convert_bids_to_nnUNetV2.py - add support of data types other than anat

[rohanbanerjee]

Fixes #43

This PR solves two things,

1. data_type can be given as a flag
2. It removes the hard-coded anat data-type in the files and should possibly work with all types of BIDS data-types.

The PR can be tested for a fMRI data with the following steps:

1. Clone this utilities repository
2. cd utilities/data_conversion
3. Run the following command:

python convert_bids_to_nnUNetV2.py --path-data /home/GRAMES.POLYMTL.CA/robana/duke/temp/rohan/fmri_sc_seg/datasets/data_all --path-out /home/GRAMES.POLYMTL.CA/robana/duke/temp/rohan/fmri_sc_seg/nnUNet_raw --split 0.8 0.2 --seed 42 --contrast bold --label-suffix seg-manual --data-type func --dataset-name spinefmri --dataset-number 516 --copy True

[valosekj]

Thank you for opening the PR! 👍🏻 let me know once it is ready for review.

[rohanbanerjee]

Thanks @valosekj for looking into this, ready for review now!

[valosekj]

Thank you! 👍🏻

Tested with datatype anat and working fine:

convert_bids_to_nnUNetV2.py 
--path-data sci-paris 
--path-out sci-paris_nnunet_test
--contrast T2w
--label-suffix seg-manual
--data-type anat

According to the command in your original comment, I guess you tested the script with datatype func; if so, you can merge.

BTW. I added a few basic unit tests and CI workflow in 8937bb5 to make the testing of the script easier in the future.