What are you trying to do? I'm using the toolbox to perform functional gradient analysis, and plot the cortex mapping
If you've tried running this with BrainSpace code already, how did you do so and what went wrong? I used to use the functions and code smoothly, but when I switch to my new PC and reinstall the package, things goes wrong. I can not even plot by using the tutorial code. It shows an error with VTK. I tried several different versions of vtk but seems not work and the same error remains.
Please tell us about your computing environment: I used python 3.12 with spacebrain 0.1.10 and vtk 9.3.0.
Other information code: from brainspace.datasets import load_group_fc, load_parcellation, load_conte69

First load mean connectivity matrix and Schaefer parcellation

conn_matrix = load_group_fc('schaefer', scale=400) labeling = load_parcellation('schaefer', scale=400, join=True)

mask = labeling != 0

and load the conte69 hemisphere surfaces

surf_lh, surf_rh = load_conte69()

import numpy as np

from brainspace.gradient import GradientMaps from brainspace.plotting import plot_hemispheres from brainspace.utils.parcellation import map_to_labels

kernels = ['pearson', 'spearman', 'normalized_angle']

gradients_kernel = [None] * len(kernels) for i, k in enumerate(kernels): gm = GradientMaps(kernel=k, approach='dm', random_state=0) gm.fit(conn_matrix)

gradients_kernel[i] = map_to_labels(gm.gradients_[:, i], labeling, mask=mask,
                                    fill=np.nan)

label_text = ['Pearson', 'Spearman', 'Normalized\nAngle'] plot_hemispheres(surf_lh, surf_rh, array_name=gradients_kernel, size=(1200, 600), cmap='viridis_r', color_bar=True, label_text=label_text, zoom=1.45)

Error:

TypeError Traceback (most recent call last) File ~\AppData\Local\Programs\Python\Python312\Lib\site-packages\vtkmodules\util\vtkAlgorithm.py:152, in VTKPythonAlgorithmBase.InternalAlgorithm.ProcessRequest(self, vtkself, request, inInfo, outInfo) 151 def ProcessRequest(self, vtkself, request, inInfo, outInfo): --> 152 return vtkself.ProcessRequest(request, inInfo, outInfo)

File ~\AppData\Local\Programs\Python\Python312\Lib\site-packages\vtkmodules\util\vtkAlgorithm.py:198, in VTKPythonAlgorithmBase.ProcessRequest(self, request, inInfo, outInfo) 196 return self.RequestUpdateExtent(request, inInfo, outInfo) 197 elif request.Has(vtkDemandDrivenPipeline.REQUEST_DATA()): --> 198 return self.RequestData(request, inInfo, outInfo) 200 return 1

File ~\AppData\Local\Programs\Python\Python312\Lib\site-packages\brainspace\vtk_interface\io_support\gifti_support.py:89, in vtkGIFTIReader.RequestData(self, request, inInfo, outInfo) 87 def RequestData(self, request, inInfo, outInfo): 88 opt = vtkPolyData.GetData(outInfo, 0) ---> 89 s = _read_gifti(self._FileName, self._fnames_pointdata) 90 opt.ShallowCopy(s) 91 return 1

File ~\AppData\Local\Programs\Python\Python312\Lib\site-packages\brainspace\vtk_interface\io_support\gifti_support.py:32, in _read_gifti(ipth, ipths_pointdata) 30 points = g.get_arrays_from_intent(INTENT_POINTS)[0].data 31 cells = g.get_arrays_from_intent(INTENT_CELLS)[0].data ---> 32 s = build_polydata(points, cells=cells) 34 # for pth_data, keys in ipths_pointdata.items(): 35 # d = nb.load(pth_data) 36 # if len(d.darrays) != len(keys): (...) 48 # # random array names 49 # s.append_array(a1.data, name=None, at='p') 50 return s.VTKObject

File ~\AppData\Local\Programs\Python\Python312\Lib\site-packages\brainspace\mesh\mesh_creation.py:54, in build_polydata(points, cells) 52 s.SetLines(cells) 53 else: ---> 54 s.SetPolys(cells) 56 # Triangulation needed 57 return serial_connect(s, vtkTriangleFilter())

File ~\AppData\Local\Programs\Python\Python312\Lib\site-packages\brainspace\vtk_interface\wrappers\data_object.py:502, in BSPolyData.SetPolys(self, polys) 492 """Set polys. 493 494 Parameters (...) 499 500 """ 501 if isinstance(polys, np.ndarray): --> 502 polys = self._numpy2cells(polys) 503 self.VTKObject.SetPolys(polys)

File ~\AppData\Local\Programs\Python\Python312\Lib\site-packages\brainspace\vtk_interface\wrappers\data_object.py:459, in BSPolyData._numpy2cells(cells) 457 # cells = dsa.numpyTovtkDataArray(vtk_cells, array_type=VTK_ID_TYPE) 458 ca = BSCellArray() --> 459 ca.SetCells(n_cells, vtk_cells) 460 return ca.VTKObject

File ~\AppData\Local\Programs\Python\Python312\Lib\site-packages\brainspace\vtk_interface\decorators.py:99, in unwrap_input.._wrapper_decorator.._wrapper_wrap(*args, *kwds) 95 @functools.wraps(func) 96 def _wrapper_wrap(args, kwds): 97 args, kwds = _unwrap_input_data(args, kwds, xargs, skip=skip, 98 vtype=vtype) ---> 99 data = func(args, kwds) 100 return data

File ~\AppData\Local\Programs\Python\Python312\Lib\site-packages\brainspace\vtk_interface\wrappers\misc.py:97, in BSCellArray.SetCells(self, n_cells, cells) 95 @unwrap_input(2, vtype={2: VTK_ID_TYPE}) 96 def SetCells(self, n_cells, cells): ---> 97 self.VTKObject.SetCells(n_cells, cells)

TypeError: SetCells argument 2:

ValueError Traceback (most recent call last) Cell In[2], line 31 26 gradients_kernel[i] = map_tolabels(gm.gradients[:, i], labeling, mask=mask, 27 fill=np.nan) 30 label_text = ['Pearson', 'Spearman', 'Normalized\nAngle'] ---> 31 plot_hemispheres(surf_lh, surf_rh, array_name=gradients_kernel, size=(1200, 600), 32 cmap='viridis_r', color_bar=True, label_text=label_text, zoom=1.45)

File ~\AppData\Local\Programs\Python\Python312\Lib\site-packages\brainspace\vtk_interface\decorators.py:41, in wrap_input.._wrapper_decorator.._wrapper_wrap(*args, *kwds) 38 @functools.wraps(func) 39 def _wrapper_wrap(args, kwds): 40 args, kwds = _wrap_input_data(args, kwds, xargs, skip=skip) ---> 41 data = func(args, kwds) 42 return data

File ~\AppData\Local\Programs\Python\Python312\Lib\site-packages\brainspace\plotting\surface_plotting.py:557, in plot_hemispheres(surf_lh, surf_rh, array_name, color_bar, color_range, label_text, layout_style, cmap, nan_color, zoom, background, size, interactive, embed_nb, screenshot, filename, scale, transparent_bg, **kwargs) 555 if isinstance(an, np.ndarray): 556 name = surf_lh.append_array(an[:n_pts_lh], at='p') --> 557 surf_rh.append_array(an[n_pts_lh:], name=name, at='p') 558 array_name2.append(name) 559 to_remove.append(name)

File ~\AppData\Local\Programs\Python\Python312\Lib\site-packages\brainspace\vtk_interface\wrappers\data_object.py:214, in BSDataSet.append_array(self, array, name, at, convert_bool, overwrite) 211 raise ValueError('Array shape is not valid.') 213 if at in ['point', 'p']: --> 214 _array_overwrite(self.PointData, to_point) 215 elif at in ['cell', 'c']: 216 _array_overwrite(self.CellData, to_cell)

File ~\AppData\Local\Programs\Python\Python312\Lib\site-packages\brainspace\vtk_interface\wrappers\data_object.py:211, in BSDataSet.append_array.._array_overwrite(attributes, has_same_shape) 208 warnings.warn('Array was not appended. Array name already ' 209 'exists.') 210 else: --> 211 raise ValueError('Array shape is not valid.')

ValueError: Array shape is not valid.

MICA-MNI / BrainSpace

error in ploting #118

First load mean connectivity matrix and Schaefer parcellation

and load the conte69 hemisphere surfaces

Error:

TypeError: SetCells argument 2:

TypeError: SetCells argument 2: