Network Neuroscience - Structural

Structural connectivity.

Let's start by learning a little bit about structural connectivity. Diffusion MRI measures how anisotropic the movement of water is, with the basic principle that myelinated tissue will create more anisotropic water movement. Structural connectivity is one type of analysis that describes the structural organization of the white matter using diffusion MRI data. This type of analysis characterizes how connected different regions are by computing the number of diffusion tractography streamlines that terminate into a particular region. The rationale is that regions that have greater density of streamline terminations have greater connectivity with the regions where those streamlines also terminate. These density values are stored in what is known as a connectivity matrix. Each position in the matrix represents the connectivity between two particular regions.

From these matrices, scientists can then examine properties that describe the inter-relatedness of many regions. These properties can be used to identify network-level, inter-individual differences in a large cohort.

This page demonstrates how to generate structural connectivity matrices on brainlife.io. The goal of this tutorial is to show you how to generate structural connectivity matrices following dMRI preprocessing and tractography. This tutorial will be using Multi-atlas Transfer Tool (MaTT) to map the Glasser 180-node cortical atlas to the preprocessed Freesurfer surfaces, anatomically-constrained tractography to generate whole-brain tractograms, and network matrices to compute the connectivity between each region in the atlas.

This tutorial will use a combination of skills developed in the Introduction tutorial and presumes that you have data processed using dMRI Preprocessing and diffusion tractography. If you are not comfortable archiving, staging, and running apps on brainlife.io, please go back through the introduction tutorial before beginning this one.

1. Anatomical preprocessing.

The first step of structural network generation often involves processing the anatomical images. In order to guarantee that any generalizations regarding location made from the preprocessed diffusion data is anatomically-informed, we must have both of our anatomical (T1w or T2w) images and our diffusion MRI images aligned. One way we can make this easier for MRTrix3 Preprocessing is by aligning the anatomical images in such a way that the center of the brain is centered in the image. We refer to this as ACPC-aligned, as we are aligning the data to the anterior commissure-posterior comissure plane. This is the first step in dMRI preprocessing, and is typically done with the FSL Anat (T1w) app. In order to map the Glasser 180-node atlas using the Multi-atlas Transfer Tool (MaTT) and compute the streamline density between each region, we first need to generate cortical and white matter surfaces and brain region parcellations using Freesurfer. Once our anatomical image is aligned, our surfaces are generated, and the Glasser 180-node cortical atlas is mapped, we can move on to diffusion preprocessing.

2. Diffusion preprocessing

The next step in diffusion preprocessing is to actually preprocess the diffusion data. dMRI data, like any other MRI dataset, is quite noisy. Just like fMRI, dMRI data is sensitive to susceptibility distortions. This is when regions of the brain look "wavy" or fold inward or outward on itself in images. This is due to how the scanner sweeps across the entire brain during acquisition. Also, dMRI data is very susceptible to motion. Because some scans take a long time, it is nearly impossible for a participant to lie completely motionless. Even the most subtle movements can alter the results in a specific region and make your data less accurate. Finally, movement of the magnetic gradients can induce electromagnetic currents which can affect the measurement in any given location. These electromagnetic currents are called eddy currents, and they are due to the fact that electricity and magnetism are part of the same field, otherwise known as an electromagnetic field. Thankfully, we can use brainlife.io to correct for all of these common artifacts using MRTrix3 Preprocessing.

In addition to these artifacts, dMRI has very low signal-to-noise ratio (SNR), which directly impacts how well you can fit microstructural models and analyze diffusion data. This means that in any given location, the amount of diffusion signal is very low compared to the "noise" of the scanner. There are methods to lower the amount of noise across the brain, and thus increase the SNR. MRTrix3 Preprocessing has the capability to identify and remove noise using principal components analysis (PCA) and Rician analysis.

On top of these issues, dMRI data is sensitive to other artifacts and non-regularities, including gibbs ringing and bias field inhomogeneities, which can affect the quality of the data and how well measures can be derived from the data. MRTrix3 Preprocessing can deal with all of these issues for us!

Finally, once the dMRI data is preprocessed and cleaned, MRTrix3 Preprocessing will align the dMRI data to the anatomical data. This will ensure that any analyses we do with the dMRI data will be anatomically-informed and biologically-relevant.

Useful information about the preprocessing pipeline that MRTrix3 Preprocessing is designed to run -- Diffusion Parameter EStimation with Gibbs and NoisE Removal (DESIGNER) -- can be found in this original Neuroimage paper.

3. Diffusion modeling & anatomically-informed tractography.

Once the dMRI data has been cleaned and aligned to the anatomical (T1w) image, the next step is to map the underlying white matter anatomy using diffusion tractography. Diffusion tractography works by modeling how water is moving throughout the brain based on the principle of anisotropy -- that water will move unequally in a particular direction given a physical constraint. In the case of diffusion MRI, this constraint comes from the myelin wrapping the many axons arranged into bundles known as fascicles. Diffusion tractography generates streamlines that act as evidence of underlying white matter organization. We can bundle these streamlines into common white matter tracts digitally, just as we can bundle fascicles into tracts using histological methods.

The first step is to fit models of diffusion at each location in the dMRI image that can be used as a guide for the tractography algorithms. The most popular model for this is known as constrained spherical deconvolution, or CSD. CSD allows for the possibility of multiple fascicles entering a single location that may have different trajectories, which is a major advantage of this model over other models of diffusion. The CSD model at each location can tell the tracking algorithm how strongly and in what direction water is diffusing in the brain, and thus where organized and myelinated white matter is likely to be.

Once we know the direction of water movement using the CSD model, we can then perform diffusion tractography to map the underlying organized white matter. Diffusion tractography sews together regions with common directions of water movement into streamlines that provide evidence for organized, myelinated white matter. These operations can be done millions of times across the entire brain to form tractograms. There are many algorithms for doing this that fall into two main categories: deterministic and probabilistic. Deterministic algorithms work by strictly following the directions of water movement, while probabilistic algorithms infer a probability of different directions of water movement at any given location. Deterministic tractography tends to be an overly conservative representation of the white matter, as modeling is never perfectly accurate. Probabilistic tractography tends to provide hairy streamline representations, as the model allows for a probability of different directions of water movement at any given location. Recently, it was discovered that combining both algorithms, or ensembling them, provides the most anatomically-accurate tractograms.

On brainlife.io, we have many options for performing tractography! For this tutorial, we will focus on Probabilistic tractography, using the mrtrix3 - WMC Anatomically Constrained Tractography (ACT) app, which restricts streamline representations to those that are biologically-plausible (i.e. not crossing CSF or gray matter)! Within this app, both the CSD and DTI models will be fit to the diffusion data and returned as outputs!

More information on ensemble tractography can be found in this PLOS Computational Biology article paper. More information on ACT can be found in this Neuroimage publication.

4. Generate structural connectivity matrices.

Once the whole-brain tractograms have been generated, we can now compute the streamline density between each region and generate our structural connectivity matrices. These matrices can then be used to derive network-related measures of the white matter organization of an individual or of common properties amongst groups. For this tutorial, we will use network matrices to generate our structural connectivity matrix.

Now, let's get to work! The following steps of this tutorial will show you how to:

1. ACPC-align the anatomical (T1w) image,
2. Generate Freesurfer surfaces and parcellations,
3. Map Glasser 180-node cortical atlas to the surface,
4. Preprocess dMRI data,
5. Perform diffusion tractography,
6. and generate network matrices from the regions of the Glasser 180-node atlas.
7. convert to conmat datatype
8. convert to network datatype

Copy appropriate data over from a single subject in the Tutorial data project

1. Click the following link to go to the project's page for the Tutorial
2. Click the 'Archive' tab at the top of the screen to go to the Archives page.
3. Select the following datatypes from one subject by clicking the boxes next to the data for subject 'test001':
   • dwi
     • Both dwi files (AP and PA dataset-tagged)
   • anat/t1w
   • anat/t2w
4. Click the 'Stage to process' button on the right side of the screen
   • For 'Project', select your project from the drop-down menu.
   • For 'Process,' select 'Create New Process' and title it "Network neuroscience - structural tutorial." Hit 'Submit.'
     • This will take you to the process on your Projects page
5. Archive the data in your project by clicking the 'Archive' button next to each dataset.

Your data should now be staged for processing and archived in your projects page! You're now ready to move onto the first step: preprocessing of the anatomical (T1w & T2w) images!

Preprocess anatomical (T1w & T2w) data using FSL

T1w data

1. On the 'Process' tab of your project, click 'Submit App' to submit a new application.
   • In the search bar, type 'FSL Anat (T1w).'
   • Click the app card.
2. On the 'Submit App' page, select the following:
   • For input, select the staged raw anatomical (T1w) image by clicking the drop-down menu and finding the appropriate datasets.
   • Select the boxes for 'crop' and 'reorient'. Leave all other defaults the same.
   • Select the box for 'Archive all output datasets when finished'
     • For 'Dataset Tags,' type and enter 'fsl_anat'
   • Hit 'Submit'
3. Once the app is finished running, view the results by clicking the 'eye' icon to the right of the dataset
   • Choose 'FSLeyes' as your viewer
     • This will load the the preprocessed T1w data.

T2w data

1. On the 'Process' tab of your project, click 'Submit App' to submit a new application.
   • In the search bar, type 'FSL Anat (T2w).'
   • Click the app card.
2. On the 'Submit App' page, select the following:
   • For input, select the staged raw anatomical (T2w) image by clicking the drop-down menu and finding the appropriate datasets.
   • Select the boxes for 'crop' and 'reorient'. Leave all other defaults the same.
   • Select the box for 'Archive all output datasets when finished'
     • For 'Dataset Tags,' type and enter 'fsl_anat'
   • Hit 'Submit'
3. Once the app is finished running, view the results by clicking the 'eye' icon to the right of the dataset
   • Choose 'FSLeyes' as your viewer
     • This will load the the preprocessed T2w data.

Once you're happy with the surfaces, you can move onto running Freesurfer!

Freesurfer.

1. On the 'Process' tab of your project, click 'Submit App' to submit a new application.
   • In the search bar, type 'Freesurfer 7.1.1'
   • Click the app card.
2. On the 'Submit App' page, select the following:
   • For input, select the staged preprocessed, 'acpc_aligned'-tagged anatomical (T1w & T2w) images by clicking the drop-down menu and finding the appropriate datasets.
   • Select the boxes for 'hippocampal' and 'thalamicnuclei'. Leave all other defaults the same
   • Select the box for 'Archive all output datasets when finished'
     • For 'Dataset Tags,' type and enter 'fsl_anat'
   • Hit 'Submit'
3. Once the app is finished running, view the results by clicking the 'eye' icon to the right of the dataset
   • Choose 'freeview' as your viewer
     • This will load the following volumes and surfaces: aseg, brainmask, white matter mask, T1, left/right hemisphere pial (cortical), and white (white matter) surfaces.
   • To view the aparc.a2009s segmentation on an inflated surface, do the following:
     • Click File --> Load surface
       • Choose the lh.inflated and rh.inflated surfaces
       • Hit 'OK'
     • Select inflated surface of choice (i.e. left or right hemisphere)
     • Click the drop-down menu next to 'Annotation' and choose 'Load from file'
       • Choose the appropriate hemisphere aparc.a2009s.annot file (lh.aparc.a2009s.annot)
       • Hit 'OK'
       • The aparc.a2009s parcellation should be overlaid on your inflated surface! Now, repeat the process on the other hemisphere.

Once you're happy with the surfaces, you can move onto running Multi-Atlas Transfer Tool!

Map the Glasser 180-node atlas:

1. On the 'Process' tab, click 'Submit App' to submit a new application.
   • In the search bar, type 'Multi-Atlas Transfer Tool'
   • Click the app card.
2. On the 'Submit App' page, select the following:
   • For input, select the staged Freesurfer output generated above by clicking the drop-down menu and finding the appropriate dataset.
   • For 'space,' select 'hcp-mmp-b' from the drop-down menu.
   • Select the box for 'Archive all output datasets' when finished
     • For 'Dataset Tags,' type and enter 'Glasser'
   • Hit 'Submit'

Once the app is finished, you're ready to move on to the final step: network matrix generation!

Preprocess diffusion MRI data with MRTrix3 preproc.

1. On the 'Process' tab, click 'Submit App' to submit a new application.
   • In the search bar, type 'MRTrix3 preproc'
   • Click the app card.
2. On the 'Submit App' page, select the following:
   • For anat/t1w, select the staged ACPC-aligned anatomical (T1w) image by clicking the drop-down menu and finding the appropriate dataset.
   • For dwi, select the dwi image with the tag "PA" by clicking the drop-down menu and finding the appropriate dataset.
   • For dwi (reverse), select the dwi image with the tag "AP" by clicking the drop-down menu and finding the appropriate dataset.
   • for acqd, choose 'posterior -> anterior (y) (PA) by clicking the drop-down menu and finding the appropriate choice.
   • Leave all the other options as default
   • Select the box for 'Archive all output datasets when finished'
     • For 'Dataset Tags,' type and enter 'acpc_aligned'
   • Hit 'Submit'
3. Once the app is finished running, view the results by clicking the 'eye' icon to the right of the dataset
   • Choose 'fsleyes' as your viewer
   • Only have the file titled 'dwi.nii.gz' selected in the viewer
4. You can also generate a QA image of the DWI-T1 alignment by running the 'Generate images of DWI overlaid on T1' using the ACPC-aligned anatomical image and the preprocessed dMRI image generated above! Archive the results and save with the tag 'qa dmri-t1 overlay'.

Once you're happy with the results, you can move on to fitting the CSD, DTI, and performing tractography!

Fit the CSD & DTI models, perform diffusion tractography.

1. On the 'Process' tab, click 'Submit App' to submit a new application.
   • In the search bar, type 'MRTrix3 - WMC Anatomically Constrained Tractography (ACT)'
   • Click the app card.
2. On the 'Submit App' page, select the following:
   • For dwi, select the preprocessed dMRI image generated above by clicking the drop-down menu and finding the appropriate dataset.
   • For anat, select the ACPC-aligned T1w image generated above by clicking the drop-down menu and finding the appropriate dataset.
   • Leave all other options as defaults
   • Select the box for 'Archive all output datasets when finished'
     • For 'Dataset Tags,' type and enter 'whole_brain_tractography'
   • Hit 'Submit'
3. Once the app is finished running, view the results by clicking the 'eye' icon to the right of the dataset
   • Choose 'mrview' as your viewer
     • This will overlay the tractogram on the generated fractional anistropy (FA) image
4. You can also generate a QA image of the whole-brain tractograms by running the 'Generate figures of whole-brain tractogram (tck)' using the whole-brain tractogram (tck) generated above! Archive the results and save with the tag 'qa whole brain tractogram'.

If you're happy with the results, you're ready to move on to structural connectivity generation!

Generate structural connectivity matrix.

1. On the 'Process' tab, click 'Submit App' to submit a new application.
   • In the search bar, type 'Structural Connectome MRTrix3 (SCMRT)'
   • Click the app card.
2. On the 'Submit App' page, select the following:
   • For parcellation/volume, select the Glasser volume generated above by clicking the drop-down menu and finding the appropriate dataset.
   • For track/tck, select the whole brain tractogram generated above by clicking the drop-down menu and finding the appropriate dataset.
   • For tensor, select the DTI tensor output generated above by clicking the drop-down menu and finding the appropriate dataset.
   • Leave all other options empty or as defaults.
   • Select the box for 'Archive all output datasets when finished'
     • For 'Dataset Tags,' type and enter 'structural_matrix'
   • Hit 'Submit'

Once the app is finished, you can now move on to converting the matrices to the appropriate datatypes!

Convert conmat to network datatype:

1. On the 'Process' tab, click 'Submit App' to submit a new application.
   • In the search bar, type ' Conmat to network'
   • Click the app card.
2. On the 'Submit App' page, select the following:
   • For conmat, select the neuro/conmat (datatype-tag: density) datatype generated above by clicking the drop-down menu and finding the appropriate dataset.
   • Select the box for 'Archive all output datasets when finished'
     • For 'Dataset Tags,' type and enter 'structural connectivity networks'
   • Hit 'Submit'

Nice work! Now that the app is finished, you're ready to perform group analyses on your connectivity matrices and examine the network structure of your data!!!!