Update README.md

Updates publications, other minor fixes

README.md

@@ -9,7 +9,6 @@
 
 This tool aims to automatically model the topological folding structure
 of the human hippocampus, and computationally unfold it.
-https://raw.githubusercontent.com//khanlab/hippunfold/master/docs/images/subfields_foldunfold.png
 ![Hippo Fold Unfold](https://raw.githubusercontent.com//khanlab/hippunfold/master/docs/images/subfields_foldunfold.png)
 
 This is especially useful for:
@@ -25,7 +24,7 @@ Major changes include the addition of unfolded space registration to a reference
 
 *Note: this replaces the default workflow, however you can revert to the legacy workflow, disabling unfolded space registration, by setting `--atlas bigbrain` or `--no-unfolded-reg`*
 
-Read more in our [preprinted manuscript](https://www.biorxiv.org/content/10.1101/2023.03.30.534978v1)
+Read more in our [ manuscript](https://doi.org/10.7554/eLife.88404.3)
 
 Also the ability to specify a new **experimental** UNet model that is contrast-agnostic using [synthseg](https://github.com/BBillot/SynthSeg) and trained using more detailed segmentations. This generally produces more detailed results but has not been extensively tested yet. 
 
@@ -46,11 +45,22 @@ For plotting, mapping fMRI, DWI or other data, and manipulating surfaces, see [h
 
 For statistical testing (spin tests) in unfolded space, see [here](https://github.com/Bradley-Karat/Hippo_Spin_Testing)
 
-## Relevant papers:
-- DeKraker, J., Palomero-Gallagher, N., Kedo, O., Ladbon-Bernasconi, N., Muenzing, S. E., Axer, M., ... & Evans, A. C. (2023). Evaluation of surface-based hippocampal registration using ground-truth subfield definitions. bioRxiv, 2023-03. [link](https://www.biorxiv.org/content/10.1101/2023.03.30.534978v1)
+## Publications
+
+### HippUnfold methods paper
+
 - DeKraker, J., Haast, R. A., Yousif, M. D., Karat, B., Lau, J. C., Köhler, S., & Khan, A. R. (2022). Automated hippocampal unfolding for morphometry and subfield segmentation with HippUnfold. Elife, 11, e77945. [link](https://doi.org/10.7554/eLife.77945)
-- DeKraker J, Ferko KM, Lau JC, Köhler S, Khan AR. Unfolding the hippocampus: An intrinsic coordinate system for subfield segmentations and quantitative mapping. Neuroimage. 2018 Feb 15;167:408-418. doi: 10.1016/j.neuroimage.2017.11.054. Epub 2017 Nov 23. PMID: 29175494. [link](https://pubmed.ncbi.nlm.nih.gov/29175494/)
-- DeKraker J, Lau JC, Ferko KM, Khan AR, Köhler S. Hippocampal subfields revealed through unfolding and unsupervised clustering of laminar and morphological features in 3D BigBrain. Neuroimage. 2020 Feb 1;206:116328. doi: 10.1016/j.neuroimage.2019.116328. Epub 2019 Nov 1. PMID: 31682982. [link](https://pubmed.ncbi.nlm.nih.gov/31682982/)
+  -  **Please cite this if you use any version of HippUnfold)**
+
+### Unfolded space registration and multihist7 atlas
+- DeKraker Jordan, Palomero-Gallagher Nicola, Kedo Olga, Ladbon-Bernasconi Neda, Muenzing Sascha E.A., Axer Markus, Amunts Katrin, Khan Ali R., Bernhardt Boris, Evans Alan C. (2023) Evaluation of surface-based hippocampal registration using ground-truth subfield definitions eLife 12:RP88404 [link](https://doi.org/10.7554/eLife.88404.3)
+  -  **Please cite this if you use HippUnfold version >= 1.3.0)**
+
+### Commentary on surface-based hippocampal segmentation
 - DeKraker J, Köhler S, Khan AR. Surface-based hippocampal subfield segmentation. Trends Neurosci. 2021 Nov;44(11):856-863. doi: 10.1016/j.tins.2021.06.005. Epub 2021 Jul 22. PMID: 34304910. [link](https://pubmed.ncbi.nlm.nih.gov/34304910/)
 
+### Related papers
 
+- DeKraker J, Ferko KM, Lau JC, Köhler S, Khan AR. Unfolding the hippocampus: An intrinsic coordinate system for subfield segmentations and quantitative mapping. Neuroimage. 2018 Feb 15;167:408-418. doi: 10.1016/j.neuroimage.2017.11.054. Epub 2017 Nov 23. PMID: 29175494. [link](https://pubmed.ncbi.nlm.nih.gov/29175494/)
+- DeKraker J, Lau JC, Ferko KM, Khan AR, Köhler S. Hippocampal subfields revealed through unfolding and unsupervised clustering of laminar and morphological features in 3D BigBrain. Neuroimage. 2020 Feb 1;206:116328. doi: 10.1016/j.neuroimage.2019.116328. Epub 2019 Nov 1. PMID: 31682982. [link](https://pubmed.ncbi.nlm.nih.gov/31682982/)
+- Karat BG, DeKraker J, Hussain U, Köhler S, Khan AR. Mapping the macrostructure and microstructure of the in vivo human hippocampus using diffusion MRI. Hum Brain Mapp. 2023 Nov;44(16):5485-5503. Epub 2023 Aug 24. PMID: 37615057; PMCID: PMC10543110.[link](https://doi.org/10.1002/hbm.26461)