tsantini/ashs repository overview

⁠Example of usage

For T1w+T2w pairs docker run -e ATLAS=ashs_atlas_magdeburg_7t_20180416_denoised -v $PWD:$PWD -w $PWD --rm tsantini/ashs TSE.nii MPRAGE.nii

For T1w only docker run -e ATLAS=ashs_atlas_magdeburg_7t_20180416_denoised -v $PWD:$PWD -w $PWD --rm tsantini/ashs MPRAGE.nii MPRAGE.nii

Atlases options:

T1w+T2w:
ashs_atlas_magdeburg_7t_20180416
ashs_atlas_magdeburg_7t_20180416_denoised
ashs_atlas_abc_prisma_20200406
ashs_atlas_abc_prisma_20200406_denoised
T1w only:
ashs_atlas_upennpmc_t1ext_20240617
ashsT1_atlas_upennpmc_wm_07172023

If no atlas is provided, the code will use ashs_atlas_magdeburg_7t_20180416_denoised

⁠References

https://github.com/pyushkevich/ashs⁠

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.466–482.

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.

Xie, L., Wisse L.E.M., Wang J., Ravikumar S., Khandelwal P., Glenn T., Luther A., Lim S., Wolk D.A., Yushkevich P.A., 2023. Deep label fusion: A generalizable hybrid multi-atlas and deep convolutional neural network for medical image segmentation. Medical Image Analysis: 83.

Niyousha Sadeghpour, Sydney A. Lim, Anika Wuestefeld, Amanda E. Denning, Ranjit Ittyerah, Winifred Trotman, Eunice Chung, Shokufeh Sadaghiani, Karthik Prabhakaran, Madigan L. Bedard, Daniel T. Ohm, Emilio Artacho-Pérula, Maria Mercedes Iñiguez de Onzoño Martin, Monica Muñoz, Francisco Javier Molina Romero, José Carlos Delgado González, María del Mar Arroyo Jiménez, Maria del Pilar Marcos Rabal, Ana María Insausti Serrano, Noemí Vilaseca González, Sandra Cebada Sánchez, Carlos de la Rosa Prieto, Ricardo Insausti, Corey McMillan, Edward B. Lee, John A. Detre, Sandhitsu R. Das, Long Xie, M. Dylan Tisdall, David J. Irwin, David A. Wolk, Paul A. Yushkevich, Laura EM. Wisse. Developing an anatomically valid segmentation protocol for anterior regions of the medial temporal lobe for neurodegenerative diseases. BioRxiv 2025

Santini T, Koo M, Farhat N, Campos VP, Alkhateeb S, Vieira MAC, Butters MA, Rosano C, Aizenstein HJ, Mettenburg J, Novelli EM, Ibrahim TS. Analysis of hippocampal subfields in sickle cell disease using ultrahigh field MRI. Neuroimage Clin. 2021;30:102655. doi: 10.1016/j.nicl.2021.102655. Epub 2021 Apr 3. PMID: 34215139; PMCID: PMC8102634.