Prerequisites for Data Organisation

For effective target localisation, you’ll need tract-density maps corresponding to your chosen seed mask. For instance, if you aim to localise the ventral intermediate nucleus of the thalamus (Vim) within thalamic masks, ensure you have the necessary tract-density maps.

It’s crucial to maintain a consistent file organization across subjects. Adopting this consistency simplifies further steps in the analysis pipeline. Below is a suggested file structure:

subject001/
├── tracts
│   ├── left
│       ├── seeds_to_target1.nii.gz
│       ├── seeds_to_target2.nii.gz
│       ├── ....
│   ├── right
│       ├── seeds_to_target1.nii.gz
│       ├── seeds_to_target2.nii.gz
│       ├── ....
├── masks
│   ├── left
│       ├── thalamus.nii.gz
│   ├── right
│       ├── thalamus.nii.gz
├── atlases_in_subject_space
│   ├── left
│       ├── vim.nii.gz
│   ├── right
│       ├── vim.nii.gz
└── otherfiles
subject002/
subject003/
...

For example:

• Anatomical masks can be stored in directories like masks/left/ and masks/right/ for each subject.

• Tract-density maps can be placed in tracts/left and tracts/right.

If you’ve prepared your masks and tract-density maps following the Prepare Your Data guide, your files should already be in this consistent format.