TubeTK/TBI Data

Image Format

Images are presented in the nii format. Each image can be loaded by any program that supports nii format, including most ITK and VTK-based applications (e.g., Slicer).

There are two patient data sets. For each of them, there are datasets for 4 different modalities for both Acute and Chronic Stage. These modalities are:

• T1-weighted MRI: These are standard basic scans that are used to differentiate fat from water. They show water darker and fat lighter.

• T2-weighted MRI: These are another standard basic scans that are used to differentiate fat from water. The difference of this data set from T1 is that they show fat darker, and water lighter.

• Fluid-attenuated inversion recovery (FLAIR) data set: It is an advanced magnetic resonance imaging sequence that reveals tissue T2 prolongation with cerebrospinal fluid suppression, allowing detection of superficial brain lesions [1].

• Gradient Recalled Echo (GRE) data set [2] [3]: These images are used to generate contrast (by enhancing at high magnetic fields (7 T and above)) in MRI of the human brain. The main advantage of this data set is that it allows to visualize biological structures within gray matter (GM) and white matter (WM) that are not usually available with conventional MRI (e.g., blood deoxyhemoglobin, tissue lipid, and non-heme iron content.) [4]

Preliminary brain, ventricle, and pathology segmentations are provided based on the T1 images for both patients at both acute and chronic time points. The relevant files are:

• [Acute/Chronic]_T1_brain.nii: Skull-stripped version of T1 image.
• [Acute/Chronic]_T1_labels(2).mha: Label maps for pathology regions and ventricles.
• [Acute/Chronic]_T1_lesion.vtk: 3D mesh model of pathology segmentation.
• [Acute/Chronic]_T1_ventricles.vtk: 3D mesh model of ventricle segmentation.

Susceptibility-weighted imaging (SWI) and DTI data sets are not available at the moment.

Detailed information about each data sets are provided in the table belows:

Data Set for Patient A

Acute/Chronic Time Point	Flair	GRE	T1	T2
Resolution	384x512x50	384x512x50	256x256x176	320x320x 50
Spacing	0.46875x0.46875x3.00000	0.46875x0.46875x3.00000	1x1x1	0.75x0.75x3.0
Origin	90, -105.12446594, -70.34745789	90, -105.12446594, -70.34745789	128, -102.42373657, -75.87287903	120, -104.84321594, -70.34745789

Data Set for Patient B

Acute Time Point	Flair	GRE	T1	T2
Resolution	384x512x53	384x512x53	256x256x176	260x320x53
Spacing	0.46875x0.46875x3.00000	0.46875x0.46875x3.00000	1x1x1	0.75x0.75x3.0
Origin	84.55205536, -105.60873413, -70.13075256	84.55205536, -105.60873413, -70.13075256	128, -106.418884, -85.684021	92.05205536, -105.32748413, -70.13075256

Data Set for Patient B

Chronic Time Point	Flair	GRE	T1	T2
Resolution	384x512x50	384x512x50	256x256x176	512x512x50
Spacing	0.46875x0.46875x3.0000033	0.46875x0.46875x3.0000033	1x1x1	0.4687500x0.4687500x3.0000033
Origin	96.05750275, -80.31092072, -43.31170654	96.05750275, -80.31092072, -43.31170654	133.73010254, -72.58300781, -70.52586365	126.04978180, -80.41034698, -43.98503113

Terms of Use

This database is provided without charge for use in research, teaching, and commercial developments that advance the medical field. Uses outside of the medical field require prior written approval from Kitware. These data may not be redistributed except when a few cases are distributed as part of an electronic publication in which the author of the publication has added significant value to the publication, beyond the value of the cases being redistributed. In all other situations, citations and links to this webpage should be used.

We request that any publication or project that uses this data do the following:

a) Cite the following paper XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

b) Include the following text (or something similar) in your acknowledgements XXXXXXXXXXXXXXXXXX