fmri_regionmask

Description

FMRI_REGIONMASK Binary brain mask for one or more atlas regions. Returns a vectorized binary mask (228453 x 1) that is 1 for all voxels belonging to the specified region(s) in the given atlas. Accepts a vector of region numbers to combine multiple ROIs into a single mask.

Usage

[mask, regionname] = fmri_regionmask(regionnumber)
[mask, regionname] = fmri_regionmask(regionnumber, atlasnumber)

Inputs

  • REGIONNUMBER: Region number(s), scalar or vector. Use fmri_roin for interactive selection or fmri_regionnumber to look up numbers.

  • ATLASNUMBER: Atlas number (see atlas list below). Default: 1 (AAL).

Outputs

  • MASK: Binary vectorized mask (228453 x 1). 1 = in region.

  • REGIONNAME: Cell array of region name strings for each requested number.

Examples

% Left hippocampus mask (AAL region 57)
mask = fmri_regionmask(57);
% Combine L+R hippocampus
mask = fmri_regionmask([57 58]);
% Sphere intersected with anatomical region
roi = fmri_spheremask(fmri_mni2sub([20 -58 18]), 5) & fmri_regionmask(6);
Atlas numbers:
1  = AAL / MarsBar (Automated Anatomical Labeling, 116 ROIs, default)
2  = Harvard-Oxford Subcortical Structural Atlas (21 ROIs)
3  = Harvard-Oxford Cortical Structural Atlas (48 ROIs)
4  = Cerebellar Atlas (MNI152, FLIRT affine, 28 ROIs)
5  = Cerebellar Atlas (MNI152, FNIRT nonlinear, 28 ROIs)
6  = JHU ICBM-DTI-81 White-Matter Labels (48 ROIs)
7  = JHU White-Matter Tractography Atlas (20 ROIs)
8  = Juelich Histological Atlas (62 ROIs)
9  = MNI Structural Atlas (9 ROIs)
10  = Oxford-Imanova Striatal Structural Atlas (3 ROIs)
11  = Oxford-Imanova Striatal Connectivity Atlas, 3 sub-regions
12  = Oxford-Imanova Striatal Connectivity Atlas, 7 sub-regions
13  = Oxford Thalamic Connectivity Probability Atlas (25 ROIs)
14  = Craddock Parcellation 200 ROI
15  = Craddock Parcellation 400 ROI
16  = Craddock Parcellation 500 ROI
17  = Craddock Parcellation 600 ROI
18  = Craddock Parcellation 950 ROI
19  = Brodmann Areas (48 regions)

See Also

  • fmri_regionnumber

  • fmri_nregion

  • fmri_roin

  • fmri_spheremask