Projects/Diffusion/2007 Project Week Contrasting Tractography Measures/ROI Definitions

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Boundaries for the ROI's, mainly using FA maps & color by orientation, followed by the color coding of the labelmaps.

This page describes the definition of the regions of interest for five fiber bundles: the Internal Capsule, the Uncinate Fasciculus, the Fornix, the Arcuate Fasciculus and the Cingulum Bundle. Seed points were defined using a two ROIs approach. Each ROI was drawn on FA and color by orientation maps according to the criteria defined below:

IC - Internal Capsule

ROI 1) We found the anterior commisure in the axial view (Fig.1) and drew ROI on coronal slice on each side on midsag line

Figure1. Axial View of the Anterior Commisure, which serves as the bottom boundary of ROI 1

Figure 2. Coronal View of ROI 1 (left and right), showing the inferior boundary (in purple)

Color Palette

Top boundary for ROI 1: Caudate/putamen line

Bottom boundary for ROI 1: draw entire plane of AC (Fig.1); IC is only superior to AC line.

ROI 2) go to the anterior most point of the corpus collosum according to sagittal view (Fig 3). Draw ROI so it covers entire (left or right) hemisphere of brain on the perpendicular Coronal Slice (Fig 4).

Figure 3.Internal Capsule ROI's 1 and 2 (left)

Figure 4.Coronal View of ROI 2 (left and right)

The color coding of the resulting ROIs is as follows:

ROI 1: Left(7) - Right(8)

ROI 2: Left(11) - Right(12)

Inferior Boundary = color 15... do not track from this.

unc - Uncinate Fasciculus

Find the most prominant (central) slice of the fornix according to sagittal view (Fig. 5). Go one slice anterior to the most anterior point of the fornix and draw Left and Right ROI 1 and ROI 2 (Fig. 6).

The color coding of the resulting ROIs is as follows:

ROI 1: Left(7) - Right(8)

ROI 2: Left(11) - Right(12)

Figure 5. Sagittal view of the fornix, located centrally in the brain

Figure 6. Coronal View of ROI 1 and ROI 2, (left and right)

Figure 7.Uncinate Fasciculus ROI's 1 and 2 (left)

Fornix

ROI 1) on Coronal view, the first (most anterior) slice where the middle cerebellar peduncles are present (Fig. 8 & 10)

ROI 2) posterior to ROI 1; large blobs drawn on coronal view where the middle cerebellar peduncle is clearly connected at bottom of slice (Fig. 9 & 11)

The color coding of the resulting ROIs is as follows:

ROI 1: Left & Right (7)

ROI 2: Left(11 or 13) - Right(12 or 14)

Figure 8. Coronal View of ROI 1

Figure 9. Coronal View of ROI 2 (left=11, right=13)

Figure 10. Sagittal View of Fornix, ROI 1 (both left and right)

Figure 11. Sagittal View of Fornix, ROI 2 (right)

Arcuate Fasciculus

These labelmaps ('caseD00XXX-FS-arcuate-final.nhdr') were created using automatic gray matter parcellation in Freesurfer and coregistered in Slicer to corresponding DTI dataset. The labelmaps were dilated in Slicer to increase coverage of gray matter.

The color coding of the resulting ROIs is as follows:

ROI 1: Superior Temporal Gyrus - Left(5) - Right(6)

ROI 2:Inferior Frontal Gyrus- Left(13) - Right (14)

Figure 12. Gray matter ROI's for Arcuate Fasciculus tractography

Figure 13. Gray matter ROIs (right side) in 3D

Figure 14. Arcuate tractography

Cingulum Bundle

ROI 1) on the superior side of the corpus, flush with the most anterior part of the corpus (based on sag view, but drawn on coronal view) (Fig. 15 & 18)

ROI 2) on the first coronal slice where the L & R corpus connect, on the superior side of the corpus. (Fig. 16 & 18)

ROI 3) on the first coronal slice where the L & R corpus connect, on the inferior side of the corpus. (Fig. 16 & 18)

ROI 4) on the first coronal slice where the middle cerebellar peduncle is present.(Fig. 17 & 19)

The color coding of the resulting ROIs is as follows:

ROI 1: Left(7) - Right(8)

ROI 2: Left(9) - Right(16)

ROI 3: Left(11) - Right(12)

ROI 4: Left(13) - Right(14)