NAMIC: Brain Mutlimodality (Size: 6Gb Downloads: 435)
> In community MIDAS/National Alliance for Medical Image Computing (NAMIC)
There are 20 cases; ten are Normal Controls and ten are Schizophrenic.
In each case folder, there are 10 files, described here:
  • 01###-t1w.nrrd is the weighted T1 scan.
  • 01###-t2w.nrrd is the weighted T2 scan.
  • 01###-t2w_mask.nrrd is a labelmap of the ICC based on the T2.
  • 000008.SER-anon.tgz is the fMRI scan (zipped tar ball) - - Note: there in no fMRI scan for case01073
  • 01###-dwi.nhdr (references 01###-dwi.raw.gz) is the raw DTI scan.
  • 01###-dwi-filt-Ed.nhdr (references 01###-dwi-filt-Ed.raw.gz) is the dwi scan after noise filtering and eddy current and head motion correction.
  • brainmask.mgz is a T1 grayscale image that has the skull & dura-matter stripped.
  • aparc+aseg.mgz is a freesurfer segmentation of the t1w image.
Data Description:
  • Structural MRI (sMRI) For the Structural MRI volume measurements, images will be acquired using a 3T GE) at BWH in Boston, MA. We will use an 8 Channel coil in order to perform parallel imaging using ASSET (Array Spatial Sensitivity Encoding techniques, GE) with a SENSE-factor (speed-up) of 2. The structural MRI acquisition protocol will include two MRI pulse sequences. The first results in contiguous spoiled gradient-recalled acquisition (fastSPGR) with the following parameters; TR=7.4ms, TE=3ms, TI=600, 10 degree flip angle, 25.6cm^2 field of view, matrix=256x256. The voxel dimensions are 1x1x1 mm. The second- XETA (eXtended Echo Train Acquisition) produces a series of contiguous T2-weighted images (TR=2500ms, TE=80ms, 25.6 cm^2 field of view, 1 mm slice thickness). Voxel dimensions are 1x1x1 mm.
  • Diffusion Tensor Imaging (DTI) DTI scans will be acquired on a 3 Tesla GE system using an echo planar imaging (EPI) DTI Tensor sequence. We will use a double echo option to reduce eddy-current related distortions (Heid 2000; Alexander 1997). To reduce impact of EPI spatial distortion, we will use an 8 Channel coil that will allow us to perform parallel imaging using ASSET (Array Spatial Sensitivity Encoding Techniques, GE) with a SENSE-factor (speed-up) of 2. We will acquire 51 directions with b=*9*00, 8 baseline scans with b=0. The following scan parameters will be used: TR 17000 ms, TE 78 ms, FOV 24 cm, 144x144 encoding steps, 1.7 mm slice thickness. We will acquire 85 axial slices parallel to the AC-PC line covering the whole brain. In addition, Bo field inhomogeneity maps will be collected.
  • Resting State fMRI This sequence is an additional EPI BOLD sequence that requires Brain Wave software, available only with 8 Channel coil. It's a resting state fMRI that was 10 minutes long, and contains 200 repetitions of a high resolution EPI scan (96x96 in plane, 3mm thickness, TR-3000 ms, TE=30, 39 slices, ASSETT). Subjects closed their eyes and rested while the magnet is running.

 
 
Please use this identifier to cite or link to this collection: http://hdl.handle.net/1926/1687

21 items within this collection

  • last update on 2010-02-09 13:42:38 (99 KB in 1 files)
  • Administrative Information
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  • last update on 2011-02-22 11:50:10 (357.1 MB in 13 files)
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case01011
01011-FA.nrrd
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case01011
01011-freesurferseg-def.nrrd
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case01011
01011-t2w-mask.nrrd
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case01011
01011-WM.nrrd
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  • filt
  • last update on 2010-02-09 12:00:12 (377.6 MB in 15 files)
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case01015
01015-dwi-filt-Ed.nhdr
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case01015
01015-dwi.nhdr
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case01015
01015-freesurferseg-def.nrrd
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case01015
01015-WM.nrrd
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case01015
01015-FA.nrrd
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  • last update on 2010-02-09 12:01:29 (215.7 MB in 13 files)
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case01017
01017-t2w-mask.nrrd
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case01017
01017-freesurferseg-def.nrrd
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case01017
01017-WM.nrrd
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case01017
01017-FA.nrrd
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  • filt
  • last update on 2010-02-09 12:03:06 (386.9 MB in 14 files)
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case01018
01018-dwi-filt-Ed.nhdr
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case01018
01018-freesurferseg-def.nrrd
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case01018
01018-dwi.nhdr
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case01018
01018-dti-filt-Ed.nrrd
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case01018
01018-FA.nrrd
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  • filt
  • last update on 2010-02-09 12:04:43 (375.3 MB in 16 files)
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case01019
01019-dwi.nhdr
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case01019
01019-dti-filt-Ed.nrrd
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case01019
01019-dwi-filt-Ed.nhdr
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case01019
01019-WM-modified.nrrd
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case01019
01019-WM-dilated.nrrd
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  • filt
  • last update on 2010-02-09 12:06:12 (386.1 MB in 14 files)
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case01020
01020-dti-filt-Ed.nrrd
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case01020
01020-WM.nrrd
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case01020
01020-dwi-filt-Ed.nhdr
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case01020
01020-freesurferseg-def.nrrd
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case01020
01020-FA.nrrd
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  • filt
  • last update on 2010-02-09 12:07:40 (375.5 MB in 15 files)
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case01025
01025-dti-filt-Ed.nrrd
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case01025
01025-WM-dilated.nrrd
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case01025
01025-t2w-mask.nrrd
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case01025
01025-WM.nrrd
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case01025
01025-freesurferseg-def.nrrd
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  • filt
  • last update on 2010-02-09 12:09:08 (374.5 MB in 13 files)
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case01026
01026-freesurferseg-def.nrrd
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case01026
01026-dti-filt-Ed.nrrd
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case01026
01026-dwi.nhdr
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case01026
01026-t2w-mask.nrrd
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case01026
01026-FA.nrrd
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  • filt
  • last update on 2010-02-09 12:10:24 (373.7 MB in 15 files)
  • Download this study: All the data
case01028
01028-dwi-filt-Ed.nhdr
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case01028
01028-WM-dilated.nrrd
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case01028
01028-freesurferseg-def.nrrd
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case01028
01028-dti-filt-Ed.nrrd
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case01028
01028-FA.nrrd
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If you have any questions about the data, please contact Sylvain Bouix (sylvain@bwh.harvard.edu) or Doug Terry (dougt@bwh.harvard.edu) at Harvard.

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