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# Repository of data for Jonas Yeung's Ccl2 CRT 4CG publication         #
# Mouse Imaging Centre, Hospital for Sick Children, Toronto, ON, Canada #
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The data here was used for a project that investigated the effects of cranial radiation therapy (CRT) on Ccl2 knockout in four core genotype (FCG) mice. 

A known sex difference was found in Ccl2 knockouts where male mice responded better than females. Sex differences are fundamentally attributed to either sex hormones or sex chromosomes. This can be distinguished by the FCG model which decouples the sex determining region (SRY) from the Y chromosome by moving SRY onto an autosome. Therefore, there are four core sex genotypes: XX NULL, XY NULL, XX SRY, and XY SRY. Moreover, mice were also either Ccl2 wildtype (+/+) and Ccl2 knockouts (-/-) or irradiated (7Gy) and Sham (0Gy). In total our dataset consisted of 16 groups. 

We used longutidinal MRI to evaluate brain changes over time across 5 timepoints (i.e., P14, P23, P42, P63, and P98). Volumes from these images were segmented into label files where the volumes were extracted for each of the 183 structures delineated in our atlas.

Image registration and segmentation were accomplished through the PydPiper toolkit (https://github.com/Mouse-Imaging-Centre/pydpiper/tree/v2.0.19.1) where MBM.py and the MAGeT algorithm were used. Volumes were extracted using the RMINC toolkit (https://github.com/Mouse-Imaging-Centre/RMINC). 

How to read df_micevolumes:
-ID: unique mouse identifier 
-DOB..P0: date-of-birth which is considered at P0
-Ccl2: genotype status of Ccl2, either +/+ (wildtype) or -/- (homozygous knockout)
-Dose: cranial radiation therapy dose, either 0Gy (sham) or 7Gy (irradiated)
-Timepoint: postnatal day at which the mouse was scanned. 
-file: structural MR image.
-voted_path: path to the voted file (in labels.tar.gz) to obtain structure volumes. 
-amygdala...pituitary_gland: 183 structure volumes (mm^3) of the brain.

Images.tar.gz contains all the images used in the analysis. These files represent the files corrected for translations and rotations (lsq6) to a reference alignment, with nonuniformity and intensity normalization applied.

Labels.tar.gz contains all the segmentations for the corresponding lsq6 image in Images.tar.gz.

final_average.mnc is the representative average of all images after registration together to a common space.

final_labels.mnc is the segmentation of final_average.mnc by voting across the all segmentations.