Whole Pig Brain DataSet

Göttinge Mini Pig Brain: Whole Brain Diffusion MRI Dataset

dig pigThis dataset has been used for validation of probabilistic tractography agains two simultaneously injected in vivo invasive tracers: Manganese and BDA, as described in Dyrby et al 2007. Therefore the dataset is suitable for testing of existing or new fibre reconstruction models and tractography methods. The dataset available for download is that referred to as "pig1" in Dyrby et al 2007 and the pig brain shown in Figure 7 of Dyrby et al 2011. The original tracer data is available for collaborators only.

For validation of different tractography methods, the same seed ROI must be used. Seed ROIs for download and details of how they were defined are descibed in Dyrby et al 2007.

Facts about the dataset:dig3 1

Sequence: diffusion weighted pulse gradient spin echo (PGSE) with single line readout. The whole brain dataset (no gap) is a concatenation of odd and even slices acquired, for practical reasons, separately but within the same scanning session. For details see Dyrby et al 2011. Imaging protocol used: Image matrix: 256x128, Voxel size: 0.51x0.51x0.5 mm^3, slices: 35 (full brain coverage), TR=6500 ms, TE= 67.1 ms, gap 0.5 mm. Diffusion weighted gradient strength*: 56 mT/m, small delta: 27 ms, big delta: 33.5 ms, a b-value of 4009 s/mm^2 that was acquired on a unit-shell in 61 non-colinear directions. A Camino scheme was used. Three b=0 s/mm^2. 

dig3 2

To cite:

If you use the data, please cite the following in describing how data was acquired (selection of the b-value):  
Dyrby TB, Baaré WF, Alexander DC, Jelsing J, Garde E, Søgaard LV, An ex vivo imaging pipeline for producing high-quality and high-resolution diffusion weighted imaging datasets, Human Brain mapping, April,2011 

Please also cite the following if a seed ROI or tractography has been applied to the dataset:
Dyrby TB, Sogaard LV, Parker GJ, Alexander DC, Lind NM, Baare WF, Hay-Schmidt A, Eriksen N, Pakkenberg B, Paulson OB, Jelsing J., Validation of in vitro probabilistic tractography. Neuroimage, Vol 37, pp. 1267-1277. 2007

Download the diffusion MRI dataset of "pig1" here which also include a camino scheme file for data reconstruction and seed regions for: the Prefrontal cortex (PFC), Somatosensory cortex (SM) and Motor cortex (MC) used in Dyrby et al 2007. Six screenshots show in different views on pig glass-brain the placement of the seed regions.

Observed problems or artefacts: A weak DC off-set that in the dataset has been corrected in the uploaded dataset. In the original image volume, the artefact exist in a single voxel placed at the same position though all slices, and appears weakly higher intense than surrounding voxels. We have reduced the artefact by replacing the intensity of the voxel in each slice with the average of the neighbouring voxels.


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