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These tools provide feedback via various atlases included in the + href="atlas-descriptions.html">atlases included in the FSL/FSLView distributions. Labels from selected atlases can be displayed, summary images overlaid, structures located and single structure probabilty maps shown.
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+ +Atlases come in two flavours: + +
Tag name | Description | Attributes |
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Tags in header section | ||
name | +A text sting to be displayed in any tools when refering to this atlas. | +|
type | +Probabilistic, Label. | +|
imagefile | +Relative path to the location of the atlas image | +|
summaryimagefile | +Relative path to the location of the atlas summary image | +|
Tags in data section | ||
label | +Text corresponding to this volume's label | +
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+<?xml version="1.0" encoding="ISO-8859-1"?> +<atlas version="1.0"> + <header> + <name>MNI Structural Probability Atlas</name> + <type>Probabalistic</type> + <images> + <imagefile>/MNI/MNI-prob-2mm</imagefile> + <summaryimagefile>/MNI/MNI-maxprob-thr25-2mm</summaryimagefile> + <images> + </header> + <data> + <label index="0" x="39" y="73" z="35">Caudate</label> + <label index="1" x="34" y="32" z="15">Cerebellum</label> + <label index="2" x="45" y="90" z="29">Frontal Lobe</label> + <label index="3" x="27" y="73" z="30">Insula</label> + <label index="4" x="50" y="20" z="37">Occipital Lobe</label> + <label index="5" x="45" y="33" z="61">Parietal Lobe</label> + <label index="6" x="56" y="69" z="34">Putamen</label> + <label index="7" x="16" y="53" z="35">Temporal Lobe</label> + <label index="8" x="48" y="55" z="38">Thalamus</label> + </data> +</atlas> ++ + +
+ Harvard-Oxford cortical and subcortical structural atlases +Probabilistic atlases covering 48 cortical and 21 + subcortical structural areas, derived from structural data + and segmentations kindly provided by + the Harvard + Center for Morphometric Analysis. +T1-weighted images of 21 healthy male and 16 healthy + female subjects (ages 18-50) were individually segmented + by the CMA using semi-automated tools developed + in-house. The T1-weighted images were affine-registered to + MNI152 space using FLIRT (FSL), and the transforms then + applied to the individual labels. Finally, these were + combined across subjects to form population probability + maps for each label. +We are very grateful to the following for providing the + segmentations used to create these atlases: David Kennedy + and Christian + Haselgrove, Centre for + Morphometric Analysis, Harvard; Bruce Fischl, + the Martinos Center + for Biomedical Imaging, MGH (NIH grants + P41-RR14075, R01 RR16594-01A1, R01 NS052585-01); Janis + Breeze and Jean Frazier from + the Child + and Adolescent Neuropsychiatric Research Program, + Cambridge Health Alliance; Larry Seidman and Jill + Goldstein from + the Department of + Psychiatry of Harvard Medical School. + |
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+ Jülich histological (cyto- and myelo-architectonic) atlas + +A probabilistic atlas created by averaging multi-subject + post-mortem cyto- and myelo-architectonic segmentations, + performed by the team of Profs Zilles and Amunts at the Research + Center Jülich and kindly provided by Simon + Eickhoff. + +The atlas contains 32 grey matter structures and 10 white + matter structures. This is the same data as used in + Eickhoff's + Anatomy Toolbox v1.5. The atlas is based on the + miscroscopic and quantitative histological examination of + ten human post-mortem brains. The histological volumes of + these brains were 3D reconstructed and spatially + normalised into the space of the MNI single subject + template to create a probabilistic map of each area. For + the FSL version of this atlas, these probabilistic maps + were then linearly transformed into MNI152 space. + +Main references (to reference individual + structures' maps, please see the publication list at the start + of the Anatomy Toolbox manual):
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+ JHU DTI-based white-matter atlases +There are two white-matter atlases, both kindly provided + by Dr. Susumu + Mori, Laboratory of + Brain Anatomical MRI, Johns Hopkins + University: + +In the ICBM-DTI-81 white-matter labels atlas, 50 white + matter tract labels were created by hand segmentation of a + standard-space average of diffusion MRI tensor maps from + 81 subjects; mean age 39 (18:59), M:42, F: 39. The + diffusion data was kindly provided by the ICBM DTI + workgroup. + +In the JHU white-matter tractography atlas, 20 + structures were identified probabilistically by averaging + the results of running deterministic tractography on 28 + normal subjects (mean age 29, M:17, F:11). + +References: +
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Oxford thalamic connectivity atlas +A probabilistic atlas of 7 sub-thalamic regions, segmented according to their + white-matter connectivity to cortical areas, kindly provided + by Heidi Johansen-Berg and Timothy Behrens, FMRIB. +This connectivity atlas reports probability of anatomical + connection from points in the thalamus to each of 7 cortical + zones. These probabilties are calculated using + probabilistic diffusion tractography in multiple + subjects. For more details see + the Thalamic + Connectivity Atlas web page. +References:
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+ A conversion of the original Talairach structural + labellings, kindly provided by Jack Lancaster and Diana + Tordesillas Gutiérrez at + the Research Imaging + Center, UTHSCSA, Texas. +This is a digitised version of the original (coarsely + sliced) Talairach atlas (Lancaster 2000) after the + application of a correcting affine transform (Lancaster + 2007) to register it into MNI152 space. +References: +
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+ 9 anatomical structural regions, kindly provided by Jack + Lancaster at + the Research Imaging + Center, UTHSCSA, Texas (originally from + the McConnell + Brain Imaging Centre, MNI). +A single subject's structural image was hand segmented, + and the labels were then propagated to more than 50 + subjects' structural images using nonlinear + registration. Each resulting labelled brain was then + transformed into MNI152 space using affine registration, + before averaging segmentations across subjects to produce + the final probability images. For more details see the + Talairach Daemon. +References: +
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