Rodent DTI Connectomics

Shellscripts for DTI connectomics generation from rodent data.

• mouse_singleShell_dtiConnectomics
• mouse_multiShell_dtiConnectomics
• rat_singleShell_dtiConnectomics
• rat_multiShell_dtiConnectomics

Prerequisites

You need to have these programmed installed.

• FSL
• ANTs
• MRtrix

Instructions

Folder Structure

.
├── dat                   # each subdirectory contains a dataset
│   ├── dataset1
│   ├── dataset2
│   └── ...
└── shellscripts          # download and save the shellscripts here

List of Input Files

For Preprocessing step

• grad.txt (grad_xx.txt; diffusion-weighted gradient scheme in MRtrix format)
• dwi.nii (dwi_xx.nii)
• rc_mt2.nii / rc_t2.nii (SPM biasfield-corrected/uncorrected t2 coregistered to dwi)
• rc_ix_AVGTmask.nii (mask image)
• c_t2.nii requires preprocessing in ANTx2 toolbox https://github.com/ChariteExpMri/antx2

For Connectome generation

• ANO_DTI.nii (atlas)
• ANO_DTI.txt (6 columns: ID, LabelName, R, G, B, A)
• atlas_lut.txt (identical to ANO_DTI.txt, but make sure ID is sequential with no gaps)

Usage

In terminal, go to the dat directory. Run the 'complete' file in the shellscripts folder. E.g.

cd /path/to/directory/dat
./../shellscripts/mouse_dti_complete_7texpmri.sh