This repository takes clinical T1 (T2, FLAIR) and DWI BIDS-formatted data and prepares it for lesion tracing.

Typically, I would recommend cloning this into <bids-dir>/code (I will update this to be <bids-dir>/code/bids_lesion_code in the future to match YODA principles.

The main script is: prep_for_ITKSNAP.sh:

It cleans up T1w files, and T2 and FLAIR files if present, and stores them in:
<bids_dir>/derivatives/lesions/<participant_id>/anat

and generates/registers DWI, ADC, b0, and b1000 images to T1w space in:
<bids_dir>/derivatives/lesions/<participant_id>/dwi

For the T1w input, it expects the following naming convention:
<bids_dir>/<participant_id>/anat/<participant_id>_T1w.nii.gz

If this is not available, it will combine axial and coronal clinical scans into a 1mm iso T1:
<bids_dir>/<participant_id>/anat/<participant_id>_acq-ax_T1w.nii.gz
<bids_dir>/<participant_id>/anat/<participant_id>_acq-sag_T1w.nii.gz

For the dwi input, it expects the following naming convention:
<bids_dir>/<participant_id>/dwi/<participant_id>_dwi.nii.gz
<bids_dir>/<participant_id>/dwi/<participant_id>_desc-adc_dwi.nii.gz

Optional (if not present, will assume last frame is b = 1000):
<bids_dir>/<participant_id>/dwi/<participant_id>_dwi.bval
<bids_dir>/<participant_id>/dwi/<participant_id>_desc-b0_dwi.nii.gz
<bids_dir>/<participant_id>/dwi/<participant_id>_desc-b1000_dwi.nii.gz

The files we want to use are:

`<bids_dir>/derivatives/lesions/<participant_id>/dwi/<participant_id>_T1w.nii.gz`  
`<bids_dir>/derivatives/lesions/<participant_id>/dwi/<participant_id>_desc-b1000_dwi.nii.gz`  
`<bids_dir>/derivatives/lesions/<participant_id>/dwi/<participant_id>_desc-adc_dwi.nii.gz`  

If you want to look at the T2w/FLAIR images in the same frame of reference, they are here:
<bids_dir>/derivatives/lesions/<participant_id>/anat/<participant_id>_space-T1w_T2w.nii.gz
<bids_dir>/derivatives/lesions/<participant_id>/anat/<participant_id>_space-T1w_FLAIR.nii.gz

If you have both a B0 image and a B1000 image, you can try getting an automatic segmentation from DeepNeuro (requires a CUDA-capable card): <bids_dir>/code/segment_with_DeepNeuro.sh <bids_dir>/derivatives/lesions/<participant_id>/dwi <participant_id>

And for now, name your lesion tracings with the following pattern:

<bids_dir>/derivatives/lesions/<participant_id>/<participant_id>_space-T1w_desc-lesion<your_initials>_mask.nii.gz

To register individual-space T1ws and lesions to MNI space from BIDS-format, use: <bids_dir>/code/ants_Lesion_in_T1w_space_to_MNI_bids.sh (NOT FINISHED YET)

(NON-BIDS QUICK SCRIPT): To register a single individual-space T1w and lesion to MNI space from specific dir, use:

<working_dir>/code/ants_Lesion_in_T1w_space_to_MNI_quick.sh

Either of these will change the "space" descriptor:
<bids_dir>/derivatives/lesions/<participant_id>/<participant_id>_space-MNI152NLin2009cAsym_desc-lesion_mask.nii.gz

Several of these scripts are from: https://neuroimaging-core-docs.readthedocs.io/, which is a GREAT collection of tutorials and examples.

Combining clinical T1w into a single HQ iso T1w is done with: https://github.com/gift-surg/NiftyMIC

Registering T2, FLAIR, and DWI images to T1 is done with: https://github.com/ANTsX/ANTs antsRegistrationSyNQuick.sh

Initial segmentation of the DWI images is done with: https://github.com/QTIM-Lab/DeepNeuro/tree/master/deepneuro/pipelines/Ischemic_Stroke