cortex.align.manual

cortex.align.manual(subject, xfmname, reference=None, **kwargs)

Open GUI for manually aligning a functional volume to the cortical surface for subject. This creates a new transform called xfm. The name of a nibabel-readable file (e.g. nii) should be supplied as reference. This image will be copied into the database.

To modify an existing functional-anatomical transform, reference can be left blank, and the previously used reference will be loaded.

<<ADD DETAILS ABOUT TRANSFORMATION MATRIX FORMAT HERE>>

When the GUI is closed, the transform will be saved into the pycortex database. The GUI requires Mayavi support.

Parameters

subjectstr

Subject identifier.

xfmnamestr

String identifying the transform to be created or loaded.

referencestr, optional

Path to a nibabel-readable image that will be used as the reference for this transform. If given the default value of None, this function will attempt to load an existing reference image from the database.

kwargsdict

Passed to mayavi_aligner.get_aligner.

Returns

m2D ndarray, shape (4, 4)

Transformation matrix.