py-neuromodulation 0.0.3__py3-none-any.whl → 0.0.4__py3-none-any.whl

py_neuromodulation/ConnectivityDecoding/_get_grid_hull.m

@@ -0,0 +1,34 @@
+addpath('C:\code\wjn_toolbox');
+addpath(genpath('C:\code\leaddbs'));
+addpath(genpath('C:\code\spm12'));
+
+
+%%
+ctx = wjn_mni_cortex();
+downsample_ctx=ctx.vertices(1:20:end,:); %downsample by 10
+
+save("downsampled_cortex.mat", "downsample_ctx")
+
+figure;
+scatter3(downsample_ctx(:,1), downsample_ctx(:,2), downsample_ctx(:,3), 'filled');
+title('3D Scatter Plot Example');
+xlabel('X-axis');
+ylabel('Y-axis');
+zlabel('Z-axis');
+grid on;
+
+
+
+PATH_OUT = "D:\Connectome_RMAP_OUT\ROIs";
+
+for a =1:size(downsample_ctx,1)
+    disp(a)
+    roiname  = fullfile(PATH_OUT, strcat('ROI-', string(a), '.nii'));
+    mni = [downsample_ctx(a, 1) downsample_ctx(a, 2) downsample_ctx(a, 3)];
+    wjn_spherical_roi(roiname,mni,4);
+end
+
+
+
+
+

py_neuromodulation/ConnectivityDecoding/_get_grid_whole_brain.py

@@ -0,0 +1,106 @@
+import nibabel as nib
+import numpy as np
+import scipy.io as sio
+import os
+from matplotlib import pyplot as plt
+
+
+class NiiToMNI:
+
+    def __init__(
+        self,
+        PATH_nii_file: str = r"C:\code\RMap_ROI_Estimation\Automated Anatomical Labeling 3 (Rolls 2020).nii",
+    ) -> None:
+
+        self.img = nib.load(PATH_nii_file)
+        self.data = self.img.get_fdata()
+
+    def downsample_nii(
+        self,
+        resampling_factor: int = 150,
+    ):
+
+        # PATH_MNI_TO_ATLAS = r"C:\code\mni_to_atlas\src\mni_to_atlas\atlases\AAL.nii"
+        # img_mni_to_atlas = nib.load(PATH_MNI_TO_ATLAS)
+
+        x_dim, y_dim, z_dim = self.data.shape
+
+        # Create arrays of voxel coordinates
+        x_coords, y_coords, z_coords = np.meshgrid(
+            range(x_dim), range(y_dim), range(z_dim), indexing="ij"
+        )
+
+        # Downsample here the voxels --> check lateron if the voxels have non-zero values
+        x_c_flatten = x_coords.flatten()[::resampling_factor]
+        y_c_flatten = y_coords.flatten()[::resampling_factor]
+        z_c_flatten = z_coords.flatten()[::resampling_factor]
+
+        # Combine coordinates into a single array
+        voxel_coordinates = np.column_stack(
+            (
+                x_c_flatten,
+                y_c_flatten,
+                z_c_flatten,
+                np.ones(x_c_flatten.shape[0]),
+            )
+        )
+
+        aff_m = self.img.affine
+        aff_m[0, 0] = 2
+        aff_m[0, 3] = -90
+
+        mni_coordinates = np.dot(aff_m, voxel_coordinates.T).T[:, :3]
+
+        return mni_coordinates
+
+    def select_non_zero_voxels(
+        self,
+        mni_coordinates: np.array,
+    ):
+
+        coords = np.hstack(
+            (mni_coordinates, np.ones((mni_coordinates.shape[0], 1)))
+        )
+
+        # and transform back to get the voxel values
+        voxels_downsampled = np.array(
+            np.linalg.solve(self.img.affine, coords.T).T
+        ).astype(int)[:, :3]
+
+        ival = []
+        coord_ = []
+        for i in range(voxels_downsampled.shape[0]):
+            ival.append(self.data[tuple(voxels_downsampled[i, :])])
+            coord_.append(mni_coordinates[i, :])
+
+        # get only voxel values non-zero
+        ival = np.array(ival)
+        coord_ = np.array(coord_)
+        ival_non_zero = ival[ival != 0]
+        coord_non_zero = coord_[ival != 0]
+        print(coord_non_zero.shape)
+
+        return coord_non_zero, ival_non_zero
+
+    def plot_3d_coordinates(self, coord_non_zero: np.array):
+        fig = plt.figure()
+        ax = fig.add_subplot(111, projection="3d")
+        ax.scatter(
+            coord_non_zero[:, 0],
+            coord_non_zero[:, 1],
+            coord_non_zero[:, 2],
+            s=50,
+            alpha=0.2,
+        )
+        plt.show()
+
+
+if __name__ == "__main__":
+
+    nii_to_mni = NiiToMNI(
+        PATH_nii_file=r"C:\code\py_neuromodulation\ConnectivityDecoding\Automated Anatomical Labeling 3 (Rolls 2020).nii"
+    )
+    mni_coordinates = nii_to_mni.downsample_nii(resampling_factor=150)
+    coord_non_zero, ival_non_zero = nii_to_mni.select_non_zero_voxels(
+        mni_coordinates
+    )

py_neuromodulation/ConnectivityDecoding/_helper_write_connectome.py

@@ -0,0 +1,119 @@
+import nibabel as nib
+import numpy as np
+import scipy.io as sio
+import os
+from matplotlib import pyplot as plt
+
+
+def write_connectome_mat(
+    PATH_Fingerprints: str = r"D:\Connectome_RMAP_OUT\ROIs\HCP1000 6K",
+    PATH_CONNECTOME: str = os.path.join(
+        "py_neuromodulation",
+        "ConnectivityDecoding",
+        "connectome_struct.mat",
+    ),
+    func_: bool = False,
+):
+
+    # connectome = sio.loadmat(PATH_CONNECTOME)  # check if read was successful
+
+    # load all fingerprints and put them in .npy
+    dict_connectome = {}
+    if func_ is False:
+        files_fps = [f for f in os.listdir(PATH_Fingerprints) if ".nii" in f]
+    else:
+        files_fps = [
+            f
+            for f in os.listdir(PATH_Fingerprints)
+            if "func_seed_AvgR_Fz.nii" in f
+        ]
+
+    # I except 1025 files, check which ones are missing
+    missing_files = []
+
+    for i in range(1, 1026):
+
+        MISSING = False
+
+        if func_ is False:
+            if f"ROI-{i}_struc_seed.nii" not in files_fps:
+                missing_files.append(f"ROI-{i}_struc_seed.nii")
+                MISSING = True
+        else:
+            if f"ROI-{i}_func_seed_AvgR_Fz.nii" not in files_fps:
+                missing_files.append(f"ROI-{i}_func_seed_AvgR_Fz.nii")
+                MISSING = True
+
+        if MISSING:
+            ROI_file = os.path.join(
+                r"D:\Connectome_RMAP_OUT\whole_brain\ROIs", f"ROI-{i}.nii"
+            )
+            # copy the ROI file to the following folder:
+            PATH_ROI_OUT = (
+                r"D:\Connectome_RMAP_OUT\whole_brain\ROI_missing_struc"
+            )
+            import shutil
+
+            shutil.copy(ROI_file, os.path.join(PATH_ROI_OUT, f"ROI-{i}.nii"))
+
+    for idx, f in enumerate(files_fps):
+        # load the .nii file and put it all in in a dictionary with the name of the file
+        fp = (
+            nib.load(os.path.join(PATH_Fingerprints, f))
+            .get_fdata()
+            .astype(np.float16)
+        )
+        if "struc" in f:
+            dict_connectome[f[f.find("ROI-") + 4 : f.find("_struc")]] = fp
+        else:
+            dict_connectome[
+                f[f.find("ROI-") + 4 : f.find("_func_seed_AvgR_Fz.nii")]
+            ] = fp
+
+        print(idx)
+    # save the dictionary
+    sio.savemat(
+        PATH_CONNECTOME,
+        dict_connectome,
+    )
+
+
+if __name__ == "__main__":
+
+    write_connectome_mat(
+        PATH_Fingerprints=r"D:\Connectome_RMAP_OUT\whole_brain\struc\HCP1000 6K",
+        PATH_CONNECTOME=os.path.join(
+            "py_neuromodulation",
+            "ConnectivityDecoding",
+            "connectome_whole_brain_struc.mat",
+        ),
+    )  # 58 files are missing
+
+    write_connectome_mat(
+        PATH_Fingerprints=r"D:\Connectome_RMAP_OUT\whole_brain\func",
+        PATH_CONNECTOME=os.path.join(
+            "py_neuromodulation",
+            "ConnectivityDecoding",
+            "connectome_whole_brain_func.mat",
+        ),
+        func_=True,
+    )
+
+    write_connectome_mat(
+        PATH_Fingerprints=r"D:\Connectome_RMAP_OUT\hull\func\GSP 1000 (Yeo 2011)_Full Set (Yeo 2011)",
+        PATH_CONNECTOME=os.path.join(
+            "py_neuromodulation",
+            "ConnectivityDecoding",
+            "connectome_hull_func.mat",
+        ),
+        func_=True,
+    )  # all there
+
+    write_connectome_mat(
+        PATH_Fingerprints=r"D:\Connectome_RMAP_OUT\hull\struc\HCP1000 6K",
+        PATH_CONNECTOME=os.path.join(
+            "py_neuromodulation",
+            "ConnectivityDecoding",
+            "connectome_hull_struc.mat",
+        ),
+    )  # 5 missing

py_neuromodulation/data/README

@@ -0,0 +1,6 @@
+References
+----------
+Appelhoff, S., Sanderson, M., Brooks, T., Vliet, M., Quentin, R., Holdgraf, C., Chaumon, M., Mikulan, E., Tavabi, K., Höchenberger, R., Welke, D., Brunner, C., Rockhill, A., Larson, E., Gramfort, A. and Jas, M. (2019). MNE-BIDS: Organizing electrophysiological data into the BIDS format and facilitating their analysis. Journal of Open Source Software 4: (1896). https://doi.org/10.21105/joss.01896
+
+Holdgraf, C., Appelhoff, S., Bickel, S., Bouchard, K., D'Ambrosio, S., David, O., … Hermes, D. (2019). iEEG-BIDS, extending the Brain Imaging Data Structure specification to human intracranial electrophysiology. Scientific Data, 6, 102. https://doi.org/10.1038/s41597-019-0105-7
+

py_neuromodulation/data/dataset_description.json

@@ -0,0 +1,8 @@
+{
+    "Name": " ",
+    "BIDSVersion": "1.7.0",
+    "DatasetType": "raw",
+    "Authors": [
+        "[Unspecified]"
+    ]
+}

py_neuromodulation/data/participants.json

@@ -0,0 +1,32 @@
+{
+    "participant_id": {
+        "Description": "Unique participant identifier"
+    },
+    "age": {
+        "Description": "Age of the participant at time of testing",
+        "Units": "years"
+    },
+    "sex": {
+        "Description": "Biological sex of the participant",
+        "Levels": {
+            "F": "female",
+            "M": "male"
+        }
+    },
+    "hand": {
+        "Description": "Handedness of the participant",
+        "Levels": {
+            "R": "right",
+            "L": "left",
+            "A": "ambidextrous"
+        }
+    },
+    "weight": {
+        "Description": "Body weight of the participant",
+        "Units": "kg"
+    },
+    "height": {
+        "Description": "Body height of the participant",
+        "Units": "m"
+    }
+}

py_neuromodulation/data/participants.tsv

@@ -0,0 +1,2 @@
+participant_id	age	sex	hand	weight	height
+sub-testsub	n/a	n/a	n/a	n/a	n/a

py_neuromodulation/data/sub-testsub/ses-EphysMedOff/ieeg/sub-testsub_ses-EphysMedOff_space-mni_coordsystem.json

@@ -0,0 +1,5 @@
+{
+    "iEEGCoordinateSystem": "Other",
+    "iEEGCoordinateSystemDescription": "n/a",
+    "iEEGCoordinateUnits": "m"
+}

py_neuromodulation/data/sub-testsub/ses-EphysMedOff/ieeg/sub-testsub_ses-EphysMedOff_space-mni_electrodes.tsv

@@ -0,0 +1,11 @@
+name	x	y	z	size	impedance
+LFP_RIGHT_0	0.0118280802308701	-0.0151597482742092	-0.00776909845640809	n/a	n/a
+LFP_RIGHT_1	0.0123908351968705	-0.0142925082817827	-0.0059367986990887	n/a	n/a
+LFP_RIGHT_2	0.012930849148285701	-0.0134128499400548	-0.00409165661961333	n/a	n/a
+ECOG_RIGHT_0	0.037318173999999996	-0.048610126639999994	0.06179765474	n/a	n/a
+ECOG_RIGHT_1	0.0401598943	-0.037315929830000004	0.06431171618	n/a	n/a
+ECOG_RIGHT_2	0.040943035780000005	-0.02721778456	0.06409518407999999	n/a	n/a
+ECOG_RIGHT_3	0.03978395522	-0.01700523081	0.06386618136	n/a	n/a
+ECOG_RIGHT_4	0.03968813641	-0.005528024572	0.06168254254	n/a	n/a
+ECOG_RIGHT_5	0.03751915924	0.004304913414	0.060541263549999995	n/a	n/a
+MOV_RIGHT	n/a	n/a	n/a	n/a	n/a

py_neuromodulation/data/sub-testsub/ses-EphysMedOff/ieeg/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_channels.tsv

@@ -0,0 +1,11 @@
+name	type	units	low_cutoff	high_cutoff	description	sampling_frequency	status	status_description
+LFP_RIGHT_0	DBS	µV	0.0	500.0	Deep Brain Stimulation	1000.0	good	n/a
+LFP_RIGHT_1	DBS	µV	0.0	500.0	Deep Brain Stimulation	1000.0	good	n/a
+LFP_RIGHT_2	DBS	µV	0.0	500.0	Deep Brain Stimulation	1000.0	good	n/a
+ECOG_RIGHT_0	ECOG	µV	0.0	500.0	Electrocorticography	1000.0	good	n/a
+ECOG_RIGHT_1	ECOG	µV	0.0	500.0	Electrocorticography	1000.0	good	n/a
+ECOG_RIGHT_2	ECOG	µV	0.0	500.0	Electrocorticography	1000.0	good	n/a
+ECOG_RIGHT_3	ECOG	µV	0.0	500.0	Electrocorticography	1000.0	good	n/a
+ECOG_RIGHT_4	ECOG	µV	0.0	500.0	Electrocorticography	1000.0	good	n/a
+ECOG_RIGHT_5	ECOG	µV	0.0	500.0	Electrocorticography	1000.0	good	n/a
+MOV_RIGHT	MISC	µV	0.0	500.0	Miscellaneous	1000.0	good	n/a

py_neuromodulation/data/sub-testsub/ses-EphysMedOff/ieeg/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_ieeg.json

@@ -0,0 +1,18 @@
+{
+    "TaskName": "gripforce",
+    "Manufacturer": "Brain Products",
+    "PowerLineFrequency": 60.0,
+    "SamplingFrequency": 1000.0,
+    "SoftwareFilters": "n/a",
+    "RecordingDuration": 19.0,
+    "RecordingType": "continuous",
+    "iEEGReference": "n/a",
+    "ECOGChannelCount": 6,
+    "SEEGChannelCount": 3,
+    "EEGChannelCount": 0,
+    "EOGChannelCount": 0,
+    "ECGChannelCount": 0,
+    "EMGChannelCount": 0,
+    "MiscChannelCount": 1,
+    "TriggerChannelCount": 0
+}

py_neuromodulation/data/sub-testsub/ses-EphysMedOff/ieeg/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_ieeg.vhdr

@@ -0,0 +1,35 @@
+Brain Vision Data Exchange Header File Version 1.0
+; Written using pybv 0.7.5
+
+[Common Infos]
+Codepage=UTF-8
+DataFile=sub-testsub_ses-EphysMedOff_task-gripforce_run-0_ieeg.eeg
+MarkerFile=sub-testsub_ses-EphysMedOff_task-gripforce_run-0_ieeg.vmrk
+DataFormat=BINARY
+; Data orientation: MULTIPLEXED=ch1,pt1, ch2,pt1 ...
+DataOrientation=MULTIPLEXED
+NumberOfChannels=10
+; Sampling interval in microseconds
+SamplingInterval=1000.0
+
+[Binary Infos]
+BinaryFormat=IEEE_FLOAT_32
+
+[Channel Infos]
+; Each entry: Ch<Channel number>=<Name>,<Reference channel name>,
+; <Resolution in "Unit">,<Unit>, Future extensions..
+; Fields are delimited by commas, some fields might be omitted (empty).
+; Commas in channel names are coded as "\1".
+Ch1=LFP_RIGHT_0,,0.1,µV
+Ch2=LFP_RIGHT_1,,0.1,µV
+Ch3=LFP_RIGHT_2,,0.1,µV
+Ch4=ECOG_RIGHT_0,,0.1,µV
+Ch5=ECOG_RIGHT_1,,0.1,µV
+Ch6=ECOG_RIGHT_2,,0.1,µV
+Ch7=ECOG_RIGHT_3,,0.1,µV
+Ch8=ECOG_RIGHT_4,,0.1,µV
+Ch9=ECOG_RIGHT_5,,0.1,µV
+Ch10=MOV_RIGHT,,0.1,µV
+
+[Comment]
+

py_neuromodulation/data/sub-testsub/ses-EphysMedOff/ieeg/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_ieeg.vmrk

@@ -0,0 +1,13 @@
+Brain Vision Data Exchange Marker File, Version 1.0
+; Exported using pybv 0.7.5
+
+[Common Infos]
+Codepage=UTF-8
+DataFile=sub-testsub_ses-EphysMedOff_task-gripforce_run-0_ieeg.eeg
+
+[Marker Infos]
+; Each entry: Mk<Marker number>=<Type>,<Description>,<Position in data points>,
+;             <Size in data points>, <Channel number (0 = marker is related to all channels)>
+;             <Date (YYYYMMDDhhmmssuuuuuu)>
+; Fields are delimited by commas, some fields might be omitted (empty).
+; Commas in type or description text are coded as "\1".

py_neuromodulation/data/sub-testsub/ses-EphysMedOff/sub-testsub_ses-EphysMedOff_scans.tsv

@@ -0,0 +1,2 @@
+filename	acq_time
+ieeg/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_ieeg.vhdr	n/a

py_neuromodulation/grid_cortex.tsv

@@ -0,0 +1,40 @@
+x	y	z
+-13.1	-67.7	69.1
+-35.5	-60.0	66.0
+-48.3	-55.1	58.2
+-60.0	-51.8	48.0
+-16.9	-51.6	78.0
+-34.8	-49.3	71.7
+-67.5	-47.1	31.0
+-46.1	-43.7	61.1
+-59.8	-39.6	53.3
+-14.2	-39.1	81.1
+-28.3	-31.2	76.0
+-42.3	-30.7	70.2
+-67.6	-30.1	41.2
+-50.5	-24.4	64.4
+-14.6	-22.7	80.2
+-60.9	-18.7	50.9
+-31.6	-16.9	75.2
+-5.1	-12.6	77.3
+-65.6	-10.8	37.8
+-41.8	-10.2	67.0
+-55.1	-4.01	53.2
+-22.7	1.2	72.0
+-5.8	2.8	74.8
+-49.2	3.7	54.7
+-34.5	3.9	66.5
+-61.55	6.2	35.9
+-63.6	8.3	25.7
+-40.4	11.8	60.7
+-48.7	14.5	50.5
+-21.8	16.0	68.9
+-58.2	18.2	27.3
+-7.0	18.4	70.3
+-36.3	19.9	59.6
+-48.1	24.6	44.0
+-56.8	28.52	20.8
+-7.3	33.8	61.7
+-22.2	35.0	57.2
+-36.8	35.4	47.0
+-46.8	35.6	36.0