# Readme
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.

In this article, we employed a recently validated method (MALPEM) for robust cross-sectional and longitudinal segmentation of MR brain images from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) cohort. Specifically, we segmented 5074 MR brain images into 138 anatomical regions and extracted time-point specific structural volumes and volume change during follow-up intervals of 12 or 24 months.

The 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 from the ADNI cohort**

-   List of all 5074 images (baseline and follow up images, incl. VISCODE) [[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 (incl. disease label) 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 baseline and m12 follow up image pairs (incl. disease label) 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 baseline and m24 follow up image pairs (incl. disease label) 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, asymmetry) 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
[![License: CC BY-NC 4.0](https://img.shields.io/badge/License-CC%20BY--NC%204.0-lightgrey.svg)](https://creativecommons.org/licenses/by-nc/4.0/)

The data in this repository is distributed under the terms of the Creative Commons Attribution-NonCommercial 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

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)


## References

**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.

## Acknowledgements
Data used in preparation of this article were obtained from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) database [[link]][adni]. As such, the investigators within the ADNI contributed to the design and implementation of ADNI and/or provided data but did not participate in analysis or writing of this report. A complete listing of ADNI investigators can be found at: [[link]][adni_ack]

[adni]: adni.loni.usc.edu
[adni_ack]: http://adni.loni.usc.edu/wp-content/uploads/how_to_apply/ADNI_Acknowledgement_List.pdf