HCP Tractography Atlas


Yeh, F. C., Panesar, S., Fernandes, D., Meola, A., Yoshino, M., Fernandez-Miranda, J. C., ... & Verstynen, T. (2018). Population-averaged atlas of the macroscale human structural connectome and its network topology. NeuroImage, 178, 57-68. PubMed: https://www.ncbi.nlm.nih.gov/pubmed/29758339

This atlas is shared under the Creative Commons Attribution-ShareAlike 4.0 International License. It is free for all purposes provided its citation (2018 Neuroimage Paper, see below) is attributed as the source.

The HCP842 tractography atlas and the most recent HCP1065 atlas are derived from data acquired by the Human Connectome Project and may require additional acknowledgment.


HCP1065 tractography atlas (April 2020)

    HCP1065 atlas is an updated atlas from HCP842 atlas. The new atlas is baes on "ICBM 2009a Nonlinear Asymmetric" (https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009) space, whereas HCP842 is based on FSL's FA map ( 58 FA images averaged to old MNI152).
    The new atlas further provides subcomponents for cingulum, SLF, corticopontine track, corticostriatal track, corticothalamic track (renamed as thalamic radiation).

    Citation: Since the atlas is transformed or derived from HCP842, please cite the original HCP842 atlas paper (Yeh, 2018), and mentioned an updated version is used to get tracks in the ICBM152 nonlinear space.

        (DSI Studio can open *.tt.gz and *trk.gz directly without decompressing them)
     To view these tract files, please download the HCP-1065 template fib file and open it in DSI Studio at [Step T3 Fiber Tracking]. The *.tt.gz files can be loaded using [Tracts][Open Tracts]. The ICBM152 images can be loaded using [Edit][Insert T1W/T2W].

HCP842 tractography files (2018)

    HCP842 tractography atlas uses FSL's FA map as its reference space (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlases), which averages from 58 FA images in the MNI152 coordinate

     A total of 80 nifti files are available in the download link. Each file records the voxel-based mask converted from the trajectories of fiber bundle. The original tracks has a much high resolution, and the conversion to a voxel mask loses a substantial amount of spatial information. 
     A total of 80 TRK files are available in the download link. To view these TRK file, please download the HCP-842 template here: https://pitt.box.com/v/HCP842T. open it in DSI Studio at [Step T3 Fiber Tracking]. The TRK files can be loaded using [Tracts][Open Tracts]
     The pictures show views of the fiber pathways from 6 different directions in a higher resolution. The images were created using DSI Studio.
     Connectograms of each fiber pathway generated using an AAL-based brain parcellation.

Integration with MGH's 100-micron human scan

Follow the above steps to view tracks in 3D. 
Download MGH's 100-micron human scan in the MNI space at https://pitt.app.box.com/s/416430693p6kjmwknpdheu3ah9en71rn and load it using [Slices][Insert T1W/T2W]
The 100-micron MGH data are redistributed by CC-BY license. The source is from https://www.biorxiv.org/content/10.1101/649822v1

Other Resources:

    Trk files converted to MNI space using Dipy RecoBundle: https://figshare.com/articles/Simple_model_bundle_atlas_for_RecoBundles/6483614

    The abbreviation list is attached at the bottom of this page.


White matter localization

The HCP842 tractography atlas can be matched with the TBSS or VMB mask to explore which pathways are involved in the finding. The following steps describe how to do this.

1. Download DSI Studio at dsi-studio.labsolver.org
2. Download HCP842 template file:  https://pitt.box.com/v/HCP8421MM
3. Download HCP842 tractography TRK files: https://pitt.app.box.com/v/SCA-TRACK   
    I recommend download only the projection, association, and commissural pathway. The following steps can be repeated for each pathway system, respectively.
4. Run DSI Studio (unzip dsi_Studio_64.zip to a folder and click dsi_studio.exe)
5. Click [STEP3 Fiber Tracking] and open HCP842_1mm.fib.gz (the HCP842 template file)
6. Load the TBSS or VBM mask file as a region by [Regions][Open Region]. 
    You may check the ROI window at the left bottom window to make sure that the mask appears correctly
7. Load the tractography TRK files by [Tracts][Open Tracts] and select the TRK files of a pathway system (e.g. TRK files in the projection folder)
8. [Tracts][Filter Tracts by ROI/ROA/END] to remove tracks that are not passing through the mask
9. [Tracts][Statistics] and save the results as a text file. 
10. Open the text file in Excel. Check out "a number of tracks" row to see the streamline count in the remaining tractography. If the number of tracks is 0, then it means the pathway does not go through the mask. A higher streamline count indicates a possible higher chance the pathway is related to the mask region.


[1]Yeh, F. C., S. Panesar, D. Fernandes, A. Meola, M. Yoshino, J. C. Fernandez-Miranda, J. M. Vettel, and T. Verstynen. "Population-averaged atlas of the macroscale human structural connectome and its network topology." NeuroImage (2018).