This is a functional index of methods available on a region object.
A region is a class for groups of voxels defined as anatomical or
functional regions (contiguous voxels above a threshold in an analysis,
parcels from an atlas, etc.). The class replaces the older clusters
struct from the scnlab toolbox; the class definition adds error
checking and structured methods (visualization, tabling, conversion to
other image types).
region is a standalone class (not a subclass of image_vector), so
it does NOT inherit image_vector methods. Instead, several region
methods convert to and from image_vector / fmri_data / atlas so
that those classes' tooling can be applied. Type methods(my_obj) in
MATLAB for the live list on any instance.
| Property | Description |
|---|
title | Title of the region object |
shorttitle | Short title (used as label) |
descrip1 | Description string 1 |
descrip2 | Description string 2 (lists key methods) |
XYZ | [3 x voxels] voxel coordinates within the region |
XYZmm | [3 x voxels] world (mm) coordinates within the region |
val | Per-voxel values (typically the input mask values) |
val_descrip | Description of values stored in val |
Z | Per-voxel max-stat / Z-scores (legacy field, still widely used) |
Z_descrip | Description of values stored in Z (legacy) |
threshold | (legacy) Threshold associated with the region, kept for compatibility |
voxSize | Voxel size in mm (3-vector from the affine) |
M | Affine matrix (4x4) inherited from the source mask |
dim | Image dimensions (3-vector) |
numVox | Number of voxels in the region |
numpeaks | Number of peaks within the region |
center | Voxel-coordinate center of mass |
mm_center | mm-coordinate center of mass |
timeseries | Per-region timeseries (if extracted) |
contrastdata | Per-region contrast data (if extracted) |
dat | Per-region averaged data (images x 1 vector when extracted) |
all_data | Full per-voxel data extracted from a source image set |
source_images | Filenames of images data were extracted from |
custom_info1 | Custom info slot 1 (often the source mask filename) |
custom_info1_descrip | Description for custom_info1 |
custom_info2 | Custom info slot 2 |
custom_info2_descrip | Description for custom_info2 |
| Method | From | One-liner |
|---|
merge | @region | Merge two or more regions into one, combining fields appropriately |
posneg_separate | @region | Split regions into positive- and negative-valued sub-regions |
subdivide_by_atlas | @region | Subdivide each blob by anatomical atlas parcels |
subdivide_by_local_max | @region | Subdivide regions by local peak Z-score / maxima |
reparse_continguous | @region | Re-define regions based on contiguous blobs (note: spelling is continguous in source) |
select_coordinates_near_regions | @region | Filter MNI mm coordinates by minimum distance to the region object |
| Method | From | One-liner |
|---|
montage | @region | Slice montage of region object on canonical anatomy |
orthviews | @region | SPM orthviews via cluster_orthviews with hot/cool colormap |
surface | @region | Render region blobs on cutaway / canonical surfaces |
isosurface | @region | One 3-D isosurface per region, with optional L/R color matching |
labelled_surface | @region | Transparent isosurfaces with centroid labels and text annotations |
match_colors_left_right | @region | Assign matched colors to symmetric L/R regions |
| Method | From | One-liner |
|---|
table | @region | Print and return a labeled table of all regions (positive and negative) |
table_simple | @region | Simple one-row-per-region results table (useful after atlas subdivision) |
table_of_atlas_regions_covered | @region | Tabulate atlas parcels covered by the regions |
ttest_table_by_condition | @region | Per-region means + stats tables for an fmri_data object across conditions |
autolabel_regions_using_atlas | @region | Auto-label regions using an atlas object |
| Method | From | One-liner |
|---|
extract_data | @region | Extract data and apply local patterns from an image_vector for the region's voxels |
check_extracted_data | @region | Verify region-average data via re-extraction from source images |
Conversion to and from other CANlab object classes, and basic predicates.
| Method | From | One-liner |
|---|
region2atlas | @region | Convert a region object to an atlas object |
region2fmri_data | @region | Convert a region object to an fmri_data object |
region2imagevec | @region | Convert a region object to an image_vector object |
region2struct | @region | Convert a region object to a plain MATLAB struct array (legacy compatibility) |
isempty | @region | True iff region array is empty or its first XYZ is empty |