This app implements the "segmentation mode" (fast) Automated Hippocampus Segmentation Algorithm (ASHS), version 2.0.0. This algorithm uses ANTs to automatically label hippocampal subfields using MRI.
More information on ASHS can be found here: http://picsl.upenn.edu/software/ashs/
- Sophia Vinci-Booher ([email protected])
- Soichi Hayashi ([email protected])
- Franco Pestilli ([email protected])
We kindly ask that you cite the following articles when publishing papers and code using this code.
Avesani, P., McPherson, B., Hayashi, S. et al. The open diffusion data derivatives, brain data upcycling via integrated publishing of derivatives and reproducible open cloud services. Sci Data 6, 69 (2019). https://doi.org/10.1038/s41597-019-0073-y
MIT Copyright (c) 2020 brainlife.io The University of Texas at Austin and Indiana University
Primary Citation Please cite this paper in reference to ASHS software and the UPenn PMC atlas:
Yushkevich PA, Pluta J, Wang H, Ding SL, Xie L, Gertje E, Mancuso L, Kliot D, Das SR and Wolk DA, "Automated Volumetry and Regional Thickness Analysis of Hippocampal Subfields and Medial Temporal Cortical Structures in Mild Cognitive Impairment", Human Brain Mapping, 2014, 36(1), 258-287. http://www.ncbi.nlm.nih.gov/pubmed/25181316
Additional Citations: Papers describing the earlier version of ASHS (2010) and the VACIND atlas:
Yushkevich, Paul A., Hongzhi Wang, John Pluta, Sandhitsu R. Das, Caryne Craige, Brian B. Avants, Michael W. Weiner, and Susanne Mueller. "Nearly automatic segmentation of hippocampal subfields in in vivo focal T2-weighted MRI." Neuroimage 53, no. 4 (2010): 1208-1224. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2939190/
Pluta, John, Paul Yushkevich, Sandhitsu Das, and David Wolk. "In vivo analysis of hippocampal subfield atrophy in mild cognitive impairment via semi-automatic segmentation of T2-weighted MRI." Journal of Alzheimer's Disease 31, no. 1 (2012): 85-99. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3391337/
We currently provide the UPenn PMC ASHS Atlas for segmentation:
Yushkevich PA, Pluta J, Wang H, Ding SL, Xie L, Gertje E, Mancuso L, Kliot D, Das SR and Wolk DA, "Automated Volumetry and Regional Thickness Analysis of Hippocampal Subfields and Medial Temporal Cortical Structures in Mild Cognitive Impairment", Human Brain Mapping, 2014, 36(1), 258-287. http://www.ncbi.nlm.nih.gov/pubmed/25181316
Please note that this atlas does not segment the head (voxel value = 5) and tail (voxel value = 6). Note also that the voxel value 9 does not exist.
We plan to provide 5 additional ASHA Atlases (listed below) in the future when they are updated for compatibility with (fast) Automated Hippocampus Segmentation Algorithm (ASHS), version 2.0.0. Citations are provided for each atlas:
- Princeton Young Adult 3T ASHS Atlas
Hindy, N. C., Ng, F. Y., & Turk-Browne, N. B. (2016). Linking pattern completion in the hippocampus to predictive coding in visual cortex. Nature Neuroscience, 19(5), 665\u2013667.
- UMC Utrecht 7T ASHS Atlas
Wisse, L.E.M., Kuijf, H.J., Honingh, A.M., Wang, H., Pluta, J.B., Das, S.R., Wolk, D.A., Zwanenburg, J.J.M., Yushkevich, P.A. and Geerlings, M.I., 2016. Automated Hippocampal Subfield Segmentation at 7T MRI. American Journal of Neuroradiology.
… and space permitting, please also cite ...
Yushkevich, P.A., Pluta, J.B., Wang, H., Xie, L., Ding, S.L., Gertje, E.C., Mancuso, L., Kliot, D., Das, S.R. and Wolk, D.A., 2015. Automated volumetry and regional thickness analysis of hippocampal subfields and medial temporal cortical structures in mild cognitive impairment. Human brain mapping, 36(1), pp.258-287.
- UMC Utrecht 7T ASHS Atlas
Berron, D., Vieweg, P., Hochkeppler, A., Pluta, J.B., Ding, S.-L., Maass, A., Luther, A., Xie, L., Das, S.R., Wolk, D.A., Wolbers, T., Yushkevich, P.A., Düzel, E., Wisse, L.E.M., 2017. A protocol for manual segmentation of medial temporal lobe subregions in 7 Tesla MRI. NeuroImage: Clinical 15, pp.466\u2013482.
- UT Austin 3T, separated
Schlichting, M. L., Mack, M. L., Guarino, K. F., & Preston, A. R. (2019). Performance of semi-automated hippocampal subfield segmentation methods across ages in a pediatric sample. NeuroImage, 191, 49–67.
- UT Austin 3T, combined
Schlichting, M. L., Mack, M. L., Guarino, K. F., & Preston, A. R. (2019). Performance of semi-automated hippocampal subfield segmentation methods across ages in a pediatric sample. NeuroImage, 191, 49–67.
- IKND Magdeburg Young Adult 7T Atlas
Berron, D., Vieweg, P., Hochkeppler, A., Pluta, J.B., Ding, S.-L., Maass, A., Luther, A., Xie, L., Das, S.R., Wolk, D.A., Wolbers, T., Yushkevich, P.A., Düzel, E., Wisse, L.E.M., 2017. A protocol for manual segmentation of medial temporal lobe subregions in 7 Tesla MRI. NeuroImage: Clinical 15, pp.466\u2013482.
This App only requires singularity to run (https://singularity.lbl.gov/install-request). If you don't have singularity, you will need to install following dependencies.
ashs_atlas_upenpmc_20170810.tar: https://www.nitrc.org/frs/?group_id=370 FSL: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation ANTS: http://stnava.github.io/ANTs/ ITK-SNAP: http://www.itksnap.org/pmwiki/pmwiki.php?n=Downloads.SNAP3 jsonlab: https://www.mathworks.com/matlabcentral/fileexchange/33381-jsonlab-a-toolbox-to-encode-decode-json-files