Brockton MRI Scan Parameters
Scanner:
1.5 Tesla GE Echospeed system (General Electric Medical Systems, Milwaukee, WI).
Raw Data:
- Coronal series of contiguous spoiled gradient (SPGR) images (124 slices of 1.5 mm thickness, voxel dimensions 0.9375 x 0.9375 x 1.5 mm). The corresponding files on the BIRN site are:
- HUVA########_spgr.nhdr (ASCII header)
- HUVA########_spgr.img (binary file: 256x256x124 big endian shorts)
- Axial series of contiguous double-echo images (Proton Density and T2 Weighted, 108 slices of 3 mm slice thickness, voxel dimensions 0.9375 x 0.9375 x 3 mm). We split the input into two volumes:
- HUVA########_t2w.nhdr (ASCII header)
- HUVA########_t2w.img (binary file: 256x256x552 big endian shorts)
- HUVA########_pd.nhdr (ASCII header)
- HUVA########_pd.img (binary file: 256x256x552 big endian shorts)
In theory, and most of the time in practice the t2w and pd volumes are perfectly aligned with each other. This is not the case with the SPGR image.
Label Maps:
Two types of label maps are drawn some on the raw spgr scan, some on a realigned resampled version of the spgr scan. The realignment process consists of setting the midsagittal plane of the brain in a vertical position and the Anterior Commissure (AC) - Posterior Commissure (PC) line to be horizontal. The spgr volume is transformed and resampled into a .9375x.9375x.9375 isotropic volume.
- ROIs drawn on original SPGR:
- HUVA########_STG (256x256x124 big endian shorts)
- HUVA########_caudate (256x256x124 big endian shorts)
- Realigned/Resampled SPGR:
- HUVA########_realigned (256x256xS big endian shorts, S varies from case to case, check header)
- ROIs drawn on Realigned/Resampled data:
- HUVA########_MTG_ITG (256x256xS big endian shorts, S varies from case to case, check header)
- HUVA########_TP_insula (256x256xS big endian shorts, S varies from case to case, check header)
'The exact labels and structures present in each of these files can be found in [Morph-ROI-description.xls] '
Here is a ppt presentation about nrrd and its integration with ITK/slicer Nrrd-namic2.ppt.
