Coverage for data/spheremodel/create_subject_spheremodel.py: 100%
105 statements
« prev ^ index » next coverage.py v7.5.1, created at 2024-05-17 07:31 +0000
1import pynibs
2import copy
3import numpy as np
5from inspect import getsourcefile
6import os
8# path of create_subject_XXXXX.py file (has to be in subjects root directoy
9subject_folder = os.path.split(os.path.abspath(getsourcefile(lambda: 0)))[0]
11# subject information
12########################################################################################################################
13subject_id = 'spheremodel'
14fn_subject_obj = subject_folder + '/spheremodel.hdf5'
16# mri information
17########################################################################################################################
18mri = [dict()]
19mri[0]['fn_mri_T1'] = subject_folder + '/mri/0/T1_sphere.nii.gz'
20mri[0]['fn_mri_T2'] = None
21mri[0]['fn_mri_DTI'] = None
22mri[0]['fn_mri_DTI_rev'] = None
23mri[0]['fn_mri_DTI_bvec'] = None
24mri[0]['fn_mri_DTI_bval'] = None
25mri[0]['dti_readout_time'] = None
26mri[0]['dti_phase_direction'] = None
28# mesh information
29########################################################################################################################
30mesh = dict()
32mesh_id = '02_make_mesh_from_mri_simnibs4'
33mesh_dict = dict()
34mesh_dict['info'] = 'charm --v 1.0 (simnibs 4.0 beta)'
35mesh_dict['approach'] = 'charm'
36mesh_dict['mesh_folder'] = os.path.join(subject_folder, 'mesh', mesh_id)
37mesh_dict['vertex_density'] = None
38mesh_dict['fn_mesh_msh'] = os.path.join(mesh_dict['mesh_folder'], f'm2m_{subject_id}', f'{subject_id}.msh')
39mesh_dict['fn_mesh_hdf5'] = os.path.join(mesh_dict['mesh_folder'], f'm2m_{subject_id}', f'{subject_id}.hdf5')
40mesh_dict['fn_tensor_vn'] = None
41mesh_dict['mri_idx'] = 0
42mesh_dict['fn_mri_conform'] = f"m2m_{subject_id}/T1.nii.gz"
43mesh_dict['fn_lh_wm'] = None
44mesh_dict['fn_rh_wm'] = None
45mesh_dict['fn_lh_gm'] = None
46mesh_dict['fn_rh_gm'] = None
47mesh_dict['fn_lh_gm_curv'] = None
48mesh_dict['fn_rh_gm_curv'] = None
49mesh_dict['fn_lh_midlayer'] = f'm2m_{subject_id}/surfaces/lh.central.gii'
50mesh_dict['fn_rh_midlayer'] = f'm2m_{subject_id}/surfaces/rh.central.gii'
51mesh_dict['smooth_skin'] = .8
52mesh[mesh_id] = mesh_dict
54mesh_id = '03_refine_mesh'
55mesh_dict = dict()
56mesh_dict['info'] = 'charm --v 1.0 (simnibs 4.0 beta)'
57mesh_dict['approach'] = 'charm'
58mesh_dict['mesh_folder'] = os.path.join(subject_folder, 'mesh', mesh_id)
59mesh_dict['vertex_density'] = None
60mesh_dict['fn_mesh_msh'] = os.path.join(mesh_dict['mesh_folder'], f'm2m_{subject_id}', f'{subject_id}.msh')
61mesh_dict['fn_mesh_hdf5'] = os.path.join(mesh_dict['mesh_folder'], f'm2m_{subject_id}', f'{subject_id}.hdf5')
62mesh_dict['fn_tensor_vn'] = None
63mesh_dict['mri_idx'] = 0
64mesh_dict['fn_mri_conform'] = f"m2m_{subject_id}/T1.nii.gz"
65mesh_dict['fn_lh_wm'] = None
66mesh_dict['fn_rh_wm'] = None
67mesh_dict['fn_lh_gm'] = None
68mesh_dict['fn_rh_gm'] = None
69mesh_dict['fn_lh_gm_curv'] = None
70mesh_dict['fn_rh_gm_curv'] = None
71mesh_dict['fn_lh_midlayer'] = f'm2m_{subject_id}/surfaces/lh.central.gii'
72mesh_dict['fn_rh_midlayer'] = f'm2m_{subject_id}/surfaces/rh.central.gii'
73mesh_dict['smooth_skin'] = .8
74mesh_dict['refinement_roi'] = 'midlayer_m1s1pmd'
75mesh_dict['refinemement_element_size'] = 1
76mesh[mesh_id] = mesh_dict
78# roi information (first index: mesh, second index: roi)
79########################################################################################################################
80roi = {}
82# create the same roi for each mesh
83for mesh_id in mesh.keys():
84 roi[mesh_id] = {}
85 roi[mesh_id]['midlayer_m1s1pmd'] = {}
86 roi[mesh_id]['midlayer_m1s1pmd']['type'] = 'surface'
87 roi[mesh_id]['midlayer_m1s1pmd']['info'] = 'freesurfer PMd, M1 and somatosensory cortex'
88 roi[mesh_id]['midlayer_m1s1pmd']['gm_surf_fname'] = mesh[mesh_id]['fn_lh_gm']
89 roi[mesh_id]['midlayer_m1s1pmd']['wm_surf_fname'] = mesh[mesh_id]['fn_lh_wm']
90 roi[mesh_id]['midlayer_m1s1pmd']['midlayer_surf_fname'] = mesh[mesh_id]['fn_lh_midlayer']
91 roi[mesh_id]['midlayer_m1s1pmd']['refine'] = False
92 roi[mesh_id]['midlayer_m1s1pmd']['delta'] = 0.5
93 roi[mesh_id]['midlayer_m1s1pmd']['X_ROI'] = None
94 roi[mesh_id]['midlayer_m1s1pmd']['Y_ROI'] = None
95 roi[mesh_id]['midlayer_m1s1pmd']['Z_ROI'] = None
96 roi[mesh_id]['midlayer_m1s1pmd']['layer'] = 3
97 roi[mesh_id]['midlayer_m1s1pmd']['fn_mask'] = f"roi/midlayer_m1s1pmd/mask_{subject_id}m1pmdss.mgh"
98 roi[mesh_id]['midlayer_m1s1pmd']['fn_mask_avg'] = '/data/pt_01756/masks/lefthandknob_M1S1PMd.overlay'
99 roi[mesh_id]['midlayer_m1s1pmd']['hemisphere'] = "lh"
101# experiment information
102########################################################################################################################
103exp = dict()
104exp["reg_isi_05"] = dict()
105exp["reg_isi_05"]['info'] = ['TMS-MEP M1 Regression study (random sampling), ISI=5']
106exp["reg_isi_05"]['date'] = ['09/04/2021']
107exp["reg_isi_05"]['nnav_system'] = 'Localite'
108exp["reg_isi_05"]['fn_tms_nav'] = [[
109 f'{subject_folder}/exp/reg_isi_05/tms_navigator/Claudia_20210401_15484.08_68a4e7d6/Sessions'
110 f'/Session_20210409134021231/TMSTrigger/TriggerMarkers_Coil1_20210409170817799.xml',
111 '']]
112exp["reg_isi_05"]['fn_data'] = [[f'{subject_folder}/exp/reg_isi_05/mep/tms_mapping_210409_000.mat']]
113exp["reg_isi_05"]['fn_intensity'] = None
114exp["reg_isi_05"]['mep_onsets'] = [[0]]
115exp["reg_isi_05"]['fn_exp_csv'] = [f'{subject_folder}/exp/reg_isi_05/experiment.csv']
116exp["reg_isi_05"]['fn_exp_hdf5'] = [f'{subject_folder}/exp/reg_isi_05/experiment.hdf5']
117exp["reg_isi_05"]['fn_coil'] = [['/data/pt_01756/coils/Magventure MCF-B65/Medtronic_MCF_B65_REF.nii.gz']]
118exp["reg_isi_05"]['fn_mri_nii'] = [[
119 f'{subject_folder}/exp/reg_isi_05/tms_navigator/Claudia_20210401_15484.08_68a4e7d6/BinData/NIFTI'
120 f'/15484.08_T1fs_conform.nii']]
121exp["reg_isi_05"]['cond'] = [[""]]
122exp["reg_isi_05"]['channels'] = ["FDI", "ADM", "APB"]
123exp["reg_isi_05"]['tms_pulse_time'] = 0.3
124exp["reg_isi_05"]['experimenter'] = 'Konstantin Weise'
125exp["reg_isi_05"]['mep_fit_info'] = [""]
126exp["reg_isi_05"]['incidents'] = []
127exp["reg_isi_05"]['postproc'] = [dict()]
128exp["reg_isi_05"]['postproc'][0]['info'] = 'None'
129exp["reg_isi_05"]['postproc'][0]['cmd'] = ' '
131# # add plot settings for c=1/dE of |E| (MEP vs E shift) 21/06/2018
132# ######################################################################################################################
133ps = None
134# save subject information in hdf5 file
135pynibs.save_subject(fname=fn_subject_obj,
136 mri_dict=mri,
137 mesh_dict=mesh,
138 roi_dict=roi,
139 exp_dict=exp,
140 ps_dict=ps,
141 subject_id=subject_id,
142 subject_folder=subject_folder,
143 verbose=False)
145print(f'Created subject .hdf5 file: {fn_subject_obj}')