Longitudinal Skull Strip

A Product of the IDeA Lab

Mario Ortega

The Olden Days…• We have received over 3800 scans form the Framingham Project.• All of these scans have been traced by trained analysts with a ICC’s (Intra-

class Correlation Coefficient) of 0.95, from 2000 to present.• The process of Hand-Tracing takes roughly 30 minutes to simply acquire a

Filtered Total Cranial Volume (No RoI’s).• Recently, a different approach was studied to reduce man-hours, and

increase tracing accuracy, this approach we called Longitudinal Skull-Strip.• LGS is comprised of several components that allow it to work more

accurately and efficiently than a complete hand-traced image.• The general idea is to use an existing hand-traced TCV, and use it to

“cookie-cut” the later images.• The Steps are 1. Loading images, 2. Slicealign 3. LincoregL3 (Linear

Coregistration) 4. SVCleanup …all on one easy interface.

Longitudinal Skull Strip Process Steps

1. Loading images

2. Slicealign

3. LincoregL3 (Linear Coregistration)

4. SVCleanup …all in one easy to use interface.

Longitudinal Skull Strip Interface

User Friendly interfaceFast and easy to use, only Step 5 requires user visualization and minor cleanup of images.

SliceAlignment

• The DSE scan is a subtraction of the T2 (time2 relaxation) from the PD image (proton density).

• The problems this causes is excessive ghosting of the image if the patient moves between acquisitions. When the images are placed together, this causes a “wiggle” effect.

• The sliceAlign tool is used to remove this “wiggle” from pseudo-T1 images made from the PD-T2 difference.

• Framingham acquires DSE scans in the coronal plane, this would cause excessive translational movement in the X and Y direction, as well as some rotation if the individual tilts their head about the occipital bone.

Slice Alignment

The effects of Slice Align can best be seen in the axial and sagittal plane.On the far left is the image before slicealign was implemented, the right image has been corrected.The result is that the DSE_COR image was fixed for excessive movement in the X and Y direction. This process is implemented on all images through Longitudinal Skull Strip.

Linear Alignment• Linear Alignment aligns a pair of images together using up to 12 parameters. These

are rotations, translations, scaling, and shears.• For this longitudinal project however, we will not be using scaling and shear

adjustments, because the individuals skull does not change over time.

Image Pre-Alignment

•These are unaligned, notice that the images do not lie in the same space. I have drawn

three lines at the edge of the skull, to show how the acquisitions differ.

•LinCoreg will align the year 2000 scan individually to the 3 other dates.

Year 2000

Year 2002 Year 2004 Year 2005

Linear Alignment results

• Every Pair of images is an aligned Time1 (year 2000), to the respective second year.• Once the images are aligned, we use the alignment parameters to create a “cookie cutter” to cut out the brain of the second paired image.• Brain Matter changes over time, but the total area in the cranial vault is constant, so the TCV’s should be near identical.

SVCLEANUP and FILTER

When the Time1 TCV is stamped onto the TimeX (any future scan), there is usually a small amount of correction required on a few slices of the image. (shown at right)• Is all of this work worth it?• Time to trace 3 images is cut down by half.• Accuracy?

Results

Longitudinal Skull Strip ID# 0-1183

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HAND TRACE

AUTO TRACE (no correction)

AUTO TRACE (with sliceAligncorrection)

• 4 Longitudinal Scans, first analyzed by different analysts from 2000 to 2006. Below are the Segmented Brain Matter volumes.• Notice the smooth decline of the Auto trace with the “wiggle” slice align correction.• The most linear slope accurately depicts the loss of brain matter over time.In this case, LGStrip reduced the error of the different individuals who originally traced these images.

LGStrip versus Hand Tracing

• Above is a graph showing the Total Cranial Volume, Segmented Brain Matter Volume, and CSF Volume.• In red are the numbers generated through LGstrip, by analyst MP, in black is the entirely manual traced version. • The Linearity of the red TCV line suggests there was very little variability of volumes. • The TCV volumes created through LGStrip only varied by 7 cc’s! (2002-2005)

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Hand Traced TCV

Hand Segmented Brain

Hand Segmented CSF

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AutoSegment Maria

AutoSegCSFMaria

These are the TCV volumes

These are segmented Brain volumes

These are the CSF volumes

The volumes acquired through hand-tracingAre in BLACK, The volumes acquired through LGStrip are in Red.

LGStrip versus Hand (ex.2)

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Hand Traced TCV

Hand SegmentedBrain

Hand Segmented CSF

AutoTCV Lauren

AutoSegBrain Lauren

AutoSegCSF Lauren

Here is another example of a series dataset run through Longitudinal Skull Strip. The smooth linear appearance of the green curve has an accurate fit, this individual is possibly a normal individual, reflecting the stable brain volume shown. Manual tracing was longitudinally inconsistent as shown by the constant rise and fall of the blue TCV and CSF lines.

These are the TCV volumes

These are segmented Brain volumes

These are the CSF volumes

The volumes acquired through hand-tracingAre in blue-dashed, The volumes acquired through LGStrip are in Green.

Summary

•As seen through the graphs, the Longitudinal Skull Strip Process, is reducing the human error over time.• It also cuts down on hand-tracing time.• It is not limited to doing the same subject over 4 years… It can load up 5+ different patient DSE scans, and do them as pairs.• LGStrip only works for longitudinal sets of images, and requires one accurate preliminary scan to use as a template.• LGStrip will be implemented into the framingham analysis protocol in the next weeks.• Work is in progress to also transport ROI’s across serial scans…