Difference between revisions of "DTI Tractography Challenge Datasets"

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T1 SPGR: TR=7500 ms; TE=30 ms; matrix 256x256; FOV 25.6 cm ; 1-mm slice thickness <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>
 
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; 55 gradient directions, 1 baseline ; b-value = 1000 s/mm2 ; matrix 128x128; 2.6 mm slice thickness <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.  
 
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==
 
== 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 the T1 and T2 images of the same two subjects.
+
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.  
  
−
Here are the details of the DTI acquisition parameters:
+
Details of the DWI acquisition parameters:
−
* 25 directions + 1 B0
+
* 25 gradient directions + 1 baseline
−
* Variable b-value (range between 50 and 1000) - Each diffusion weighted image has a different b value.
+
* Variable b-value (range between 40 and 1000): each diffusion weighted image has a different b value.
 
* Spacial resolution of 1.97x1.97x2mm
 
* Spacial resolution of 1.97x1.97x2mm
 
* Image size 96x96x81
 
* 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'''==
 
=='''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
 
  
 +
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 (voxelized binary image of the tracts): 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, 4) a set of intuitive neurosurgical views 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 <br>
 +
patient1_right_tract.vtk <br>
 +
patient1_left_enveloppe.nhdr <br>
 +
patient1_left_enveloppe.raw <br>
 +
patient1_right_enveloppe.nhdr <br>
 +
patient1_right_enveloppe.raw <br>
 +
...<br>
 +
patient1_left_tract_axial_view.png <br>
 +
patient1_left_tract_coronal_view.png <br>
 +
patient1_left_tract_sagittal_view.png <br>
 +
patient1_right_tract_axial_view.png <br>
 +
patient1_right_tract_coronal_view.png <br>
 +
patient1_right_tract_sagittal_view.png <br>
 +
...<br>
 +
patient1_left_and_right_tract_axial_view.png <br>
 +
patient1_left_and_right_tract_coronal_view.png <br>
 +
patient1_left_and_right_tract_sagittal_view.png <br>
 +
 +
patient1_neurosurgicalview1.png<br>
 +
...<br>
 +
patient1_neurosurgicalviewN.png<br>
 +
 +
*Healthy subject1
 +
healthysubject1_scan01_left_tract.vtk <br>
 +
healthysubject1_scan01_right_tract.vtk<br>
 +
...<br>
 +
healthysubject1_scan10_left_tract.vtk <br>
 +
healthysubject1_scan10_right_tract.vtk<br>
 +
healthysubject1_scan01_left_enveloppe.nhdr <br>
 +
healthysubject1_scan01_left_enveloppe.raw <br>
 +
...<br>
 +
healthysubject1_scan10_left_enveloppe.nhdr<br>
 +
healthysubject1_scan10_left_enveloppe.raw <br>
 +
healthysubject1_scan01_right_enveloppe.nhdr <br>
 +
healthysubject1_scan01_right_enveloppe.raw <br>
 +
...<br>
 +
healthysubject1_scan01_right_enveloppe.nhdr <br>
 +
healthysubject1_scan01_right_enveloppe.raw <br>
 +
...<br>
 +
healthysubject1_scan01_left_tract_axial_view.png <br>
 +
healthysubject1_scan01_right_tract_coronal_view.png <br>
 +
patient1_left_tract_sagittal_view.png <br>
 +
patient1_right_tract_axial_view.png <br>
 +
patient1_right_tract_coronal_view.png <br>
 +
patient1_right_tract_sagittal_view.png <br>
 +
...<br>
 +
patient1_left_and_right_tract_axial_view.png <br>
 +
patient1_left_and_right_tract_coronal_view.png <br>
 +
patient1_left_and_right_tract_sagittal_view.png <br>
  
  
  
 
Back to [[Events:_DTI_Tractography_Challenge_MICCAI_2011 | DTI Tractography Challenge MICCAI 2011]]
 
Back to [[Events:_DTI_Tractography_Challenge_MICCAI_2011 | DTI Tractography Challenge MICCAI 2011]]

Latest revision as of 20:42, 9 June 2011

Home < 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 (voxelized binary image of the tracts): 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, 4) a set of intuitive neurosurgical views 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

patient1_neurosurgicalview1.png
...
patient1_neurosurgicalviewN.png

  • Healthy subject1

healthysubject1_scan01_left_tract.vtk
healthysubject1_scan01_right_tract.vtk
...
healthysubject1_scan10_left_tract.vtk
healthysubject1_scan10_right_tract.vtk
healthysubject1_scan01_left_enveloppe.nhdr
healthysubject1_scan01_left_enveloppe.raw
...
healthysubject1_scan10_left_enveloppe.nhdr
healthysubject1_scan10_left_enveloppe.raw
healthysubject1_scan01_right_enveloppe.nhdr
healthysubject1_scan01_right_enveloppe.raw
...
healthysubject1_scan01_right_enveloppe.nhdr
healthysubject1_scan01_right_enveloppe.raw
...
healthysubject1_scan01_left_tract_axial_view.png
healthysubject1_scan01_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


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