Difference between revisions of "Projects/Diffusion/2007 Project Week Contrasting Tractography Measures/ROI Definitions"
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====IC - Internal Capsule==== | ====IC - Internal Capsule==== | ||
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| + | ====Fornix==== | ||
| + | ROI 1) on Coronal view, the first slice where the middle cerebellar peduncles are present | ||
| + | <p>ROI 2) posterior to ROI 1; large blobs drawn on coronal view where the middle cerebellar peduncle is clearly connected at bottom of slice</p> | ||
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| + | ::7= ROI 1 for both Left and Right | ||
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| + | ::11 or 13 = Left ROI 2 | ||
| + | ::12 or 14 = Right ROI 2 | ||
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| + | [[Image:Fornix1ROIs.png|left|thumb|300px|Fornix ROI 1 (both left and right)]] [[Image:Fornix2ROIs.png|left|thumb|300px|Fornix ROI 2 (right)]] | ||
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===Arcuate Fasciculus=== | ===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. | 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. | ||
Revision as of 20:12, 26 July 2007
Home < Projects < Diffusion < 2007 Project Week Contrasting Tractography Measures < ROI DefinitionsContents
Boundaries for the ROI's, mainly using FA maps & color by orientation, followed by the color coding of the labelmaps.
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IC - Internal CapsuleROI 1) find anterior commisure on axial view and draw ROI on coronal slice on each side on midsag line 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.
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unc - Uncinate FasciculusFind 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.
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FornixROI 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
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Arcuate FasciculusThese 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.
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Cingulum BundleROI 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.
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