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You don't need to download the code to generate the flatmap stacks. This repository contains the code for generating the flatmap stack warping fields (See usage section below).
A flatmap extents cortical flatmaps with cortical depth. We created two kinds of mappings, based on two different, publicly available cortical marmoset flatmaps from the Marmoset Brain Mapping project [2], and the Brain/MINDS Atlas [6] (See references below). Click on the image below to see a demonstration video on youtube. You can find further details in our preprint [1].
Your image data must be aligned to one of these five marmoset brain reference image spaces
- Brain/MINDS Marmoset Connectivity Atlas (STPT template space) (https://bia.riken.jp/doku.php?id=tools:bmca) [1]
- Marmoset Brain Mapping Atlas v3.0 (https://marmosetbrainmapping.org/atlas.html) [3]
- Marmoset Brain Mapping Atlas v2.0 (https://marmosetbrainmapping.org/atlas.html) [2]
- Marmoset Brain Connectivity Atlas (https://www.marmosetbrain.org/) [4,5]
- Brain/MINDS 3D Marmoset Reference Brain Atlas (https://dataportal.brainminds.jp/atlas-package-download-main-page/bma-2019-ex-vivo) [6]
The warping fields are made for the ANTs image registration toolkit (http://stnava.github.io/ANTs/). You need to install it.
Then you need to download the warping field(s). You will find links to our data repositories on this website https://bia.riken.jp/doku.php?id=tools:bmca in the "Data download" section.
- You need to download the flatmap stack warping fields from the "Flatmap_stack_mapping" folder.
- In case your images are NOT in the STPT template space, you need to download the warping field that maps from one of the other atlases to the STPT template space (archive folder: STPT_reference_image_space/##ATLAS##/trafo).
Howto warp an image from the STPT template space to a flatmap stack based on the Marmoset Brain Mapping Atlas flatmap
antsApplyTransforms -d 3 -v --float \
-i PATH_TO_YOUR_INPUT_FILE.nii.gz \
-o PATH_TO_YOUR_OUTPUT_FILE.nii.gz \
-t flatmap_stack_trafo_l_2.nii.gz \
-r flatmap_stack_trafo_l_2.nii.gz \
Similar to the previous case, but we first flip left and right hemisphere before warping.
antsApplyTransforms -d 3 -v --float \
-i PATH_TO_YOUR_INPUT_FILE.nii.gz \
-o PATH_TO_YOUR_OUTPUT_FILE.nii.gz \
-t flatmap_stack_trafo_l_2.nii.gz \
-t -t [flip_x.itk.aff.txt,1]
-r flatmap_stack_trafo_l_2.nii.gz \
Howto warp an image from the Marmoset Brain Mapping Atlas v2 template space to a flatmap stack based on the Marmoset Brain Mapping Atlas flatmap
Just add the warping field that maps to the STPT template space last.
antsApplyTransforms -d 3 -v --float \
-i PATH_TO_YOUR_INPUT_FILE.nii.gz \
-o PATH_TO_YOUR_OUTPUT_FILE.nii.gz \
-t flatmap_stack_trafo_l_2.nii.gz \
-t MBM_2_STPT.h5 \
-r flatmap_stack_trafo_l_2.nii.gz \
- Skibbe, et al. The Brain/MINDS Marmoset Connectivity Atlas: Exploring bidirectional tracing and tractography in the same stereotaxic space. bioRxiv. 2022.
- Liu C, et al. Marmoset Brain Mapping V3: Population multi-modal standard volumetric and surface-based templates. 2021
- Liu C, et al. A resource for detailed 3D mapping of white matter pathways in the marmoset brain. Nature Neuroscience. 2020
- Majka P, et al. Open access resource for cellular-resolution analyses of corticocortical connectivity in the marmoset monkey. Nature Communications. 2020
- Majka P,et al. Towards a comprehensive atlas of cortical connections in a primate brain: Mapping tracer injection studies of the common marmoset into a reference digital template. Journal of Comparative Neurology. 2016
- Woodward,et al.Brain/MINDS 3D Marmoset Reference Brain Atlas 2019 (DataID: 4520) https://doi.org/10.24475/bma.4520