simnibs.SubjectFiles¶
- class simnibs.SubjectFiles(fnamehead: str | None = None, subpath: str | None = None)¶
Class to find files for a given subject
- Parameters:
fnamehead (str (optional)) – Path to head mesh. Either fnamehead or subpath need to be set. subpath has preference when it comes to finding other files.
subpath (str (optional)) – Path to m2m_folder. Either fnamehead or subpath need to be set. subpath has preference when it comes to finding other files
- fnamehead¶
Path to head mesh (.msh)
- Type:
str
- subpath¶
Path to m2m_folder (dir)
- Type:
str
- subid¶
The subject ID (eg: ernie)
- Type:
str
- tensor_file¶
Path to the NIfTI file with the tensor conductivity information (.nii.gz)
- Type:
str
- eeg_cap_folder¶
Path to the folder with EEG caps (dir)
- Type:
str
- segmentation_folder¶
Path to the output from the segmentation
- Type:
str
- surface_folder¶
Path to surfaces from middle GM reconstruction
- Type:
str
- label_prep_folder¶
Path to the output from upsampling
- Type:
str
- mni_transf_folder¶
Path to MNI transformations
- Type:
str
- eeg_cap_1010¶
Path to the EEG 10-10 electrode file (.csv)
- Type:
str
- reference_volume¶
Path to the reference subject volume (T1.nii.gz)
- Type:
str
- mni2conf_nonl¶
MNI to conform nonlinear transformation (.nii.gz)
- Type:
str
- conf2mni_nonl¶
Conform to MNI nonlinear tansformation (.nii.gz)
- Type:
str
- mni2conf_6dof¶
MNI to conform 6 DOF transfomation (.txt or .mat)
- Type:
str
- mni2conf_12dof¶
MNI to conform 12 DOF transfomation (.txt or .mat)
- Type:
str
- final_labels_MNI¶
Label image created from final mesh in MNI space
- Type:
str
- hemispheres¶
Hemisphere names.
- Type:
list
- surfaces¶
Dictionary of ‘standard’ surfaces which are present after running CHARM. Each entry is a dict with hemispheres as keys pointing to the corresponding surface file.
- Type:
dict
- morph_data¶
Dictionary of ‘standard’ morphometry data which os present after running CHARM. Each entry is a dict with hemispheres as keys pointing to the corresponding morph file.
- Type:
dict
- T1¶
T1 image after applying transformations
- Type:
str
- T2_reg¶
T2 image after rigid co-registration to T1
- Type:
str
- T1_denoised¶
T1 image after running filtering (optional)
- Type:
str
- T2_reg_denoised¶
T2 image after co-registration and filtering (optional)
- Type:
str
- T1_bias_corrected¶
T1 image after bias correction
- Type:
str
- T2_reg_bias_corrected¶
T2 image after bias correction
- Type:
str
- labeling¶
Output segmentation from samseg
- Type:
str
- final_labels¶
Label image created from final mesh
- Type:
str
- template_coregistered¶
Affine mapping from atlas voxel space to T1 voxel space
- Type:
str
- T1_upsampled¶
Bias corrected T1 upsampled to 0.5mm^3 resolution
- Type:
str
- T2_upsampled¶
Bias corrected T2 upsampled to 0.5mm^3 resolution
- Type:
str
- tissue_labeling_upsampled¶
Labeling mapped to conductivity values and reconstructed at 0.5mm^3 resolution
- Type:
str
- head_mesh¶
Final head mesh
- Type:
str
- cerebrum_mask¶
Mask indicating cerebrum and cerebellum. Needed for surfaces.
- Type:
str
- norm_image¶
Normalized intensity image. Needed for surfaces.
- Type:
str
- subcortical_mask¶
Mask of subcortical structures. Needed for surfaces
- Type:
str
- parahippo_mask¶
Mask of parahippocampal area. Needed for surfaces.
- Type:
str
- hemi_mask¶
Mask indicating left/right. Needed for surfaces.
- Type:
str
- charm_log¶
The charm run log (.html)
- Type:
str
- summary_report¶
html summarizing the run and linking to the reports (.html)
- Type:
str
Warning
This class does not check for existance of the files
- __init__(fnamehead: str | None = None, subpath: str | None = None)¶
Methods
__init__([fnamehead, subpath])get_eeg_cap([cap_name])Gets the name of an EEG cap for this subject
get_morph_data(hemi, data[, subsampling])Get morphometry data files, e.g., thickness.
get_surface(hemi, surface[, subsampling])Get surface files, e.g., central, pial, sphere, sphere.reg
