Robust joint registration of multiple stains and MRI for multimodal 3D histology reconstruction: Application to the Allen human brain atlas

uploaded by Adrià Casamitjana on 2021-03-29 - 3 months ago
last modified on 2021-06-07 - 14 days ago
authored by Adria Casamitjana, Marco Lorenzi, Sebastiano Ferraris, Loïc Peter, Marc Modat, Allison Stevens, Bruce Fischl, Eugenio Iglesias
0107

OpenNeuro Accession Number: ds003590
Files: 5, Size: 15.08MB, Subject: 1, Session: 1
No Available Tasks
Available Modalities: T2w

README

This repository contains the following files:

BIDS Directory Structure

Raw MRI volumes (T2w) at 7T

sub-01/ses-7T/anat/  -  MRI volume from the Allen Human Brain Atlas used as the reference for 3D histology reconstruction

Reconstructed MRI and histological data in subject space at 0.25mm isotropic

derivatives/historecon/sub-01/sub-01_res-0.25_<stain>  

Corresponding MNI coordinates form the reconstructed volumes (4D volume with RAS/image coordinates). These files lie on the space of the histology reconstructions, thus, opening it on top of any of the reconstructed contrasts will directly give the image indices on MNI space

derivatives/mni-coordinates/sub-01/mni.coords.ijk.nii.gz
derivatives/mni-coordinates/sub-01/mni.coords.ijk.nii.gz

===

Authors

  • Adria Casamitjana
  • Marco Lorenzi
  • Sebastiano Ferraris
  • Loïc Peter
  • Marc Modat
  • Allison Stevens
  • Bruce Fischl
  • Eugenio Iglesias

Dataset DOI

10.18112/openneuro.ds003590.v1.0.1

License

CC0

Acknowledgements

How to Acknowledge

Casamitjana, Adrià, et al. "Robust joint registration of multiple stains and MRI for multimodal 3D histology reconstruction: Application to the Allen human brain atlas." arXiv preprint arXiv:2104.14873 (2021).

Funding

  • This work was primarily funded by the European Research Council (Starting Grant 677697, project \BUNGEE-TOOLS").
  • EPSRC-funded UCL Centre for Doctoral Training in Medical Imaging (EP/L016478/1) 985 and Doctoral Training Grant (EP/M506448/1).
  • BRAIN Initiative (1RF1MH123195- 01, U01MH117023),
  • Biomedical Imaging and Bioengineering 990 (P41EB015896, 1R01EB023281, R01EB006758, R21EB018907, R01EB019956, P41EB030006)
  • National Institute on Aging (1R01AG070988-01, 1R56AG064027, 1R01AG064027, 5R01AG008122, R01AG016495)
  • National Institute of Men995 tal Health (R01 MH123195, R01 MH121885, 1RF1MH123195)
  • National Institute for Neurological Disorders and Stroke (R01NS0525851, R21NS072652, R01NS070963, R01NS083534, 5U01NS086625,5U24NS10059103, R01NS105820)
  • Shared Instrumentation Grants 1S10RR023401, 1S10RR019307, and 1S10RR023043.
  • NIH Blueprint for Neuroscience Research (5U01-MH093765), part 1005 of the multi-institutional Human Connectome Project.
  • Wellcome/EPSRC Centre for Medical En1015 gineering [WT203148/Z/16/Z; NS/A000049/1]
  • Alzheimer's Research UK (ARUK-IRG2019A-003)
  • NIH (1RF1MH123195-01, 1R01AG070988-01)

Ethics Approvals

How To Cite

Copy
Adria Casamitjana and Marco Lorenzi and Sebastiano Ferraris and Loïc Peter and Marc Modat and Allison Stevens and Bruce Fischl and Eugenio Iglesias (2021). Robust joint registration of multiple stains and MRI for multimodal 3D histology reconstruction: Application to the Allen human brain atlas. OpenNeuro. [Dataset] doi: 10.18112/openneuro.ds003590.v1.0.1
More citation info

Robust joint registration of multiple stains and MRI for multimodal 3D histology reconstruction: Application to the Allen human brain atlas

uploaded by Adrià Casamitjana on 2021-03-29 - 3 months ago
last modified on 2021-06-07 - 14 days ago
authored by Adria Casamitjana, Marco Lorenzi, Sebastiano Ferraris, Loïc Peter, Marc Modat, Allison Stevens, Bruce Fischl, Eugenio Iglesias
0107

OpenNeuro Accession Number: ds003590
Files: 5, Size: 15.08MB, Subject: 1, Session: 1
No Available Tasks
Available Modalities: T2w

README

This repository contains the following files:

BIDS Directory Structure

Raw MRI volumes (T2w) at 7T

sub-01/ses-7T/anat/  -  MRI volume from the Allen Human Brain Atlas used as the reference for 3D histology reconstruction

Reconstructed MRI and histological data in subject space at 0.25mm isotropic

derivatives/historecon/sub-01/sub-01_res-0.25_<stain>  

Corresponding MNI coordinates form the reconstructed volumes (4D volume with RAS/image coordinates). These files lie on the space of the histology reconstructions, thus, opening it on top of any of the reconstructed contrasts will directly give the image indices on MNI space

derivatives/mni-coordinates/sub-01/mni.coords.ijk.nii.gz
derivatives/mni-coordinates/sub-01/mni.coords.ijk.nii.gz

===

Authors

  • Adria Casamitjana
  • Marco Lorenzi
  • Sebastiano Ferraris
  • Loïc Peter
  • Marc Modat
  • Allison Stevens
  • Bruce Fischl
  • Eugenio Iglesias

Dataset DOI

10.18112/openneuro.ds003590.v1.0.1

License

CC0

Acknowledgements

How to Acknowledge

Casamitjana, Adrià, et al. "Robust joint registration of multiple stains and MRI for multimodal 3D histology reconstruction: Application to the Allen human brain atlas." arXiv preprint arXiv:2104.14873 (2021).

Funding

  • This work was primarily funded by the European Research Council (Starting Grant 677697, project \BUNGEE-TOOLS").
  • EPSRC-funded UCL Centre for Doctoral Training in Medical Imaging (EP/L016478/1) 985 and Doctoral Training Grant (EP/M506448/1).
  • BRAIN Initiative (1RF1MH123195- 01, U01MH117023),
  • Biomedical Imaging and Bioengineering 990 (P41EB015896, 1R01EB023281, R01EB006758, R21EB018907, R01EB019956, P41EB030006)
  • National Institute on Aging (1R01AG070988-01, 1R56AG064027, 1R01AG064027, 5R01AG008122, R01AG016495)
  • National Institute of Men995 tal Health (R01 MH123195, R01 MH121885, 1RF1MH123195)
  • National Institute for Neurological Disorders and Stroke (R01NS0525851, R21NS072652, R01NS070963, R01NS083534, 5U01NS086625,5U24NS10059103, R01NS105820)
  • Shared Instrumentation Grants 1S10RR023401, 1S10RR019307, and 1S10RR023043.
  • NIH Blueprint for Neuroscience Research (5U01-MH093765), part 1005 of the multi-institutional Human Connectome Project.
  • Wellcome/EPSRC Centre for Medical En1015 gineering [WT203148/Z/16/Z; NS/A000049/1]
  • Alzheimer's Research UK (ARUK-IRG2019A-003)
  • NIH (1RF1MH123195-01, 1R01AG070988-01)

Ethics Approvals

How To Cite

Copy
Adria Casamitjana and Marco Lorenzi and Sebastiano Ferraris and Loïc Peter and Marc Modat and Allison Stevens and Bruce Fischl and Eugenio Iglesias (2021). Robust joint registration of multiple stains and MRI for multimodal 3D histology reconstruction: Application to the Allen human brain atlas. OpenNeuro. [Dataset] doi: 10.18112/openneuro.ds003590.v1.0.1
More citation info

Dataset File Tree

Git Hash: 60ff30a 

BIDS Validation

Dataset File Tree

Git Hash: 60ff30a 

Comments

Please sign in to contribute to the discussion.