pyNIBS 0.2024.8__py3-none-any.whl

pynibs/tests/data/brainsight_niiImage_niifticoord_mixedtargets.txt

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+# Version: 12
+# Coordinate system: NIfTI:Scanner
+# Created by: Brainsight 2.4.9
+# Units: millimetres, degrees, milliseconds, and microvolts
+# Encoding: UTF-8
+# Notes: Each column is delimited by a tab. Each value within a column is delimited by a semicolon.
+# Target Name	Loc. X	Loc. Y	Loc. Z	m0n0	m0n1	m0n2	m1n0	m1n1	m1n2	m2n0	m2n1	m2n2
+Grid 1	-30.8428	-5.3267	64.7916	0.6378	-0.7144	0.2877	0.4953	0.6666	0.5571	-0.5898	-0.2128	0.7790
+Grid 2	-31.1844	-14.9263	63.9842	0.7363	-0.6115	0.2896	0.3934	0.7352	0.5521	-0.5505	-0.2926	0.7819
+Grid 3	-30.7333	-24.8329	62.6843	0.8303	-0.4727	0.2951	0.2630	0.7993	0.5403	-0.4913	-0.3710	0.7880
+Grid 4	-30.1749	-34.7806	60.9488	0.9044	-0.2782	0.3234	0.0730	0.8478	0.5253	-0.4203	-0.4515	0.7871
+Grid 5	-29.4729	-44.6629	58.2659	0.9257	-0.1301	0.3552	-0.0774	0.8540	0.5145	-0.3703	-0.5038	0.7804
+Grid 6	-39.0555	-5.2258	59.4733	0.5645	-0.7429	0.3598	0.4771	0.6494	0.5922	-0.6736	-0.1626	0.7210
+Grid 7	-39.9336	-15.0727	59.2835	0.6394	-0.6779	0.3628	0.4046	0.6978	0.5910	-0.6538	-0.2311	0.7205
+Grid 8	-39.6519	-24.8847	58.5993	0.7320	-0.5753	0.3649	0.3014	0.7538	0.5838	-0.6110	-0.3174	0.7252
+Grid 9	-38.7227	-34.8693	56.5547	0.8163	-0.4331	0.3822	0.1573	0.8033	0.5744	-0.5559	-0.4088	0.7238
+Grid 10	-37.2954	-44.3732	53.2071	0.8632	-0.2882	0.4145	0.0031	0.8240	0.5666	-0.5048	-0.4878	0.7122
+Grid 11	-47.1255	-5.2334	53.2950	0.4881	-0.7510	0.4448	0.4363	0.6513	0.6209	-0.7560	-0.1090	0.6455
+Grid 12	-47.0786	-14.9371	52.9875	0.5506	-0.7053	0.4465	0.3774	0.6874	0.6206	-0.7446	-0.1732	0.6447
+Grid 13	-47.2444	-24.7992	51.8260	0.6180	-0.6410	0.4552	0.2969	0.7264	0.6198	-0.7280	-0.2479	0.6393
+Grid 14	-46.3680	-34.6823	50.3981	0.7001	-0.5410	0.4661	0.1833	0.7670	0.6149	-0.6902	-0.3450	0.6361
+Grid 15	-45.1875	-43.6119	48.0059	0.7603	-0.4267	0.4897	0.0512	0.7910	0.6097	-0.6475	-0.4385	0.6233
+Sample 12	-58.9553	-33.2536	34.1801	-0.5251	0.3593	-0.7714	-0.0314	-0.9140	-0.4044	-0.8504	-0.1882	0.4913
+Sample 13	-56.2248	-7.3385	42.9699	-0.6037	0.0452	-0.7959	-0.0186	-0.9989	-0.0427	-0.7970	-0.0110	0.6039
+# Sample Name	Session Name	Index	Assoc. Target	Loc. X	Loc. Y	Loc. Z	m0n0	m0n1	m0n2	m1n0	m1n1	m1n2	m2n0	m2n1	m2n2	Dist. to Target	Target Error	Angular Error	Twist Error	Stim. Power A	Stim. Pulse Interval	Stim. Power B	Date	Time	Creation Cause	Crosshairs Driver	Offset	Comment	EMG Channels	EMG Window Start	EMG Window End
+Sample 1	Session 1	1	Grid 1	-55.1479	6.1262	44.3384	-0.6211	-0.0364	-0.7829	-0.0146	-0.9982	0.0580	-0.7836	0.0475	0.6194	33.7674	33.0508	20.8341	-129.8152	(null)	(null)	(null)	2022-05-04	12:52:28.341	Button	Mouse	0.0000	(null)	(null)	(null)	(null)
+Sample 2	Session 1	2	Grid 1	-63.6209	-23.8103	27.8907	-0.4278	0.3416	-0.8368	-0.0301	-0.9307	-0.3646	-0.9034	-0.1308	0.4085	52.7041	49.9026	28.4977	-151.7541	(null)	(null)	(null)	2022-05-04	12:52:31.431	Button	Mouse	0.0000	(null)	(null)	(null)	(null)
+Sample 3	Session 1	3	Grid 1	-44.6242	30.0542	52.5229	-0.7433	-0.0531	-0.6669	-0.0132	-0.9955	0.0939	-0.6688	0.0786	0.7392	39.9031	39.7955	17.5155	-128.5574	(null)	(null)	(null)	2022-05-04	12:52:33.542	Button	Mouse	0.0000	(null)	(null)	(null)	(null)
+Sample 4	Session 1	4	Grid 3	-35.2757	6.7944	61.7833	-0.8588	-0.0578	-0.5090	-0.0116	-0.9912	0.1321	-0.5121	0.1194	0.8506	31.9645	31.5162	28.6470	-142.9211	(null)	(null)	(null)	2022-05-04	12:52:40.717	Button	Mouse	0.0000	(null)	(null)	(null)	(null)
+Sample 5	Session 1	5	Grid 3	-13.4808	18.3753	70.2118	-0.9549	-0.0136	-0.2965	-0.0134	-0.9960	0.0887	-0.2966	0.0886	0.9509	47.1302	46.7631	30.4431	-150.6771	(null)	(null)	(null)	2022-05-04	12:52:43.158	Button	Mouse	0.0000	(null)	(null)	(null)	(null)
+Sample 6	Session 1	6	Grid 3	-18.4564	55.0287	62.4736	-0.9595	-0.0753	-0.2716	-0.0051	-0.9589	0.2838	-0.2818	0.2737	0.9196	80.7999	78.7226	40.3975	-143.2218	(null)	(null)	(null)	2022-05-04	12:52:54.934	Button	Mouse	0.0000	(null)	(null)	(null)	(null)
+Sample 7	Session 1	7	Grid 3	-32.4728	23.8971	61.7426	-0.8603	-0.0216	-0.5093	-0.0143	-0.9977	0.0665	-0.5096	0.0644	0.8580	48.7701	48.6638	25.5026	-145.8697	(null)	(null)	(null)	2022-05-04	12:52:59.357	Button	Mouse	0.0000	(null)	(null)	(null)	(null)
+Sample 8	Session 1	8	Grid 8	-23.0275	17.9829	66.6807	-0.9408	-0.0111	-0.3388	-0.0141	-0.9973	0.0717	-0.3387	0.0722	0.9381	46.6831	46.4095	30.1882	-145.5609	(null)	(null)	(null)	2022-05-04	12:53:20.086	Button	Mouse	0.0000	(null)	(null)	(null)	(null)
+Sample 9	Session 1	9	Grid 8	-57.1984	-14.2254	41.3910	-0.5961	0.1265	-0.7929	-0.0223	-0.9897	-0.1411	-0.8026	-0.0664	0.5928	26.7886	26.6000	19.7113	-146.7670	(null)	(null)	(null)	2022-05-04	12:53:22.534	Button	Mouse	0.0000	(null)	(null)	(null)	(null)
+Sample 10	Session 1	10	Grid 8	-50.2868	19.9919	49.0658	-0.7051	-0.0108	-0.7091	-0.0157	-0.9994	0.0309	-0.7090	0.0329	0.7045	47.0945	47.0383	20.9906	-139.3842	(null)	(null)	(null)	2022-05-04	12:53:24.742	Button	Mouse	0.0000	(null)	(null)	(null)	(null)
+Sample 11	Session 1	11	Grid 11	-50.2218	-22.8565	49.3190	-0.7086	0.0993	-0.6985	-0.0215	-0.9926	-0.1193	-0.7052	-0.0695	0.7055	18.3294	18.3195	5.0398	-137.1064	(null)	(null)	(null)	2022-05-04	12:53:29.390	Button	Mouse	0.0000	(null)	(null)	(null)	(null)
+Sample 12	Session 1	12	Grid 11	-58.9553	-33.2536	34.1801	-0.5251	0.3593	-0.7714	-0.0314	-0.9140	-0.4044	-0.8504	-0.1882	0.4913	35.9229	35.4280	11.3312	-151.1384	(null)	(null)	(null)	2022-05-04	12:53:32.127	Button	Mouse	0.0000	(null)	(null)	(null)	(null)
+Sample 13	Session 1	13	Grid 11	-56.2248	-7.3385	42.9699	-0.6037	0.0452	-0.7959	-0.0186	-0.9989	-0.0427	-0.7970	-0.0110	0.6039	13.9224	13.8836	6.5408	-133.2619	(null)	(null)	(null)	2022-05-04	12:53:35.327	Button	Mouse	0.0000	(null)	(null)	(null)	(null)
+Sample 14	Session 1	14	Sample 13	-46.7327	8.0539	53.1294	-0.7357	-0.0184	-0.6771	-0.0152	-0.9989	0.0436	-0.6771	0.0424	0.7346	20.7422	20.6734	10.6270	3.4988	(null)	(null)	(null)	2022-05-04	12:57:40.904	Button	Mouse	0.0000	(null)	(null)	(null)	(null)
+Sample 15	Session 1	15	Sample 13	-64.2987	17.5635	28.9303	-0.4324	-0.0517	-0.9002	-0.0144	-0.9978	0.0642	-0.9016	0.0407	0.4307	29.7053	29.6203	11.9835	5.6368	(null)	(null)	(null)	2022-05-04	12:57:43.080	Button	Mouse	0.0000	(null)	(null)	(null)	(null)
+Sample 16	Session 1	16	Sample 13	-53.5237	-38.0805	40.9321	-0.5999	0.3424	-0.7231	-0.0314	-0.9132	-0.4064	-0.7994	-0.2211	0.5586	30.9277	30.7292	12.3387	-17.8797	(null)	(null)	(null)	2022-05-04	12:57:45.816	Button	Mouse	0.0000	(null)	(null)	(null)	(null)
+# Planned Landmark Name	Loc. X	Loc. Y	Loc. Z
+LPA	-75.2492	14.8688	-53.8637
+Nasion	8.8695	102.2740	-14.0720
+RPA	83.5259	10.3013	-61.3207
+# Session Name	Loc. X	Loc. Y	Loc. Z	m0n0	m0n1	m0n2	m1n0	m1n1	m1n2	m2n0	m2n1	m2n2
+Session 1	(null)	(null)	(null)	(null)	(null)	(null)	(null)	(null)	(null)	(null)	(null)	(null)

pynibs/tests/data/create_subject_testsub.py

@@ -0,0 +1,332 @@
+import os
+import numpy as np
+from inspect import getsourcefile
+
+import pynibs
+
+# path of create_subject_XXXXX.py file (has to be in subjects root directoy
+subject_folder = os.path.split(os.path.abspath(getsourcefile(lambda: 0)))[0]
+
+# subject information
+###########################################################################################################
+subject_id = 'testsub'
+fn_subject_obj = subject_folder + f'/{subject_id}.hdf5'
+
+# mri information
+###########################################################################################################
+mri = [dict()]
+
+mri[0]['fn_mri_T1'] = subject_folder + f'/mri/0/original/nifti/t1/2_T1_mprage_iso.nii.gz'
+mri[0]['fn_mri_T2'] = subject_folder + f'/mri/0/original/nifti/t2/5_T2_cube_iso.nii.gz'
+mri[0]['fn_mri_DTI'] = subject_folder + f'/mri/0/original/nifti/dti/7_HB4_diff_64dir_PA0_112.nii.gz'
+mri[0]['fn_mri_DTI_rev'] = subject_folder + f'/mri/0/original/nifti/dti/8_HB4_diff_AP1_slice2.nii.gz'
+mri[0]['fn_mri_DTI_bvec'] = subject_folder + f'/mri/0/original/nifti/dti/7_HB4_diff_64dir_PA0_112.bvec'
+mri[0]['fn_mri_DTI_bval'] = subject_folder + f'/mri/0/original/nifti/dti/7_HB4_diff_64dir_PA0_112.bval'
+mri[0]['dti_readout_time'] = '0.08214'
+mri[0]['dti_phase_direction'] = 'y'
+
+# mesh information
+###########################################################################################################
+mesh = {'charm_refm1_sm': dict(), 'headreco': dict(), 'headreco_refined_m1': dict()}
+
+mesh['charm_refm1_sm']['info'] = 'charm --v 1.0 (simnibs 4.0 beta)'
+mesh['charm_refm1_sm']['approach'] = 'charm'
+mesh['charm_refm1_sm']['mesh_folder'] = os.path.join(subject_folder, 'testsub/mesh', 'charm_refm1_sm')
+mesh['charm_refm1_sm']['vertex_density'] = None
+mesh['charm_refm1_sm']['fn_mesh_msh'] = os.path.join(mesh['charm_refm1_sm']['mesh_folder'], f'm2m_{subject_id}',
+                                                     f'{subject_id}.msh')
+mesh['charm_refm1_sm']['fn_mesh_hdf5'] = os.path.join(mesh['charm_refm1_sm']['mesh_folder'], f'm2m_{subject_id}',
+                                                      f'{subject_id}.hdf5')
+mesh['charm_refm1_sm']['fn_tensor_vn'] = f'm2m_{subject_id}/DTI_coregT1_tensor.nii.gz'
+mesh['charm_refm1_sm']['mri_idx'] = 0
+mesh['charm_refm1_sm']['fn_mri_conform'] = f"m2m_{subject_id}/T1.nii.gz"
+
+mesh['charm_refm1_sm']['fn_lh_wm'] = None
+mesh['charm_refm1_sm']['fn_rh_wm'] = None
+mesh['charm_refm1_sm']['fn_lh_gm'] = None
+mesh['charm_refm1_sm']['fn_rh_gm'] = None
+mesh['charm_refm1_sm']['fn_lh_gm_curv'] = None
+mesh['charm_refm1_sm']['fn_rh_gm_curv'] = None
+mesh['charm_refm1_sm']['fn_lh_midlayer'] = f'm2m_{subject_id}/surfaces/lh.central.gii'
+mesh['charm_refm1_sm']['fn_rh_midlayer'] = f'm2m_{subject_id}/surfaces/rh.central.gii'
+mesh['charm_refm1_sm']['smooth_skin'] = .8
+mesh['charm_refm1_sm']['refinement_roi'] = 'midlayer_m1s1pmd'
+mesh['charm_refm1_sm']['refinemement_element_size'] = 1
+
+mesh['headreco']['info'] = 'headreco --v 1.0 (simnibs 3.1)'
+mesh['headreco']['approach'] = 'headreco'
+mesh['headreco']['mesh_folder'] = os.path.join(subject_folder, 'testsub/mesh', 'headreco')
+mesh['headreco']['vertex_density'] = 1.0
+mesh['headreco']['fn_mesh_msh'] = os.path.join(mesh['headreco']['mesh_folder'], f'{subject_id}.msh')
+mesh['headreco']['fn_mesh_hdf5'] = os.path.join(mesh['headreco']['mesh_folder'], f'{subject_id}.hdf5')
+mesh['headreco']['fn_tensor_vn'] = f'd2c_{subject_id}_PA/CTI_vn_tensor.nii'
+mesh['headreco']['mri_idx'] = 0
+mesh['headreco']['fn_lh_wm'] = None
+mesh['headreco']['fn_rh_wm'] = None
+mesh['headreco']['fn_lh_gm'] = None
+mesh['headreco']['fn_rh_gm'] = None
+mesh['headreco']['fn_lh_gm_curv'] = None
+mesh['headreco']['fn_rh_gm_curv'] = None
+mesh['headreco']['fn_lh_midlayer'] = f'fs_{subject_id}/surf/lh.central'
+mesh['headreco']['fn_rh_midlayer'] = f'fs_{subject_id}/surf/rh.central'
+
+mesh['headreco_refined_m1']['info'] = 'headreco --v 1.0 (simnibs 3.1)'
+mesh['headreco_refined_m1']['approach'] = 'headreco'
+mesh['headreco_refined_m1']['mesh_folder'] = os.path.join(subject_folder, 'testsub/mesh', 'headreco_refined_m1')
+mesh['headreco_refined_m1']['vertex_density'] = 1.0
+mesh['headreco_refined_m1']['center'] = [-41.33, -49.37, 73.78]
+mesh['headreco_refined_m1']['radius'] = 35
+mesh['headreco_refined_m1']['element_size'] = 0.4
+mesh['headreco_refined_m1']['refine_domains'] = ["wm", "gm", "csf"]
+mesh['headreco_refined_m1']['fn_mesh_msh'] = os.path.join(mesh['headreco_refined_m1']['mesh_folder'],
+                                                          f"{subject_id}.msh")
+mesh['headreco_refined_m1']['fn_mesh_hdf5'] = os.path.join(mesh['headreco_refined_m1']['mesh_folder'],
+                                                           f"{subject_id}.hdf5")
+mesh['headreco_refined_m1']['fn_tensor_vn'] = f"d2c_{subject_id}/dti_results_T1space/DTI_conf_tensor.nii.gz"
+mesh['headreco_refined_m1']['mri_idx'] = 0
+mesh['headreco_refined_m1']['fn_mri_conform'] = f"{subject_id}_T1fs_conform.nii.gz"
+mesh['headreco_refined_m1']['smooth_domains'] = ['skin']
+
+mesh['headreco_refined_m1']['fn_lh_wm'] = None
+mesh['headreco_refined_m1']['fn_rh_wm'] = None
+mesh['headreco_refined_m1']['fn_lh_gm'] = None
+mesh['headreco_refined_m1']['fn_rh_gm'] = None
+mesh['headreco_refined_m1']['fn_lh_gm_curv'] = None
+mesh['headreco_refined_m1']['fn_rh_gm_curv'] = None
+mesh['headreco_refined_m1']['fn_lh_midlayer'] = f"fs_{subject_id}/surf/lh.central"
+mesh['headreco_refined_m1']['fn_rh_midlayer'] = f"fs_{subject_id}/surf/rh.central"
+
+# roi information (first index: mesh, second index: roi)
+###########################################################################################################
+roi = {'headreco': {'midlayer_lh_rh': dict(), 'midlayer_m1s1pmd': dict()},
+       'headreco_refined_m1': {'midlayer_lh_rh': dict(), 'midlayer_m1s1pmd': dict(),
+                               'midlayer_m1s1pmd_refined': dict()},
+       'charm_refm1_sm': {'midlayer_lh_rh': dict(), 'midlayer_m1s1pmd': dict()}}
+
+roi['charm_refm1_sm']['midlayer_lh_rh']['type'] = 'surface'
+roi['charm_refm1_sm']['midlayer_lh_rh']['info'] = 'freesurfer lh + rh whole brain midlayer'
+roi['charm_refm1_sm']['midlayer_lh_rh']['gm_surf_fname'] = [mesh['charm_refm1_sm']['fn_lh_gm'],
+                                                            mesh['charm_refm1_sm']['fn_rh_gm']]
+roi['charm_refm1_sm']['midlayer_lh_rh']['wm_surf_fname'] = [mesh['charm_refm1_sm']['fn_lh_wm'],
+                                                            mesh['charm_refm1_sm']['fn_rh_wm']]
+roi['charm_refm1_sm']['midlayer_lh_rh']['midlayer_surf_fname'] = [mesh['charm_refm1_sm']['fn_lh_midlayer'],
+                                                                  mesh['charm_refm1_sm']['fn_rh_midlayer']]
+roi['charm_refm1_sm']['midlayer_lh_rh']['delta'] = 0.5
+roi['charm_refm1_sm']['midlayer_lh_rh']['refine'] = False
+roi['charm_refm1_sm']['midlayer_lh_rh']['X_ROI'] = None
+roi['charm_refm1_sm']['midlayer_lh_rh']['Y_ROI'] = None
+roi['charm_refm1_sm']['midlayer_lh_rh']['Z_ROI'] = None
+roi['charm_refm1_sm']['midlayer_lh_rh']['layer'] = 3
+roi['charm_refm1_sm']['midlayer_lh_rh']['fn_mask'] = None
+roi['charm_refm1_sm']['midlayer_lh_rh']['fn_mask_avg'] = None
+
+roi['charm_refm1_sm']['midlayer_m1s1pmd']['type'] = 'surface'
+roi['charm_refm1_sm']['midlayer_m1s1pmd']['info'] = 'freesurfer PMd, M1 and somatosensory cortex'
+roi['charm_refm1_sm']['midlayer_m1s1pmd']['gm_surf_fname'] = mesh['charm_refm1_sm']['fn_lh_gm']
+roi['charm_refm1_sm']['midlayer_m1s1pmd']['wm_surf_fname'] = mesh['charm_refm1_sm']['fn_lh_wm']
+roi['charm_refm1_sm']['midlayer_m1s1pmd']['midlayer_surf_fname'] = mesh['charm_refm1_sm']['fn_lh_midlayer']
+roi['charm_refm1_sm']['midlayer_m1s1pmd']['delta'] = 0.5
+roi['charm_refm1_sm']['midlayer_m1s1pmd']['refine'] = False
+roi['charm_refm1_sm']['midlayer_m1s1pmd']['X_ROI'] = None
+roi['charm_refm1_sm']['midlayer_m1s1pmd']['Y_ROI'] = None
+roi['charm_refm1_sm']['midlayer_m1s1pmd']['Z_ROI'] = None
+roi['charm_refm1_sm']['midlayer_m1s1pmd']['layer'] = 3
+roi['charm_refm1_sm']['midlayer_m1s1pmd']['fn_mask'] = f"roi/midlayer_m1s1pmd/mask_{subject_id}m1pmdss.mgh"
+roi['charm_refm1_sm']['midlayer_m1s1pmd']['fn_mask_avg'] = '/lefthandknob_M1S1PMd.overlay'
+roi['charm_refm1_sm']['midlayer_m1s1pmd']['hemisphere'] = "lh"
+
+roi['headreco']['midlayer_lh_rh']['type'] = 'surface'
+roi['headreco']['midlayer_lh_rh']['info'] = 'freesurfer lh + rh whole brain midlayer'
+roi['headreco']['midlayer_lh_rh']['gm_surf_fname'] = [mesh['headreco']['fn_lh_gm'], mesh['headreco']['fn_rh_gm']]
+roi['headreco']['midlayer_lh_rh']['wm_surf_fname'] = [mesh['headreco']['fn_lh_wm'], mesh['headreco']['fn_rh_wm']]
+roi['headreco']['midlayer_lh_rh']['midlayer_surf_fname'] = [mesh['headreco']['fn_lh_midlayer'],
+                                                            mesh['headreco']['fn_rh_midlayer']]
+roi['headreco']['midlayer_lh_rh']['delta'] = 0.5
+roi['headreco']['midlayer_lh_rh']['refine'] = False
+roi['headreco']['midlayer_lh_rh']['X_ROI'] = None
+roi['headreco']['midlayer_lh_rh']['Y_ROI'] = None
+roi['headreco']['midlayer_lh_rh']['Z_ROI'] = None
+roi['headreco']['midlayer_lh_rh']['layer'] = 3
+roi['headreco']['midlayer_lh_rh']['fn_mask'] = None
+roi['headreco']['midlayer_lh_rh']['fn_mask_avg'] = None
+
+roi['headreco']['midlayer_m1s1pmd']['type'] = 'surface'
+roi['headreco']['midlayer_m1s1pmd']['info'] = 'freesurfer PMd, M1 and somatosensory cortex'
+roi['headreco']['midlayer_m1s1pmd']['gm_surf_fname'] = mesh['headreco']['fn_lh_gm']
+roi['headreco']['midlayer_m1s1pmd']['wm_surf_fname'] = mesh['headreco']['fn_lh_wm']
+roi['headreco']['midlayer_m1s1pmd']['midlayer_surf_fname'] = mesh['headreco']['fn_lh_midlayer']
+roi['headreco']['midlayer_m1s1pmd']['delta'] = 0.5
+roi['headreco']['midlayer_m1s1pmd']['refine'] = False
+roi['headreco']['midlayer_m1s1pmd']['X_ROI'] = None
+roi['headreco']['midlayer_m1s1pmd']['Y_ROI'] = None
+roi['headreco']['midlayer_m1s1pmd']['Z_ROI'] = None
+roi['headreco']['midlayer_m1s1pmd']['layer'] = 3
+roi['headreco']['midlayer_m1s1pmd']['fn_mask'] = f"roi/midlayer_m1s1pmd/mask_{subject_id}m1pmdss.mgh"
+roi['headreco']['midlayer_m1s1pmd']['fn_mask_avg'] = '/masks/lefthandknob_M1S1PMd.overlay'
+roi['headreco']['midlayer_m1s1pmd']['hemisphere'] = "lh"
+
+roi_id = 'midlayer_lh_rh'
+roi['headreco_refined_m1'][roi_id]['type'] = 'surface'
+roi['headreco_refined_m1'][roi_id]['info'] = 'freesurfer lh + rh whole brain midlayer'
+roi['headreco_refined_m1'][roi_id]['gm_surf_fname'] = [mesh['headreco_refined_m1']['fn_lh_gm'],
+                                                       mesh['headreco_refined_m1']['fn_rh_gm']]
+roi['headreco_refined_m1'][roi_id]['wm_surf_fname'] = [mesh['headreco_refined_m1']['fn_lh_wm'],
+                                                       mesh['headreco_refined_m1']['fn_rh_wm']]
+roi['headreco_refined_m1'][roi_id]['midlayer_surf_fname'] = [mesh['headreco_refined_m1']['fn_lh_midlayer'],
+                                                             mesh['headreco_refined_m1']['fn_rh_midlayer']]
+roi['headreco_refined_m1'][roi_id]['refine'] = False
+roi['headreco_refined_m1'][roi_id]['delta'] = 0.5
+roi['headreco_refined_m1'][roi_id]['X_ROI'] = None
+roi['headreco_refined_m1'][roi_id]['Y_ROI'] = None
+roi['headreco_refined_m1'][roi_id]['Z_ROI'] = None
+roi['headreco_refined_m1'][roi_id]['layer'] = 3
+roi['headreco_refined_m1'][roi_id]['fn_mask'] = None
+roi['headreco_refined_m1'][roi_id]['fn_mask_avg'] = None
+
+roi_id = 'midlayer_m1s1pmd'
+roi['headreco_refined_m1'][roi_id]['type'] = 'surface'
+roi['headreco_refined_m1'][roi_id]['info'] = 'freesurfer PMd, M1 and somatosensory cortex'
+roi['headreco_refined_m1'][roi_id]['gm_surf_fname'] = mesh['headreco_refined_m1']['fn_lh_gm']
+roi['headreco_refined_m1'][roi_id]['wm_surf_fname'] = mesh['headreco_refined_m1']['fn_lh_wm']
+roi['headreco_refined_m1'][roi_id]['midlayer_surf_fname'] = mesh['headreco_refined_m1']['fn_lh_midlayer']
+roi['headreco_refined_m1'][roi_id]['refine'] = False
+roi['headreco_refined_m1'][roi_id]['delta'] = 0.5
+roi['headreco_refined_m1'][roi_id]['X_ROI'] = None
+roi['headreco_refined_m1'][roi_id]['Y_ROI'] = None
+roi['headreco_refined_m1'][roi_id]['Z_ROI'] = None
+roi['headreco_refined_m1'][roi_id]['layer'] = 3
+roi['headreco_refined_m1'][roi_id]['fn_mask'] = f"roi/midlayer_m1s1pmd/mask_{subject_id}m1pmdss.mgh"
+roi['headreco_refined_m1'][roi_id]['fn_mask_avg'] = '//masks/lefthandknob_M1S1PMd.overlay'
+roi['headreco_refined_m1'][roi_id]['hemisphere'] = "lh"
+
+roi_id = 'midlayer_m1s1pmd_refined'
+roi['headreco_refined_m1'][roi_id]['type'] = 'surface'
+roi['headreco_refined_m1'][roi_id]['info'] = 'freesurfer PMd, M1 and somatosensory cortex'
+roi['headreco_refined_m1'][roi_id]['gm_surf_fname'] = mesh['headreco_refined_m1']['fn_lh_gm']
+roi['headreco_refined_m1'][roi_id]['wm_surf_fname'] = mesh['headreco_refined_m1']['fn_lh_wm']
+roi['headreco_refined_m1'][roi_id]['midlayer_surf_fname'] = mesh['headreco_refined_m1']['fn_lh_midlayer']
+roi['headreco_refined_m1'][roi_id]['refine'] = True
+roi['headreco_refined_m1'][roi_id]['delta'] = 0.5
+roi['headreco_refined_m1'][roi_id]['X_ROI'] = None
+roi['headreco_refined_m1'][roi_id]['Y_ROI'] = None
+roi['headreco_refined_m1'][roi_id]['Z_ROI'] = None
+roi['headreco_refined_m1'][roi_id]['layer'] = 3
+roi['headreco_refined_m1'][roi_id]['fn_mask'] = f"roi/midlayer_m1s1pmd/mask_{subject_id}m1pmdss.mgh"
+roi['headreco_refined_m1'][roi_id]['fn_mask_avg'] = '//masks/lefthandknob_M1S1PMd.overlay'
+roi['headreco_refined_m1'][roi_id]['hemisphere'] = "lh"
+
+# experiment information
+###########################################################################################################
+exp = {'TMS_localite': dict(), 'TMS_ant': dict(), 'TMS_brainsight': dict()}
+
+exp['TMS_localite']['info'] = ['TMS-MEP template Localite (MPI)']
+exp['TMS_localite']['date'] = ['XX/XX/20XX']
+exp['TMS_localite']['nnav_system'] = 'Localite'
+exp['TMS_localite']['fn_tms_nav'] = [[subject_folder + '...xml', subject_folder + '...xml']]
+exp['TMS_localite']['fn_data'] = [[subject_folder + '/exp/0/mep/...cfs']]
+exp['TMS_localite']['fn_intensity'] = None
+exp['TMS_localite']['mep_onsets'] = [[0]]
+exp['TMS_localite']['fn_exp_csv'] = [subject_folder + '/exp/0/experiment.csv']
+exp['TMS_localite']['fn_exp_hdf5'] = [subject_folder + '/exp/0/experiment.hdf5']
+exp['TMS_localite']['fn_coil'] = [['.../MagStim_Alpha_Coil_70mm_Fig8.nii.gz']]
+exp['TMS_localite']['fn_mri_nii'] = [[subject_folder + '/exp/0/..._conform.nii']]
+exp['TMS_localite']['cond'] = [['']]
+exp['TMS_localite']['tms_pulse_time'] = None
+exp['TMS_localite']['experimenter'] = ''
+exp['TMS_localite']['mep_fit_info'] = ['']
+exp['TMS_localite']['incidents'] = ['']
+exp['TMS_localite']['postproc'] = [dict()]
+exp['TMS_localite']['postproc'][0]['info'] = ' '
+exp['TMS_localite']['postproc'][0]['cmd'] = ' '
+
+exp['TMS_ant']['info'] = ['TMS-MEP-EEG template (ANT)']
+exp['TMS_ant']['date'] = ['XX/XX/20XX']
+exp['TMS_ant']['nnav_system'] = 'Visor'
+exp['TMS_ant']['fn_data'] = [[subject_folder + '/exp/2/...cnt']]
+exp['TMS_ant']['fn_exp_hdf5'] = [subject_folder + '/exp/2/experiment.hdf5']
+exp['TMS_ant']['fn_coil'] = [['.../MagStim_Alpha_Coil_70mm_Fig8.nii.gz']]
+exp['TMS_ant']['fn_mri_nii'] = [[subject_folder + '/exp/2/..._conform.nii']]
+exp['TMS_ant']['fn_visor_cnt'] = [subject_folder + '/exp/2/...pos.cnt']
+exp['TMS_ant']['fn_visor_calibration'] = [subject_folder + '/exp/2/...calibration.xml']
+exp['TMS_ant']['fn_eeg_cnt'] = [subject_folder + '/exp/2/eeg/...cnt']
+exp['TMS_ant']['eeg_channels'] = ['all']
+exp['TMS_ant']['fn_emg_cnt'] = [subject_folder + '/exp/2/emg/...cnt']
+exp['TMS_ant']['emg_channels'] = [0]
+exp['TMS_ant']['emg_max_duration'] = [10]
+exp['TMS_ant']['eeg_max_duration'] = [10]
+exp['TMS_ant']['emg_trigger_value'] = ['4']
+exp['TMS_ant']['eeg_trigger_value'] = ['1']
+exp['TMS_ant']['cond'] = [['M1_random']]
+exp['TMS_ant']['tms_pulse_time'] = None
+exp['TMS_ant']['experimenter'] = ' '
+exp['TMS_ant']['mep_fit_info'] = [' ']
+exp['TMS_ant']['incidents'] = [' ']
+exp['TMS_ant']['fiducal_corr'] = [[0, 0, 0]]  # x,y,z in mm
+
+exp['TMS_brainsight']['info'] = ['TMS-MEP-EEG template (Brainsight)']
+exp['TMS_brainsight']['date'] = ['09/03/20222']
+exp['TMS_brainsight']['nnav_system'] = 'Brainsight'
+exp['TMS_brainsight']['fn_data'] = [subject_folder + '/Data_testsub.txt']
+exp['TMS_brainsight']['fn_exp_hdf5'] = [subject_folder + '/exp/random/experiment.hdf5']
+exp['TMS_brainsight']['fn_coil'] = [['.../Magstim_D70_AFC_force_sensor.ccd.nii.gz']]
+exp['TMS_brainsight']['fn_mri_nii'] = [[subject_folder + '/exp/random/testsub_T1.nii.gz']]
+exp['TMS_brainsight']['cond'] = [['M1_random']]
+exp['TMS_brainsight']['tms_pulse_time'] = None
+exp['TMS_brainsight']['experimenter'] = 'Zijian'
+exp['TMS_brainsight']['mep_fit_info'] = [' ']
+exp['TMS_brainsight']['incidents'] = [' ']
+exp['TMS_brainsight']['fiducal_corr'] = [[0, 0, 0]]  # x,y,z in mm
+
+# add plot settings
+###########################################################################################################
+ps = []
+
+ps.append(pynibs.create_plot_settings_dict(plotfunction_type='surface_vector_plot'))
+ps[0]['info'] = ' '
+ps[0]['plot_function'] = 'surface_vector_plot'
+ps[0]['fname_in'] = '..._data.xdmf'
+ps[0]['fname_png'] = '...png'
+ps[0]['png_resolution'] = 1.0
+ps[0]['quantity'] = [' ']
+ps[0]['vlabels'] = None
+ps[0]['vscales'] = None
+ps[0]['datarange'] = [None, None]
+ps[0]['domain_label'] = 'tissue_type'
+ps[0]['domain_IDs'] = 0
+ps[0]['colorbar_label'] = ' '
+ps[0]['colorbar_position'] = [0.45, -0.05]
+ps[0]['colorbar_orientation'] = 'Horizontal'
+ps[0]['colorbar_aspectratio'] = 20
+ps[0]['colorbar_titlefontsize'] = 12
+ps[0]['colorbar_labelfontsize'] = 12
+ps[0]['colorbar_labelformat'] = '%-#6.1f'
+ps[0]['colorbar_numberoflabels'] = 5
+ps[0]['colorbar_labelcolor'] = [0, 0, 0]
+ps[0]['view'] = [[-332.040630013204, -16.8948837495393, 256.721941018442],
+                 [-35.3111635316966, -13.6999528376981, 36.4196465112876],
+                 [0.588834647614276, -0.167617710066906, 0.790682022712606],
+                 [30, 0, 0]]
+ps[0]['interpolate'] = True
+ps[0]['edges'] = False
+ps[0]['axes'] = False
+ps[0]['colormap'] = 'Rainbow Blended White'
+ps[0]['opacitymap'] = None
+ps[0]['vscale_mode'] = ['off']
+ps[0]['vector_mode'] = {'Every Nth Point': 10}
+ps[0]['vcolor'] = None
+ps[0]['background_color'] = np.array([1, 1, 1])
+ps[0]['viewsize'] = np.array([1000, 1000])
+
+# save subject information in .hdf5 file
+###########################################################################################################
+pynibs.save_subject_hdf5(fname=fn_subject_obj,
+                         mri_dict=mri,
+                         mesh_dict=mesh,
+                         roi_dict=roi,
+                         exp_dict=exp,
+                         ps_dict=ps,
+                         subject_id=subject_id,
+                         subject_folder=subject_folder
+                         )
+
+print(f'Created subject .hdf5 file: {fn_subject_obj}')