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: https://github.com/htakemur/SIPS

We plan to include it as a part of AFQ repository in the future: https://github.com/yeatmanlab/AFQ

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

Second step is to generate whole-brain candidate streamlines using tractography. Vistasoft requires the specific format to identify streamlines, but code for the conversion from several tools (MRTrix, Camino) are available.

The recommended pipeline for identifying the human SIPS is to use CSD-based Anatomically Constrained Tractography (ACT; Smith et al. 2012 NeuroImage), implemented in MrTrix3. The documentation of ACT is here.

Defining cortical ROIs based on Freesurfer parcellation

In order to define the cortical ROI used for identifying SIPS, we need to perform following steps.

1. Convert freesurfer format into vistasoft format. We use the function named fs_roisFromAllLabels in vistasoft.

Example usage:

fs_subjid = {'HCP_001','HCP_002','HCP_003'}; 
% List of subject id used in Freesurfer processing

fsdir = '/data/freesurfer'; % Freesurfer directory
fsfile = '/mri/aparc+aseg.mgz'; % The mgz file including ROI information
anatomyfolder = '/data/HCP/anatomy'; % Path to folder with T1 anatomy file

% Loops for running individual subjects
for i = 1:length(fs_subjid)
fsIn = fullfile(fsdir, fs_subjid{i},fsfile);
outDir = fullfile(fsdir,'FSROI',fs_subjid{i}); % The directory for output files
type   = 'nifti'; % nifti or mat
refT1  = fullfile(anatomyfolder,fs_subjid{i},'t1_acpc.nii.gz'); % Full path to T1 anatomy file
    
mkdir(outDir);
% Run conversion
fs_roisFromAllLabels(fsIn,outDir,type,refT1);
end

2. Use SPIS_convertROI.m to create ROI files to identify SIPS.

% Path to the folder storing ROI file created in an above step
fsFolder = '/data/freesurfer/FSROI/HCP_001'; 
% Path to T1-weighted anatomy file
anatomyfile = '/data/HCP/anatomy/HCP_001/t1_acpc.nii.gz';
% Run
SIPS_convertROI(fsFolder, anatomyFile)

Identify human SIPS

To identify SIPS, we use a function AFQ_findSPIS. We need one ROI in superior parietal ("lh_precuneus_spl" or "rh_precuneus_spl"), and the other ROI in supramarginal gyrus ("1031_ctx-lh-supramarginal" or "2031_ctx-lh-supramarginal"). To run AFQ_findSPIS, we need to specify the path to these ROI together with a path to streamlines generated in a step above.

% Path to whole-brain streamline file (.tck or .pdb or .mat) 
fgFile = '/data/HCP/diffusion/mrtrix/HCP_001/2million_act.tck';  
% Define tract name to save
tractname = 'LH_SIPS.pdb';
% Specify ROI directory 
roiDir = '/data/freesurfer/FSROI/HCP_001';
% Define two ROI required to identify Left SIPS
targetROI1 = 'lh_precuneus_spl';
targetROI2 = '1031_ctx-lh-supramarginal';

% Run
AFQ_findSPIS(fgFile, tractname, roiDir, targetROI1, targetROI2);

Citations to this work

Uesaki, M., Takemura, H. & Ashida, H. (2018) Computational neuroanatomy of human stratum proprium of interparietal sulcus. Brain Structure and Function, 223(1), 489-507.

References

Sachs H. (1892) Das hemisphärenmark des menschlichen grosshirns. Leipzig: Verlag von georg thieme.

Vergani F, Mahmood S, Morris CM, Mitchell P, Forkel SJ. (2014) Intralobar fibers of the occipital lobe: a post mortem dissection study. Cortex. 56:145–156.