cmtklib.interfaces.pycartool module

The PyCartool module provides Nipype interfaces with Cartool using pycartool.

CartoolInverseSolutionROIExtraction

Link to code

Bases: nipype.interfaces.base.core.BaseInterface

Use Pycartool to load inverse solutions estimated by Cartool.

Examples

>>> from cmtklib.interfaces.pycartool import CartoolInverseSolutionROIExtraction
>>> cartool_inv_sol = CartoolInverseSolutionROIExtraction()
>>> cartool_inv_sol.inputs.epochs_file = 'sub-01_task-faces_desc-preproc_eeg.set'
>>> cartool_inv_sol.inputs.invsol_file = 'sub-01_eeg.LORETA.is'
>>> cartool_inv_sol.inputs.mapping_spi_rois_file = 'sub-01_atlas-L2018_res-scale1.pickle.rois'
>>> cartool_inv_sol.inputs.lamd = 6
>>> cartool_inv_sol.inputs.svd_toi_begin = 0
>>> cartool_inv_sol.inputs.svd_toi_end = 0.25
>>> cartool_inv_sol.inputs.out_roi_ts_fname_prefix = 'sub-01_task-faces_atlas-L2008_res-scale1_rec-LORETA_timeseries'
>>> cartool_inv_sol.run()  

References

• https://pycartool.readthedocs.io/en/latest/pycartool.io.html#module-pycartool.io.inverse_solution

epochs_filea string or os.PathLike object referring to an existing file

Eeg * epochs in .set format.

invsol_filea string or os.PathLike object referring to an existing file

Inverse solution (.is file loaded with pycartool).

mapping_spi_rois_filea string or os.PathLike object referring to an existing file

Cartool-reconstructed sources / parcellation ROI mapping file, loaded with pickle.

out_roi_ts_fname_prefixa string

Output name prefix (no extension) for rois * time series files.

lamban integer

Regularization weight.

svd_toi_begina float

Start TOI for SVD projection.

svd_toi_enda float

End TOI for SVD projection.

roi_ts_mat_filea string or os.PathLike object

Path to output ROI time series file in .mat format.

roi_ts_npy_filea string or os.PathLike object

Path to output ROI time series file in .npy format.

static CartoolInverseSolutionROIExtraction.apply_inverse_epochs_cartool(epochs_file, invsol_file, lamda, rois_file, svd_params)

CreateSpiRoisMapping

Link to code

Bases: nipype.interfaces.base.core.BaseInterface

Create Cartool-reconstructed sources / parcellation ROI mapping file.

Examples

>>> from cmtklib.interfaces.pycartool import CreateSpiRoisMapping
>>> createrois = CreateSpiRoisMapping()
>>> createrois.inputs.roi_volume_file = '/path/to/sub-01_atlas-L2018_res-scale1_dseg.nii.gz'
>>> createrois.inputs.spi_file = '/path/to/sub-01_eeg.spi'
>>> createrois.inputs.out_mapping_spi_rois_fname = 'sub-01_atlas-L2018_res-scale1_eeg.pickle.rois'
>>> createrois.run()  

out_mapping_spi_rois_fnamea string

Name of output sources / parcellation ROI mapping file in .pickle.rois format.

roi_volume_filea string or os.PathLike object

Parcellation file in nifti format.

spi_filea string or os.PathLike object

Cartool reconstructed sources file in spi format.

mapping_spi_rois_filea string or os.PathLike object

Path to output Cartool-reconstructed sources / parcellation ROI mapping file in .pickle.rois format.