Identify human Stratum Proprium of Interparietal Sulcus

Tutorial of human SIPS

This documentation describe how to identify the human Stratum proprium of Interparietal Sulcus (SIPS) from diffusion MRI dataset, as described in Uesaki et al. (2017). Human SIPS is a white matter tract in human parietal cortex initially identified by Sachs (1892), and later by Vergani et al. (2014).

Note: This tutorial is still under development.

Code download

The code required for human SIPS identification is hosted in following repository (open to public upon publication of the paper): https://github.com/htakemur/SIPS

We plan to include it as a part of AFQ repository in the future.

Dependency

To identify human SIPS, we need to install several different software distributions together with MATLAB.

• Freesurfer
• vistasoft
• mba

Following softwares are optional, but also highly recommended to install:

• MRTrix
• FSL

Requirement

• Preprocessed Diffusion MRI dataset (nifti format)
• T1-weighted Anatomical image (nifti format)

These images should be coregistered prior to run the subsequent analysis process.

Run whole-brain segmentation

First step of the analysis is to run the Freesurfer command for tissue segmentation, using recon-all command. This will typically require about one day for one single subject.

Example usage is: recon-all -i t1.nii.gz -subjid HCP_001 -all

where -i requires the file name of nifti file (T1-weighted image), and -subjid requires the subject ID used for defining Freesurfer subject directory.

See Freesurfer Wiki to figure out how to install and set up subject folder to run Freesurfer segmentation.

Generating whole-brain streamlines

Defining cortical ROIs based on Freesurfer parcellation

Identify human SIPS

Citations to this work

Uesaki, M., Takemura, H. & Ashida, H. (2017) Computational neuroanatomy of human stratum proprium of interparietal sulcus. bioRxiv, 126961.