ATAC data
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Repository Version: 2017.05.03

This dataset includes amygdala segmentation and tractography results from the first 50 subjects (28 female, age 22–35 years, mean 30 years) from the WU-Minn HCP Data-80 unrelated subjects release in the human connectome database (http://humanconnectome.org) [Van Essen et al., 2013].

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The study is reported in the following reference:
Aslan Abivardi & Dominik R. Bach (2017). Deconstructing White Matter Connectivity of Human Amygdala Nuclei with Thalamus and Cortex Subdivisions In Vivo. Human Brain Mapping, in press.

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File Structure:
-README.txt             // This document
-+Data                  // Folder Containing all data files
 |-amy_cortex_connection_strength.csv  \
 |-amy_cortex_connection_density.csv   | Region-wise connection strength and density from amygdala to cortex parcellations, paraventricular thalamus (PVT), and all thalamus parcellations
 |-amy_pvt_connection_strength.csv     |
 |-amy_pvt_connection_density.csv      |
 |-amy_thalamus_connection_strength.csv|
 |-amy_thalamus_connection_density.csv /
 |-probability_map_amygdala.nii.gz      \
 |-probability_map_centrocortical.nii.gz| Probability maps for amygdala subnuclei, parcellated based on tractography, and manually segmented overall amygdala, in MNI space
 |-probability_map_basolateral.nii.gz   /
 |-cortex_tracts_basolateral_mean.nii.gz      \
 |-cortex_tracts_basolateral_stdev.nii.gz     | Voxel-wise mean and standard deviation for tracts to cortex and thalamus, masked with individual cortex/thalamus masks in native space, and combined after transformation to MNI space
 |-cortex_tracts_centrocortical_mean.nii.gz   |
 |-cortex_tracts_centrocortical_stdev.nii.gz  |
 |-thalamus_tracts_basolateral_mean.nii.gz    |
 |-thalamus_tracts_basolateral_stdev.nii.gz   |
 |-thalamus_tracts_centrocortical_mean.nii.gz |
 |-thalamus_tracts_centrocortical_stdev.nii.gz/


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Data Files:
-+Connection strength and density header labels:
 |DL: Basolateral (deep) Left
 |DR: Basolateral (deep) Right
 |SL: Centrocortical (superficial) Left
 |SR: Centrocortical (superficial) right
 |Numbers for cortex refer to "List of anatomical parcellations" as published in "Christophe Destrieux, Bruce Fischl, Anders Dale, Eric Halgren, Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature, NeuroImage, Volume 53, Issue 1, 15 October 2010, Pages 1-15, ISSN 1053-8119, https://doi.org/10.1016/j.neuroimage.2010.06.010."
 | Numbers for thalamus: 1. frontal, 2. occipital, 3. parietal, 4. somatosensory, 5. motor, 6. temporal

Connection strength and density files are saved as .csv files with a comma as delimiter
Map data are stored as .nii files (NIfTI-1, Neuroimaging Informatics Technology Initiative) compressed as .gz (gzip, a GNU project). All .nii.gz files were written and compressed in MATLAB 9.1 (R2016b) with spm12 functions.