DTI Tractography Challenge Datasets
Neurosurgical Datasets
Neurosurgical Case 1
- Clinical Case: Astrocytoma, World Health Organization (WHO) grade III
- Acquistion Parameters
Data were acquired on a 3.0-T scanner (EXCITE Signa scanner,
GE Medical System, Milwaukee, Wisconsin) with Excite 14.0 using an
8-channel head coil.
T1 SPGR: TR=7500 ms; TE=30 ms; matrix 256x256; FOV 25.6 cm ; 1-mm slice thickness
T2 GRE: TR=8000 ms; TE=98 ms; matrix 512x512; voxel size 0.5 x 0.5 x 1.5 mm
DWI Singe shot EPI: TR=14 000ms; TE=30 ms; 31 gradient directions, 1 baseline ; b-value = 1000 s/mm2 ; matrix 128x128; 2.6 mm slice thickness
Segmentation: The file patient1-tumor.nhdr & raw is labelmap which contains the segmented structures: label #1 represents the solid part of the tumor; label #2 represents the cystic part of the tumor.
Neurosurgical Case 2
- Clinical Case: Oligoastrocytoma,WHO grade II
- Acquistion Parameters
Data were acquired on a 3.0-T scanner (EXCITE Signa scanner,
GE Medical System, Milwaukee, Wisconsin) with Excite 14.0 using an
8-channel head coil.
T1 SPGR: TR=7500 ms; TE=30 ms; matrix 256x256; FOV 25.6 cm ; 1-mm slice thickness
T2 GRE: TR=8000 ms; TE=98 ms; matrix 512x512; voxel size 0.5 x 0.5 x 1.5 mm
DWI Single shot EPI: TR=14 000ms; TE=30 ms; 55 gradient directions, 1 baseline ; b-value = 1000 s/mm2 ; matrix 128x128; 2.6 mm slice thickness
Segmentation: The file patient2-tumor.nhdr & raw is labelmap which contains the segmented structures: label #1 represents the solid part of the tumor; label #2 represents the cystic part of the tumor.
Neurosurgical Case 3
- Clinical Case: Pending
- Acquisition Parameters:
- T1 Axial SPGR: matrix 256x256; voxel size 1 x 1 x 1.4 mm, volume size 256 x 256 x130
- T2 matrix 512x512; voxel size 0.5 x 0.5 x 1.5 mm, volume size 512 x 512 x 100
- DWI matrix 256 x256; voxel size 1 x 1 x 2.6 mm, 31 gradient directions, 1 baseline , b-value = 1000 s/mm2; volume size 256 x 256 x 32 x 52
Neurosurgical Case 4
- Clinical Case: Pending
- Acquisition Parameters:
- T1 Axial SPGR: matrix 256x256; voxel size 1 x 1 x 1.4 mm, volume size 256 x 256 x130
- T2 matrix 512x512; voxel size 0.5 x 0.5 x 1.5 mm, volume size 512 x 512 x 100
- DWI matrix 256 x256; voxel size 1 x 1 x 2.6 mm, 31 gradient directions, 1 baseline , b-value = 1000 s/mm2; volume size 256 x 256 x 32 x 52
Control subjects Datasets
Two adult control subject datasets will be available for this challenge. For each subject we have 10 repetitions of the structural and diffusion-weighted acquisitions. All scans were acquired on the same type of scanner (Siemens Tim Trio) at 5 different institutions.
Details of the DWI acquisition parameters:
- 25 gradient directions + 1 baseline
- Variable b-value (range between 40 and 1000): each diffusion weighted image has a different b value.
- Spacial resolution of 1.97x1.97x2mm
- Image size 96x96x81
Details of DTI estimation:
- Tensor estimation using weighted least square algorithm
Details of the structural acquisition. We provide two sets of images:
- Original T1 and T2 (size: 160x224x256, spacing: 1x1x1mm)
- T1 and T2 registered and resampled to baseline (size: 96x96x81, spacing: 1.97x1.97x2mm) (Affine + BSpline)
File format and naming convention for submission
The results should be sent in a zip archive or tarball file named 'miccai2011DTIChallenge_firstAuthorName.zip'. For each case, the results should be submitted in the following formats: 1) 3D coordinate of the tracts: vtkPolydata ASCII VTK file format; 2) enveloppe of the tracts (binary image, with label = 1 if the voxel contains a tract, and label = 0 if the voxel contains no tract: ITK-readable Nrrd file format 3) anatomical views (axial, coronal, sagittal) of individual and paired corticospinal tracts with a black background, in png file format. All results (Nrrd and vtk files) should be in the original DWI image space.
An example of the naming convention to be used for Patient1 and HealthySubject1 is given below:
- Patient1:
patient1_left_tract.vtk
patient1_right_tract.vtk
patient1_left_enveloppe.nhdr
patient1_left_enveloppe.raw
patient1_right_enveloppe.nhdr
patient1_right_enveloppe.raw
patient1_left_tract_axial_view.png
patient1_left_tract_coronal_view.png
patient1_left_tract_sagittal_view.png
patient1_right_tract_axial_view.png
patient1_right_tract_coronal_view.png
patient1_right_tract_sagittal_view.png
patient1_left_and_right_tract_axial_view.png
patient1_left_and_right_tract_coronal_view.png
patient1_left_and_right_tract_sagittal_view.png
- Healthy subject1
healthysubject1_scan1_left_tract.vtk
healthysubject1_scan1_right_tract.vtk
...
healthysubject1_scan10_left_tract.vtk
healthysubject1_scan10_right_tract.vtk
healthysubject1_scan1_left_enveloppe.nhdr
healthysubject1_scan1_left_enveloppe.raw
...
healthysubject1_scan10_left_enveloppe.nhdr
healthysubject1_scan10_left_enveloppe.raw
healthysubject1_scan1_right_enveloppe.nhdr
healthysubject1_scan1_right_enveloppe.raw
...
healthysubject1_scan1_right_enveloppe.nhdr
healthysubject1_scan1_right_enveloppe.raw
healthysubject1_scan1_left_tract_axial_view.png
healthysubject1_scan1_right_tract_coronal_view.png
patient1_left_tract_sagittal_view.png
patient1_right_tract_axial_view.png
patient1_right_tract_coronal_view.png
patient1_right_tract_sagittal_view.png
patient1_left_and_right_tract_axial_view.png
patient1_left_and_right_tract_coronal_view.png
patient1_left_and_right_tract_sagittal_view.png
