This folder contains data released as part of the paper: 

"A Contrast-Agnostic Method for Ultra-High Resolution Claustrum Segmentation"
Chiara Mauri, Ryan Fritz, Jocelyn Mora, Benjamin Billot, Juan Eugenio Iglesias, Koen Van Leemput, Jean Augustinack, Douglas N Greve

The folder contains the following subdirectories:

- high-res-manual-labels: manual labels for claustrum on 18 high-resolution hemispheres (0.1-0.25 mm isotropic resolution)

	* The intensity image for ex vivo case 3 (Costantini et al., 2023) is publicly available on the DANDI platform at https://dandiarchive.org/dandiset/000026

	* Intensity image for ex vivo case 13 (Edlow et al., 2019) is publicly available on the OpenNeuro platform at https://doi.org/10.18112/openneuro.ds002179.v1.1.0 
	  and in the Dryad Digital Repository at https://doi.org/10.5061/dryad.119f80q.

	* Intensity image for in vivo case 16 (Lusebrink et al., 2017) is publicly available in the Dryad Digital Repository at http://dx.doi.org/10.5061/dryad.38s74

	* Intensity images of all other cases are not publicly available

	Please note that the manual labels are provided in cropped form to facilitate loading. However, the header information preserves the spatial origin of the crop, 
	allowing the labels to be aligned with the full-FoV image. For cases where the corresponding intensity image is publicly available, it can be downloaded using 
	the links provided above and visualized alongside the manual labels in tools such as Freeview. The images and labels are aligned in the same spatial reference frame, 
	allowing for direct overlay in Freeview.
	If you prefer to crop the intensity image to match the spatial extent of the manual label, the following FreeSurfer command can be used:

	mri_extract -like <manual label> <intensity image> <output cropped intensity image>

	For instance, for case 13:
	mri_extract -like  /path/to/data/claustrumData/high-res-manual-labels/case13_RH.label.mgz  /path/to/downloaded/intensity/Acquired_FA25_100um.nii.gz cropped_intensity_image.nii.gz

- atlas-MNI52-200um: probabilistic atlas for claustrum in MNI152 space at 0.2 mm isotropic resolution, obtained from the 18 claustrum manual labels

- IXI: automatic claustrum segmentations on T1-weigthed scans from the IXI dataset. Intensity images can be found at: http://braindevelopment.org/ixi-dataset/

- FSM: automatic claustrum segmentations on T1-weigthed (39 subjects) and T2-weighted (31 subjects) scans from the FSM dataset. 
  Intensity images can be found at:  https://doi.org/10.18112/openneuro.ds004958.v1.0.0




References:

(Costantini et al., 2023)  A cellular resolution atlas of Broca’s area. Science Advances, 9(41):eadg3844.

(Edlow et al., 2019) 7 Tesla MRI of the ex vivo human brain at 100 micron resolution. Scientific data, 6(1):244.

(Lusebrink et al., 2017)  T1-weighted in vivo human whole brain MRI dataset with an ultrahigh isotropic resolution of 250 μm. Scientific data, 4(1):1–12.
