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