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

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. IC - Internal Capsule ROI 1) We found the anterior commisure in the axial view and drew ROI on coronal slice on each side on midsag line Axial View of the Anterior Commisure, which serves as the bottom boundary of ROI 1 Coronal View of ROI 1 (left and right), showing the inferior boundary (in purple)

Top boundary for ROI 1: Caudate/putamen line Bottom boundary for ROI 1: draw entire plane of AC; IC is only superior to AC line. ROI 2) go to the anterior most point of the corpus collosum according to saggital view. Draw ROI so it covers entire (left or right) hemisphere of brain on the perpendicular Coronal Slice. Coronal View of ROI 2 (left and right)

7= Left ROI 1 11= Left ROI 2 8= Right ROI 1 12= Right ROI 2 15= Inferior Boundary... do not track from this. Internal Capsule ROI's 1 and 2 (left)

unc - Uncinate Fasciculus Find the most prominant (central) slice of the fornix according to saggital view. Go one slice anterior to the most anterior point of the fornix and draw Left and Right ROI 1 and ROI 2. 7= Left ROI 1 11= Left ROI 2 8= Right ROI 1 12= Right ROI 2 Saggital view of the fornix, located centrally in the brain Coronal View of ROI 1 and ROI 2, (left and right)

Uncinate Fasciculus ROI's 1 and 2 (left)

Fornix ROI 1) on Coronal view, the first slice where the middle cerebellar peduncles are present ROI 2) posterior to ROI 1; large blobs drawn on coronal view where the middle cerebellar peduncle is clearly connected at bottom of slice 7= ROI 1 for both Left and Right 11 or 13 = Left ROI 2 12 or 14 = Right ROI 2 Fornix ROI 1 (both left and right) 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. 5 = Left Superior Temporal Gyrus 13 = Left Inferior Frontal Gyrus 6 = Right Superior Temporal Gyrus 14 = Right Inferior Frontal Gyrus Gray matter ROI's for Arcuate Fasciculus tractography Gray matter ROIs (right side) in 3D 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) ROI 2) on the first coronal slice where the L & R corpus connect, on the superior side of the corpus. ROI 3) on the first coronal slice where the L & R corpus connect, on the inferior side of the corpus. ROI 4) on the first coronal slice where the middle cerebellar peduncle is present. 7= Left ROI 1 9= Left ROI 2 11= Left ROI 3 13= Left ROI 4 8= Right ROI 1 16= Right ROI 2 12= Right ROI 3 14= Right ROI 4 Cingulum Bundle ROI's 1, 2, and 3 Cingulum Bundle ROI 4

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