This repo conatins the dwi preprocessing and analysis code used by the Computational Neuroimaging Lab at Biocruces Bizkaia HRI.
All the code can be executed using docker. To build the image you need to install first docker and make:
sudo apt install makeBut, if you want to install all neuroimaging software used to preprocess the data, here you have the list!
Raw data should be stored in BIDS format inside a folder named "data"
Also, You need a folder with the brain extracted images and a folder with the tissue-priors segmentations. You can use our pipeline also to a better integration! compneuro-anatpreproc. But, if you want to use another software (or your own code), you need the following folder structure and files:
/path/to/your/project/
├──Preproc
│ ├── Anat
│ │ ├── sub-XXX_acpc
│ │ │ ├── sub-XXX_acpc.nii.gz
│ ├── BET
│ │ ├── sub-XXX_T1w_brain.nii.gz
│ ├── ProbTissue
│ │ ├── sub-XXX_T1w_brain_corticalGM.nii.gz
│ │ ├── sub-XXX_T1w_brain_CSF.nii.gz
│ │ ├── sub-XXX_T1w_brain_subcorticalGM.nii.gz
│ │ ├── sub-XXX_T1w_brain_WM.nii.gz
First, create an environment variable where your data is placed.
export PROJECT_PATH=/path/to/your/projectYou can now build the docker container:
sudo make build
make dev. src/dwi_launcher.sh <partition>- partition: brain partition used for computing the connectivity matrices. It should be in the MNI152_2mm space and dimensions.
The main outputs will be placed in the folder /path/to/your/project/Preproc/Dwiprep
Inside, you will find a subfolder for each subject with the tensor-fitted images (i.e. Fractional anisotropy dwi_FA.nii.gz, Medial diffusivity dwi_MD.nii.gz, Radial diffusivity dwi_RD.nii.gz, and Axial diffusivity dwi_AD.nii.gz). Furthermore you will find the SC matrices of the probabilistic iFOD2 and deterministic FACT tractographies containing the fiber counting in the partition introduced as input.
Please, if you want to use this code in your publications, cite this work:
Multimodal and multidomain lesion network mapping enhances prediction of sensorimotor behavior in stroke patients. Antonio Jimenez-Marin, Nele De Bruyn, Jolien Gooijers, Alberto Llera, Sarah Meyer, Kaat Alaerts, Geert Verheyden, Stephan P. Swinnen, Jesus M. Cortes. SciRep. 2022. doi: https://doi.org/10.1038/s41598-022-26945-x