October 07 2009 Meeting: VT-NAMIC Data review summary

We made the following observations about the data at the first time point:

• In some sobjects the FOV is axis-aligned, while in others it is tilted. These directions were not preserved in the NIFTI data we were previously using.
• We have two SPGR scans of for each subject, but the scans are not perfectly aligned. Ron: possibly due to coil heating. We cannot right away use these images to average and get better SNR, need to check with imaging people. Not sure if discrepancy is the rigid one.
• Noticeable bias field in the atlas is observed by Ron.

Other observations with illustrations:

The issue with noise in Tommy and Louis resolved: we do not know how the NIFTI images we used before for Tommy and Louis were obtained -- the DICOM data has much better noise characteristics

Tommy, DICOM Louis, DICOM

Angio sequence (right name?) has apparently been used for some (7 out of 10) subjects

Calvin axial showing vessel and volume rendering of vasculature

Strange artifact is observed in the occipital lobe for all subjects. Ron, Sandy, Sota Oguro (SPL radiologist) cannot explain the origin. See Calvin example (note the interpolation is turned off) Ron: This is fat shift artifact, bone marrow creates the shadow effect. Was fat suppression included in the sequence?

Calvin occipital lobe Calvin Calvin

Significant mis-alignment of some subjects with the template subject after FLIRT registration for some subjects is confirmed

Ralph/atlas post-FLIRT checkerboard Mark/atlas post-FLIRT overlay

Ringing artifacts for some (few) subjects

Calvin ringing artifact

Valentino has structure not consistent with the normal anatomy Ron: this is likely a cyst.

Valentino unknown structure, Fast marching segmentation ' ' Valentino unknown structure, surface model

Zero filling artifact

Calvin time point 2

Susceptibility artifacts

Calvin time point 1 Gucci time point 1