This repo conatins the anatomical (T1) 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"
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 devFor anatomical image preprocessing run:
src/apreproc_launcher.shIf you want to calculate the head size (vscale), gray matter and white matter volume of each participant, run (after apreproc_launcher):
utils/brainmeasures.shThe following outputs will be generated:
/path/to/your/project/
├──Preproc
│ ├── 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
In BET folder you will find the brain extracted images of each participant and in ProbTissue the probability maps of each brain tissue. If you run brainmeasures.sh you will also find brainmeasures.tsv in data folder.
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