mpragepre – image quality
DESCRIPTION
MPRAGEpre – Image Quality. Quality is fairly consistent throughout subjects but there are a couple notable outliers: P003 & P025. Lesion Segmentation. Process. Z-score-based (> 4) one-sided thresholding method on FLAIR registered to MNI 1mm 3 > “raw MNI FLAIR z -score masks” - PowerPoint PPT PresentationTRANSCRIPT
MPRAGEpre – Image Quality
• Quality is fairly consistent throughout subjects but there are a couple notable outliers: P003 & P025
Lesion Segmentation
Process
• Z-score-based (> 4) one-sided thresholding method on FLAIR registered to MNI 1mm3
– > “raw MNI FLAIR z-score masks”• Similar to tissue segmentation, this seemed to contain
speckling that was not clearly associated with lesions to me
• Median filtering– > “filtered MNI FLAIR z-score masks”
• Used median filtering with a kernel of (3mm)3 to reduce speckle
• I presented Hagen with the choice of editing either the raw filtered masks
Process
• Manual editing• Hagen decided to go work from the raw MNI FLAIR z-score
masks• He found the median filtering to be overly aggressive and
saw what I had considered as speckling as legitimate lesions• Basic workflow was two passes: remove non-lesion matter
such as misclassified skull, add back and correct any lesion boundaries
• Hagen focused heavily on the first step and after consideration, felt that most of the pre-lesion boundaries were adequate and actually advantageous because they were not generated by subjective human eyes
Post-Process
• Warping back to patient space, SPGR target• Thresholding to recover a binary lesion mask• Further editing?
P015 – Low CIS – MNI
P015 – Low CIS – MNI
P015 – Low CIS – FLAIR Space
P015 – Low CIS – FLAIR Space
P027 – High CIS – MNI
P027 – High CIS – MNI
P027 – High CIS – FLAIR Space
P027 – High CIS – FLAIR Space
P001 – RR – MNI
P001 – RR – MNI
P001 – RR – FLAIR Space
P001 – RR – FLAIR Space
P016 – SP – MNI
P016 – SP – MNI
P016 – SP – FLAIR Space
P016 – SP – FLAIR Space
P021 – PP – MNI
P021 – PP – MNI
P021 – PP – FLAIR Space
P021 – PP – FLAIR Space
Quality of Edits
• Free of any obvious skull defects• Many lesions remain on sulci, suspicious given
limits of standard space registration
Thresholding
• Relapsing case, P001:– Some lesions are very close to 0 in value, hard to tell if
they should be thrown out• Progressive case, P021:– Thresholds of 0.4-0.6 preserve the sometimes smooth
transition into surrounding normal tissue– For conservative lesion boundaries, 0.95 or higher
• After we settle on a value, compute the volume of “lost” voxels as a measure of how significant the reduction was
Remaining Work
• Tissue segmentation correction• Reiss group multi-spectral segmentation as an
alternative to our lesion masks