mne.SourceMorph¶
-
class
mne.
SourceMorph
(subject_from, subject_to, kind, zooms, niter_affine, niter_sdr, spacing, smooth, xhemi, morph_mat, vertices_to, shape, affine, pre_affine, sdr_morph, src_data, verbose=None)[source]¶ Morph source space data from one subject to another.
Note
This class should not be instantiated directly. Use
mne.compute_source_morph()
instead.New in version 0.17.
- Parameters
- subject_from
str
|None
Name of the subject from which to morph as named in the SUBJECTS_DIR.
- subject_to
str
|array
|list
ofarray
Name of the subject on which to morph as named in the SUBJECTS_DIR. The default is ‘fsaverage’. If morphing a volume source space, subject_to can be the path to a MRI volume. Can also be a list of two arrays if morphing to hemisphere surfaces.
- kind
str
|None
Kind of source estimate. E.g. ‘volume’ or ‘surface’.
- zooms
float
|tuple
- niter_affine
tuple
ofint
Number of levels (
len(niter_affine)
) and number of iterations per level - for each successive stage of iterative refinement - to perform the affine transform.- niter_sdr
tuple
ofint
Number of levels (
len(niter_sdr)
) and number of iterations per level - for each successive stage of iterative refinement - to perform the Symmetric Diffeomorphic Registration (sdr) transform [R4e7e360c4de9-2].- spacing
int
|list
|None
- smooth
int
|None
Number of iterations for the smoothing of the surface data. If None, smooth is automatically defined to fill the surface with non-zero values.
- xhemibool
Morph across hemisphere.
- morph_mat
scipy.sparse.csr_matrix
The sparse surface morphing matrix for spherical surface based morphing [R4e7e360c4de9-1].
- vertices_to
list
ofndarray
The destination surface vertices.
- shape
tuple
The volume MRI shape.
- affine
ndarray
The volume MRI affine.
- pre_affineinstance of
dipy.align.imaffine.AffineMap
The
dipy.align.imaffine.AffineMap
transformation that is applied before the beforesdr_morph
.- sdr_morphinstance of
dipy.align.imwarp.DiffeomorphicMap
The
dipy.align.imwarp.DiffeomorphicMap
that applies the the symmetric diffeomorphic registration (SDR) morph.- src_data
dict
Additional source data necessary to perform morphing.
- verbosebool,
str
,int
, orNone
If not None, override default verbose level (see
mne.verbose()
and Logging documentation for more).
- subject_from
References
- R4e7e360c4de9-1
Greve D. N., Van der Haegen L., Cai Q., Stufflebeam S., Sabuncu M. R., Fischl B., Brysbaert M. A Surface-based Analysis of Language Lateralization and Cortical Asymmetry. Journal of Cognitive Neuroscience 25(9), 1477-1492, 2013.
- R4e7e360c4de9-2
Avants, B. B., Epstein, C. L., Grossman, M., & Gee, J. C. (2009). Symmetric Diffeomorphic Image Registration with Cross- Correlation: Evaluating Automated Labeling of Elderly and Neurodegenerative Brain, 12(1), 26-41.
Methods
__hash__
(self, /)Return hash(self).
apply
(self, stc_from[, output, …])Morph source space data.
save
(self, fname[, overwrite, verbose])Save the morph for source estimates to a file.
-
__hash__
(self, /)¶ Return hash(self).
-
apply
(self, stc_from, output='stc', mri_resolution=False, mri_space=False, verbose=None)[source]¶ Morph source space data.
- Parameters
- stc_from
VolSourceEstimate
|VolVectorSourceEstimate
|SourceEstimate
|VectorSourceEstimate
The source estimate to morph.
- output
str
Can be ‘stc’ (default) or possibly ‘nifti1’, or ‘nifti2’ when working with a volume source space defined on a regular grid.
- mri_resolution: bool | tuple | int | float
If True the image is saved in MRI resolution. Default False. WARNING: if you have many time points the file produced can be huge. The default is mri_resolution=False.
- mri_spacebool
Whether the image to world registration should be in mri space. The default is mri_space=mri_resolution.
- verbosebool,
str
,int
, orNone
If not None, override default verbose level (see
mne.verbose()
and Logging documentation for more). Defaults to self.verbose.
- stc_from
- Returns
- stc_to
VolSourceEstimate
|SourceEstimate
|VectorSourceEstimate
|Nifti1Image
|Nifti2Image
The morphed source estimates.
- stc_to
-
save
(self, fname, overwrite=False, verbose=None)[source]¶ Save the morph for source estimates to a file.
- Parameters
- fname
str
The stem of the file name. ‘-morph.h5’ will be added if fname does not end with ‘.h5’
- overwritebool
If True, overwrite existing file.
- verbosebool,
str
,int
, orNone
If not None, override default verbose level (see
mne.verbose()
and Logging documentation for more). Defaults to self.verbose.
- fname