UPDATE: README.md

README.md

@@ -1,3 +1,78 @@
-# MALPEM_ADNI_data
+# Readme
 
-Shared Data for article "Structural brain imaging in Alzheimer's disease and mild cognitive impairment: biomarker analysis and shared morphometry database"
+This repository contains data resources accompanying the article:
+
+   [C. Ledig][cledig], [A. Schuh][schuschu], R. Guerrero, [R. Heckemann][rheckemann], [D. Rueckert][drueckert]
+   "Structural brain imaging in Alzheimer's disease and mild cognitive impairment: biomarker analysis and shared morphometry database", Scientific Reports, 2018.
+
+This work was done in the [BioMedIA][biomedia] group at
+Imperial College London, UK.
+
+[cledig]: http://www.christianledig.com
+[biomedia]: http://biomedic.doc.ic.ac.uk
+[schuschu]: http://andreasschuh.com
+[rheckemann]: https://www.soundray.org
+[drueckert]: http://wp.doc.ic.ac.uk/dr/
+
+## Citation
+Please cite as:
+    @article{Ledig2018,
+      title={Structural brain imaging in Alzheimer's disease and mild cognitive impairment: biomarker analysis and shared morphometry database},
+      author={Ledig, Christian and Schuh, Andreas and Guerrero, Ricardo and Heckemann, Rolf and Rueckert, Daniel},
+      journal={Scientific Reports},
+      year={2018},
+      publisher={Nature Publishing Group}
+    }
+      
+## File Description 
+
+**Processed Images**
+
+-   List of all 5074 images (includes baseline and follow up images) [[ADNI_MALPEM_all_5074.csv]](https://web.gin.g-node.org/ledigchr/MALPEM_ADNI_data/src/master/ADNI_MALPEM_all_5074.csv)
+-   List of 1069 baseline images used for analysis [[ADNI_MALPEM_baseline_1069.csv]](https://web.gin.g-node.org/ledigchr/MALPEM_ADNI_data/src/master/ADNI_MALPEM_baseline_1069.csv)
+-   List of 802 m12 follow up images used for analysis [[ADNI_MALPEM_m12_802.csv]](https://web.gin.g-node.org/ledigchr/MALPEM_ADNI_data/src/master/ADNI_MALPEM_m12_802.csv)
+-   List of 532 m24 follow up images used for analysis [[ADNI_MALPEM_m24_532.csv]](https://web.gin.g-node.org/ledigchr/MALPEM_ADNI_data/src/master/ADNI_MALPEM_m24_532.csv)
+
+**Features**
+
+-   All extracted cross-sectional (structural volumes) and longitudinal (volume change rate) features and selected clinical information (e.g. disease labels). Note: Not all of those features have been used in the manuscript. Please, refer to the paper for details. 
+[[features_CrossSect-5074_LongBLM12-802_LongBLM24-532.zip]](https://web.gin.g-node.org/ledigchr/MALPEM_ADNI_data/src/master/features_CrossSect-5074_LongBLM12-802_LongBLM24-532.zip)
+
+**Segmentations / Brain masks**
+
+-   5074 cross-sectional structural segmentations in 138 distinct anatomical regions (calculated with MALPEM) 
+[[MALPEM_cross-sectional_seg138_5074.zip]](http://https://web.gin.g-node.org/ledigchr/MALPEM_ADNI_data/src/master/MALPEM_cross-sectional_seg138_5074.zip)
+-   5074 binary brain masks (calculated with pincram). Masks have been quality checked (baseline: visual, followup: automatic)
+[[pincram_bin_brain_masks_5074.zip]](https://web.gin.g-node.org/ledigchr/MALPEM_ADNI_data/src/master/pincram_bin_brain_masks_5074.zip)
+-   Lookup table for all segmented 138 brain structures  [[lut.csv]](http://web.gin.g-node.org/ledigchr/MALPEM_ADNI_data/src/master/lut.csv)
+
+  
+## License
+The data in this repository is distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International Public License. See the accompanying [license file][license] for details. The license does not allow usage of this data for commercial applications. This restriction is derived from the license of the [Neuromorphometrics](http://Neuromorphometrics.com/) atlases (CC BY-NC).
+
+[license]: https://web.gin.g-node.org/ledigchr/MALPEM_ADNI_data/src/master/LICENSE
+
+## Methodology
+
+**Framework and cross-sectional segmentation** [[paper]](http://www.sciencedirect.com/science/article/pii/S136184151400187X)
+
+C. Ledig, R. A. Heckemann, A. Hammers, J. C. Lopez, V. F. J. Newcombe, A. Makropoulos, 
+J. Loetjoenen, D. Menon and D. Rueckert,
+"Robust whole-brain segmentation: Application to traumatic brain injury",
+Medical Image Analysis, 21(1), pp. 40-58, 2015.
+
+**Longitudinal segmentation**  [[paper]](http://www.christianledig.com/Publications/pdf/ISBI2014_Ledig.pdf)
+
+C. Ledig, W. Shi, A. Makropoulos, J. Koikkalainen, R. A. Heckemann, A. Hammers, J. Lötjönen, and D. Rueckert,
+"Consistent and robust 4D whole-brain segmentation: application to traumatic brain injury", Proceedings of ISBI
+2014, pp. 673-676, 2014
+
+**Brain extraction** [[paper]](http://www.plosone.org/article/Authors/info:doi/10.1371/journal.pone.0129211)
+
+R. Heckemann, C. Ledig, K. R. Gray, P. Aljabar, D. Rueckert, J. V. Hajnal, and A. Hammers,
+"Brain extraction using label propagation and group agreement: pincram",
+PLoS ONE, 10(7), pp. e0129211, 2015.
+
+Multi-Atlas Label Propagation with Expecation-Maximisation based refinement (MALPEM) including pincram brain extraction is publicly available on github: [[MALPEM]](https://github.com/ledigchr/MALPEM)
+
+We are working on releasing the actual source code of MALPEM within [[MIRTK]](https://github.com/BioMedIA/MIRTK)