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Li Jingwei
Li Jingwei v0.5.0 - Initial release of Wu2017_RegistrationFusion project
Why:

* Initial release of Wu2017_RegistrationFusion project.
* Modify a few READM.md files and comments for other stable projects.

This change addresses the need by:

* All users
Latest commit acb2262 Apr 23, 2018
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ADNIDataRelease
step1_VBM
step2_LDA
step3_analyses_internalUse
CBIG_tested_config.sh
README.md

README.md

Reference

Xiuming Zhang, Elizabeth C. Mormino, Nanbo Sun, Reisa A. Sperling, Mert R. Sabuncu, B. T. Thomas Yeo. Bayesian model reveals latent atrophy factors with dissociable cognitive trajectories in Alzheimer's disease. Proceedings of the National Academy of Sciences of the USA, 2016.


Background

Alzheimer’s disease (AD) affects 10% of the elderly population. The disease remains poorly understood with no cure. The main symptom is memory loss, but other symptoms might include impaired executive function (ability to plan and accomplish goals; e.g., grocery shopping). The severity of behavioral symptoms and brain atrophy (gray matter loss) can vary widely across patients. This variability complicates diagnosis, treatment, and prevention. A mathematical model reveals distinct brain atrophy patterns, explaining variation in gray matter loss among AD dementia patients. The atrophy patterns can also explain variation in memory and executive function decline among dementia patients and at-risk nondemented participants. This model can potentially be applied to understand brain disorders with varying symptoms, including autism and schizophrenia.


Data Release

Factor compositions of the ADNI subjects involved in this study are released as a spreadsheet in the ADNIDataRelease folder. Specifically, the spreadsheet includes 810 ADNI1-enrolled subjects’ baseline factor compositions and their factor compositions 24 months after baseline (N = 560).

Folder ADNIDataRelease/inferNew/files_LDA/model_K3 contain the probabilistic atrophy maps of the atrophy factors for the three-factor model. Maps for the two- and four-factor models are also released (folders model_K2 and model_K4). You can also view or download all of these atrophy maps online at http://neurovault.org/collections/1917/.

In folder ADNIDataRelease/inferNew/, we provide instructions and code for inferring factor compositions of your own subjects.


Code Release

The remaining folders offer our full code, allowing you to start from scratch on possibly other brain disorders.

Note that this project uses generic functions from other folders, which may be updated over time. To download the exact code utilized for the PNAS paper, you can either

or

  • run the following command, if you have Git installed
git checkout -b Zhang2016_ADFactors v0.1.3-Zhang2016_ADFactors

Updates

  • Release v0.1.3 (26/04/2017): fixing a bug in wrapper CBIG_LDA_est.sh

  • Release v0.1.2 (03/04/2017): removing hardcoded image dimensions

  • Release v0.1.1 (11/06/2016): adding README for each internal folder


Bugs and Questions

Please contact xiuming Zhang at xiuming6zhang@gmail.com and Thomas Yeo at yeoyeo02@gmail.com.

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