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README
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2016 Fetal Brain Atlas
Copyright 2016, Computational Radiology Lab, Boston Childrens Hospital
Contact:
Ali Gholipour: [email protected]
Clemente Velasco-Annis: [email protected]
This version of the Spatio-Temporal Atlas (STA) was last edited on 11/21/16
This spatio-temporal atlas and the included parcellations are not intended for medical use and have no warranty. Structures received varying amounts of attention and refinement based on the research goals at the time of creation and thus no guarantees can be made regarding the accuracy or precision of the segmentations, nor the withholding to any particular labeling convention or protocol between structures. Any output derived from the use of these atlases or parcellations shouled be checked in order to validate the accuracy of the results.
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New to this update (11/21/16) "Olympic edition":
CHANGES TO LABELING SCHEME:
The parcellation scheme (label numbers) has been reorganized
All atlas images now share the same label key
The full key can be found below
Left and right white matter have been separated into separate labels
Labels for left and right internal capsule have been added to all images
REFINEMENT TO PARCELLATIONS:
"Miscellanous_brain_tissue" has been mostly removed as most of the label was internal capsule
Developing white matter zones (SP, IZ & VZ) have been removed from STA31-33 because they were not felt to be accurate (differentiation between layers was arbitrary)
*There are two versions of the STA30 parcellation, one with developing white matter zones, one without*
Cortical plate was reduced in the region anterior to the corpus callosum (reduced the portion "wrapping" into hemisphere)
Subplate has been expanded to the appropriate width as per reviewer feedback
The intermediate zone/ventricular zone has been edited to shrink the ventricular zone in line with reviewer feedback
Deep gray matter structures have been edited to increase segmentation consistency between gestational ages
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New to this update (06/07/16):
White and gray cerebellum have been recombined because we could not ensure the accuracy of the delineation (very little refinement had been done since initial propagation of the parcellation scheme to this atlas).
The files have been renamed slightly.
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New to this update (03/30/16):
ADDED TEMPLATES:
There are now atlas images and labels for gestational age (GA) weeks 21-37.
DEVELOPING WHITE MATTER ZONES:
Labels for developing white matter zones have been added for GA 21-33
This includes left and right "ventricular zone", "intermediate zone" (similar to subventricular zone), and "subplate"
In these images, label 51 is now "miscellaneous brain tissue", mostly deep gray matter found between the larger subcortical structures
Images with the labeling convention are marked with "wmz"; for example, STA27_WMZparc.nii.gz
There are two versions of labels for STA31, STA32, and STA33
STA31_parc.nii.gz = All white matter is label 51
STA31_WMZparc.nii.gz = Developing white matter layers have been separated into miscellaneous brain tissue (#51), subplate (#73,74), intermediate zone (#75,76), and ventricular zone (#77,78)
Note: As the white matter homogenizes in composition during development, the visual differentiation between the layers also decreases. Because of this the accuracy of the developmental layers may not be great for the older brains (i.e. STA30-33). This primarily pertains to the border between intermediate zone and subplate.
ADDITIONAL ADDED LABELS:
#5: Hippocampal commisure
#6: Fornix
LABEL REFINEMENTS:
Many of the labels have been refined to increase accuracy, in particular:
hippocampus
caudate
thalamus
lentiform
corpus callosum
cortical plate
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Label key (all images):
37 Hippocampus_L
38 Hippocampus_R
41 Amygdala_L
42 Amygdala_R
71 Caudate_L
72 Caudate_R
73 Lentiform_L
74 Lentiform_R
77 Thalamus_L
78 Thalamus_R
91 CorpusCallosum
92 Lateral_Ventricle_L
93 Lateral_Ventricle_R
94 Brainstem
100 Cerebellum_L
101 Cerebellum_R
108 Subthalamic_Nuc_L
109 Subthalamic_Nuc_R
110 Hippocampal_Comm
111 Fornix
112 Cortical_Plate_L
113 Cortical_Plate_R
114 Subplate_L
115 Subplate_R
116 Inter_Zone_L
117 Inter_Zone_R
118 Vent_Zone_L
119 Vent_Zone_R
120 White_Matter_L
121 White_Matter_R
122 Internal_Capsule_L
123 Internal_Capsule_R
124 CSF
125 Misc
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Michael Ebner, Feb 16, 2018:
- All image headers have been updated using fslreorient2std using `for i in *.nii.gz; do echo $i; fslreorient2std $i $i; done`
- _mask: binarized image labels
- _mask_dil: dilated binary masks; applied to SRR it approximates brain tissue only
- templates_info.json: Additional information on templates like volume