Article Figures & Data
Figures
- Fig 1.
Atlas-to-patient registration by the outline-based SSM and the hybrid SSM method. First row: alignment of atlas data (image 3) to the subject's gross, visible thalamus outlines through a statistical shape model–based registration (image 1, red outlines: thalamus borders; image 2: 3D visualization). Second row: atlas-to-patient registration by using the hybrid SSM method. Matching is guided by the weighted contribution of the gross visible thalamus borders and the DTI-based intrathalamic markers of connectivities (panel 1: visible outlines and the center-of-mass point of the connectivity map to the postcentral gyrus in panel 2; panel 3: alignment of thalamus outlines and DTI markers). The resulting thalamus maps are given in the rightmost panel. Abbreviations of the connectivity-based landmarks are given according to the cortical target areas used. FP indicates frontal pole; MFG, middle frontal gyrus; SFG, superior frontal gyrus; CDN, caudate nucleus; SMC, supplementary motor cortex; PREC, precentral gyrus; PSC, postcentral gyrus; SPL, superior parietal lobule; CEREB, cerebellum; LOCS, lateral occipital cortex, superior division.
- Fig 2.
Postmortem evaluation of the SSM-based target map prediction method: examples for the delineation of individual visible nuclei. The generation of thalamic nuclei was performed by using visible thalamus outlines as predictors of individual geometry. Left panels: axial sections proton attenuation–weighted MR images (brain specimen 2); right panels: axial sections, T1-weighted ex situ MR images (brain specimen 5). White outlines: manual reference nuclei borders; black outlines: SSM-based prediction of nuclei borders. Top left: anterior ventral nucleus. Top right: medial geniculate nucleus. Bottom left: mediodorsal nucleus, magnocellular part. Bottom right: centromedian nucleus.
Tables
Brain Specimen No. Processed Hemispheres MRI Scanner Sequence Used for Nuclei Depiction TE/TR (ms), Averages Voxel Dimensions (mm), Acquisition Matrix Size Delineated Thalamic Nuclei 1 Left and right Philips Achieva 3T Axial, T2WI, TSE 80/3000, 4 averages 0.21 * 0.21 * 2, matrix: 400 * 394 AV 2 Left and right Philips Achieva 3T Axial, PDWI, TSE 24/3000, 30 averages 0.16 * 0.16 * 1.25, matrix: 528 * 525 AV, MDmc, MDpc + pl, CM, MGN 3 Left Philips Achieva 3T Sagittal, PDWI, TSE 24/3500, 30 averages 0.15 * 0.15 *2, matrix: 532 * 530 AV, CM, MGN, LGN 4 Left and right Philips Achieva 3T Axial, T1WI, IR, TSE 20/2000, TI: 800 ms, 8 averages 0.28 * 0.28 * 0.3, matrix: 784 * 784 AV 5 Left Philips Achieva 7T 3D, PDWI, SE 14/900, 1 scan 0.14 * 0.14 * 0.14, matrix: 768 * 768 AV, CM, MGN Note:—IR indicates inversion recovery; AV, anterior ventral nucleus; MDmc, mediodorsal nucleus magnocellular part; MDpc, mediodorsal nucleus parvocellular part; MDpl, mediodorsal nucleus paralamellar segment; CM, Centre médian nucleus; MGN, medial geniculate nucleus; LGN, lateral geniculate nucleus; PDWI, proton-density weighted imaging.
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↵a Abbreviations of thalamic nuclei are in accordance with the nomenclature used by Morel.7,9
- Table 2:
Evaluation of accuracy of various atlas-to-patient registration methods on postmortem samplesa
Structure No. Outline-Based SSM Registration 12 df Surface Matching ACPC Matching AV 8 0.77 mm D: 0.53 1.05 mm D: 0.41 1.91 mm D: 0.2 MDmc 2 0.93 mm D: 0.46 1.99 mm D: 0.41 0.73 mm D: 0.52 MDpc 2 0.52 mm D: 0.73 0.87 mm D: 0.62 0.92 mm D: 0.53 MGN 4 0.46 mm D: 0.64 1.09 mm D: 0.48 0.75 mm D: 0.57 LGN 1 1.19 mm D: 0.72 0.46 mm D: 0.39 0.91 mm D: 0.44 CM 4 0.41 mm D: 0.78 0.90 mm D: 0.57 0.92 mm D: 0.54 Thalamus outline 8 0.45 mm D: 0.89 0.54 mm D: 0.87 1.49 mm D: 0.71 Note:—D indicates the Dice coefficient of overlaps; AV, anterior ventral nucleus; MDmc, mediodorsal nucleus magnocellular part; MDpc, mediodorsal nucleus parvocellular part; CM, Centre médian nucleus; MGN, medial geniculate nucleus; LGN, lateral geniculate nucleus.
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↵a We were able to perform such validations on a limited number of reference images. Geometric errors are given as median vertex distances measured between the reference standard (manual delineation of MRI data) and the predicted meshes and as the Dice coefficient of overlaps. For predictions, we have applied the outline-based SSM, conventional ACPC matching, and a surface-based 12 df registration method. Abbreviations of thalamic nuclei are in accordance with the nomenclature used by Morel.7,9
- Table 3:
Testing the correspondences between the predicted thalamic nuclei locations and biologically coupled DTI-based thalamocortical connection mapsa
Cortical Connection Area Frontal Pole Superior Frontal Gyrus Precentral Gyrus Postcentral Gyrus Postcentral Gyrus Cerebellum Lateral Occipital Cortex Overall Results Associated nucleus VA VLa VLpv VPLa VPLp VLpv PuL ACPC registration 0.46 ± 0.14 0.31 ± 0.16 0.38 ± 0.2 0.14 ± 0.12 0.3 ± 0.19 0.09 ± 0.09 0.08 ± 0.08 0.25 ± 0.2 Outline-based SSM 0.49 ± 0.12 0.38 ± 0.15 0.41 ± 0.16 0.14 ± 0.12 0.44 ± 0.15 0.14 ± 0.09 0.16 ± 0.1 0.31 ± 0.19 Hybrid SSM 0.5 ± 0.12 0.41 ± 0.15 0.44 ± 0.14 0.17 ± 0.11 0.48 ± 0.13 0.15 ± 0.08 0.13 ± 0.1 0.33 ± 0.2 Difference between outline-based SSM and ACPC registration 6.9%b (P = .021) 22.29%c (P < .001) 7.7% (P = .212) 5.3% (P =.666) 47.7%c (P < .001) 52.8%c (P < .001) 97.2%c (P < .001) 23.3c (P < .001) Difference between hybrid SSM and ACPC registration 9.1%b (P = .011) 31.1%c (P < .001) 15.1%b (P =. 012) 24.6% (P = 056) 59.6%c (P < .001) 58.5c (P < .001001) 54.0%c (P < .001) 28.8%c (P < .001) Difference between hybrid SSM and outline-based SSM registration 2.0% (P = .214) 7.3%b (P = .023) 6.8% (P = .056) 18.3%b (P = 013) 8.0%b(P =. 019) 3.7% (P = .562) −21.9%c (P < .001) 4.5%c (P < .001) Note:—PuL indicates lateral pulvinar.
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↵a Correspondence indices (mean ± SD) are given as the ratio of tractography samples reaching 1 particular cortical area from the voxels of a nucleus and from the entire thalamus volume. Comparisons of alignment methods were tested by using a paired Student t test.
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↵b Result is significant at the .01 < P < .05 level.
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↵c Result is significant at the P < .01 level.
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