231010 \
-bids-folder ~/data/experiments/balgrist-sci/bids \ 
-participant sub-001 \
-session ses-01 \
-contrasts T2w dwi

Then, the script prints info to the user and starts the dcm2nii conversion:

----------------------------------------------------------------------------------------------------
Dicom folder: /Users/valosek/data/experiments/balgrist-sci/source_data/dir_20231010
BIDS folder: /Users/valosek/data/experiments/balgrist-sci/bids
Participant ID: sub-001
Session ID: ses-01
Log file will be stored in: /Users/valosek/data/experiments/balgrist-sci/bids/logs/dicom_to_nifti_sub-001_ses-01_20240904_132303.log
----------------------------------------------------------------------------------------------------

Info: Converted NIfTI images will be stored in: /Users/valosek/data/experiments/balgrist-sci/bids/sub-001/ses-01

Info: Creating a temporary folder for NIfTI images: /Users/valosek/data/experiments/balgrist-sci/bids/sub-001/ses-01/temp_dcm2niix

Info: Starting DICOM to NIfTI conversion using dcm2niix.

Compression will be faster with 'pigz' installed http://macappstore.org/pigz/
Chris Rorden's dcm2niiX version v1.0.20230411  Clang15.0.7 ARM (64-bit MacOS)
Found 56 DICOM file(s)
...

After the dcm2nii conversion, the script prompts the user to select the images for further processing. In this case, the script asks for T2w and DWI images.

...
----------------------------------------------------------------------------------------------------
DICOM to NIfTI is done. Please review the images and select images for further processing.
----------------------------------------------------------------------------------------------------
                  File Name      Dimensions                   Pixel Size
0  t2_sag_tse_stir_5.nii.gz  896 x 896 x 15  0.36 mm x 0.36 mm x 3.00 mm
1       DWI_ZOOMit_8.nii.gz    96 x 36 x 15  0.90 mm x 0.90 mm x 5.00 mm
2  t1_sag_flair_2D_4.nii.gz  864 x 864 x 15  0.37 mm x 0.37 mm x 3.00 mm
3  t1_sag_flair_2D_3.nii.gz   864 x 864 x 8  0.37 mm x 0.37 mm x 3.00 mm
4  t2_sag_tse_stir_6.nii.gz  896 x 896 x 15  0.36 mm x 0.36 mm x 3.00 mm
5    t2_sag_tse_2D_2.nii.gz  928 x 928 x 19  0.34 mm x 0.34 mm x 3.00 mm
6     t2_tra_me_2D_7.nii.gz  512 x 512 x 30  0.35 mm x 0.35 mm x 3.30 mm

Please specify the row number of the T2w image you want to use: 5
Selected T2w image: t2_sag_tse_2D_2.nii.gz
Please specify the row number of the dwi image you want to use: 1
Selected dwi image: DWI_ZOOMit_8.nii.gz

Info: Copying /Users/valosek/data/experiments/balgrist-sci/bids/sub-001/ses-01/temp_dcm2niix/t2_sag_tse_2D_2.nii.gz to /Users/valosek/data/experiments/balgrist-sci/bids/sub-001/ses-01/anat/sub-001_ses-01_T2w.nii.gz
Info: Copying /Users/valosek/data/experiments/balgrist-sci/bids/sub-001/ses-01/temp_dcm2niix/DWI_ZOOMit_8.nii.gz to /Users/valosek/data/experiments/balgrist-sci/bids/sub-001/ses-01/dwi/sub-001_ses-01_dwi.nii.gz

Info: Removing the temporary folder /Users/valosek/data/experiments/balgrist-sci/bids/sub-001/ses-01/temp_dcm2niix
----------------------------------------------------------------------------------------------------
All files have been successfully converted and validated. You can find the following images in the BIDS folder:
	/Users/valosek/data/experiments/balgrist-sci/bids/sub-001/ses-01
----------------------------------------------------------------------------------------------------

The output file structure then looks like this:

valosek@macbook-pro:~/data/experiments/balgrist-sci$ tree
.
├── bids
│   └── sub-001
│       └── ses-01
│           ├── anat
│           │   ├── sub-001_ses-01_T2w.json
│           │   └── sub-001_ses-01_T2w.nii.gz
│           └── dwi
│               ├── sub-001_ses-01_dwi.bval
│               ├── sub-001_ses-01_dwi.bvec
│               ├── sub-001_ses-01_dwi.json
│               └── sub-001_ses-01_dwi.nii.gz
└── source_data
    └── dir_20231010
        ├── MRc.1.3.12.2.543543
        ├── ...
        └── SRe. 1.3.12.2.5432233

[sandrinebedard]

Do you have some dicoms to test it out with?

[valosekj]

Do you have some dicoms to test it out with?

Unfortunately not publicly available. Maybe you can pick some dicoms from duke? Or what about spine-generic dicoms? Do you know if they are publicly available somewhere?

[sandrinebedard]

Unfortunately not publicly available. Maybe you can pick some dicoms from duke? Or what about spine-generic dicoms? Do you know if they are publicly available somewhere?

I don't thinl they are publicly available, they are probably not defaced, and usually dicoms contains some HIPAA identifyers (identifying data) ...

[sandrinebedard]

Unfortunately not publicly available. Maybe you can pick some dicoms from duke? Or what about spine-generic dicoms? Do you know if they are publicly available somewhere?

I don't thinl they are publicly available, they are probably not defaced, and usually dicoms contains some HIPAA identifyers (identifying data) ...

I'll take something on duke

[sandrinebedard]

Approving!

[valosekj]

Merging! I'll continue with the code for further analysis in a new branch.