View source for 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.<br>
T1 SPGR: TR=7500 ms; TE=30 ms; matrix 256x256; FOV 25.6 cm ; 1-mm slice thickness <br>
T2 GRE: TR=8000 ms; TE=98 ms; matrix 512x512; voxel size 0.5 x 0.5 x 1.5 mm <br>
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 <br>
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.<br>
T1 SPGR: TR=7500 ms; TE=30 ms; matrix 256x256; FOV 25.6 cm ; 1-mm slice thickness <br>
T2 GRE: TR=8000 ms; TE=98 ms; matrix 512x512; voxel size 0.5 x 0.5 x 1.5 mm <br>
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 <br>
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 both subjects we have 10 repetitions of the DTI acquisitions. All scans were done on the same type of scanner (Siemens Tim Trio) at 5 different institutions. We also provide structural images (T1 and T2) of the same two subjects.

Here are the details of the DWI acquisition parameters:
* 25 gradient directions + 1 baseline
* Gradient directions were obtained using the b-matrix field of the dicom header
* Variable b-value (range between 50 and 1000) - Each diffusion weighted image has a different b value.
* Spacial resolution of 1.97x1.97x2mm
* Image size 96x96x81

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'''==
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: ITK-readable Nrrd file format
<br>Naming convention: 
* zip archive file: miccaiDTIChallenge_firstAuthorName.zip
* VTK file: firstAuthorName_tract_coordinate.vtk
* Nrrd file: firstAuthorName_tract_enveloppe.nhdr and  firstAuthorName_tract_enveloppe.nhdr 
* PNG file: firstAuthorName_tract_axialView.png; firstAuthorName_tract_sagittalView.png; firstAuthorName_tract_coronalView.png




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