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FsAtlasLookup

Namespace: FSLIB  ·  Library: FreeSurfer Library

#include <fs/fs_atlas_lookup.h>

class FSLIB::FsAtlasLookup

RAS-point → anatomical-region resolver backed by a FreeSurfer volumetric parcellation.

Owns the parcellation voxel grid, its inverse RAS-to-voxel affine, and a label-id → region-name map seeded from FreeSurferColorLUT. Designed for cheap per-point queries: a labelAtRas() call is an affine transform, three bound checks and an int → QString hash lookup.

src/examples/ex_fs/main.cpp
QTemporaryDir dir;
const QString atlasPath = dir.filePath("atlas.mgh"); // normally aparc+aseg.mgz
writeAtlas(atlasPath);
FsAtlasLookup atlas;
atlas.load(atlasPath);
const QStringList regionsAt = atlas.labelsForPositions({Vector3f(-4.0f, -4.0f, -4.0f), Vector3f(2.0f, 0.0f, -2.0f), Vector3f(0.0f, 0.0f, 0.0f)});

Public Methods​

FsAtlasLookup()​

Constructs an empty atlas lookup.

load(sParcellationPath)​

Load a FreeSurfer MGH/MGZ volume parcellation.

Parameters:

  • sParcellationPath : const QString & Path to the volume file (e.g. aparc+aseg.mgz).

Returns:

  • bool — true if loaded successfully.

labelAtRas(ras)​

Look up the anatomical label at a RAS coordinate.

Parameters:

  • ras : const Eigen::Vector3f & 3D position in RAS space (in mm).

Returns:

  • QString — Label string, or "Unknown" if out of bounds or unlabeled.

labelsForPositions(positions)​

Look up labels for multiple RAS positions.

Parameters:

  • positions : const QVector< Eigen::Vector3f > & List of 3D RAS positions.

Returns:

  • QStringList — List of label strings (one per position).

isLoaded()​

Check whether a parcellation volume has been loaded.

Returns:

  • bool — true if loaded.

Example​

Used in examples​

ex_fs​

FreeSurfer library: surfaces, curvature, parcellations, labels and an atlas volume.

src/examples/ex_fs/main.cpp, line 174
QTemporaryDir dir;
const QString atlasPath = dir.filePath("atlas.mgh"); // normally aparc+aseg.mgz
writeAtlas(atlasPath);
FsAtlasLookup atlas;
atlas.load(atlasPath);
const QStringList regionsAt = atlas.labelsForPositions({Vector3f(-4.0f, -4.0f, -4.0f), Vector3f(2.0f, 0.0f, -2.0f), Vector3f(0.0f, 0.0f, 0.0f)});
// nibabel: inv(affine) maps (-4,-4,-4) to voxel (0,0,0) and (2,0,-2) to voxel (3,2,1)
ok &= expect(atlas.isLoaded() && regionsAt == QStringList({"Left-Hippocampus", "Right-Hippocampus", "Unknown"}),
             QString("atlas lookup: %1").arg(regionsAt.join(", ")));

Authors of this file​