MRI Dataset for Hippocampus Segmentation

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Welcome to the hippocampus segmentation dataset provided by the Department of Diagnostic Radiology at Henry Ford Hospital. The aim of this project is to provide a freely available infrastructure for evaluation and validation of hippocampus segmentation techniques. Hippocampus is an important brain structure. Several conditions such as epilepsy and Alzheimer’s disease are known to affect the hippocampus. Thus, segmentation of this structure is important in diagnosis, prognosis, and research.

This dataset is provided with the following specifications:

• The dataset contains 50 brain T1-weighted MRI volumes with hippocampus labels. Images are acquired at two different MRI units (with different field strengths) and thus have very different resolutions and contrasts. Twenty of these images have a higher resolution and are acquired with a relatively new 3T MRI system.

• Forty of these images belong to patients with temporal lobe epilepsy who may have atrophic hippocampi. This makes the segmentation challenging and thus evaluates the segmentation algorithms against practical problems. The remaining 10 images belong to nonepileptic subjects.

• We have divided the dataset into two groups of training and testing (50% each). Training set is provided along with the labels. However, no label is provided for the testing set. All images are in ANALYZE format.

• Special care has been taken to minimize the effect of partial volume in manual drawings. The hippocampi were reconstructed in 3D to ensure that the outlines in consecutive slices are consistent.

• You are encouraged to first work with the training set. If you are about to make a journal publication and would like to report the segmentation results on the testing set, you may send a request to Kourosh Jafari-Khouzani . You may then submit your segmentation results. We will send you a table of evaluation metrics.  Please use “Hippocampus Segmentation Dataset” in the subject of your e-mails.

• More information about the dataset may be found from the following reference. Please refer to this reference in your publications:

  K. Jafari-Khouzani, K. Elisevich, S. Patel, and H. Soltanian-Zadeh, “Dataset of magnetic resonance images of nonepileptic subjects and temporal lobe epilepsy patients for validation of hippocampal segmentation techniques,” Neuroinformatics, 2011.

• You can open the file containing the data using WinRAR.

• Please send your comments to Kourosh Jafari-Khouzani.

Click here to go to the download page. Login required.

You may also consider using the MRI data set provided You may also consider using the MRI dataset provided by Internet Brain Segmentation Repository (IBSR, http://www.cma.mgh.harvard.edu/ibsr/ ) which is provided along with the labels for a number of structures including the hippocampus.