mpragepre – image quality

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