Description
Hi,
I'm encountering an error when trying to use cortex.webgl.make_static with my subject data, although the same code works perfectly with fsaverage.
This is my code:
sub = "sub-05"
cortex_dir = f'{derivatives_pth}/pycortex/db/{sub}'
temp_dir = f'{derivatives_pth}/temp_data/{sub}_rand_ds'
os.makedirs(temp_dir,exist_ok=True)
cortex.freesurfer.import_subj(freesurfer_subject = sub, pycortex_subject = sub, freesurfer_subject_dir = setup['fsPath'], whitematter_surf = 'smoothwm')
surfs = [cortex.polyutils.Surface(*d) for d in cortex.db.get_surf(sub, "fiducials")]
num_verts = surfs[0].pts.shape[0] + surfs[1].pts.shape[0]
rand_data = np.random.randn(num_verts)
vertex_data = cortex.Vertex(rand_data, sub)
ds = cortex.Dataset(rand=vertex_data)
cortex.webgl.make_static(outpath=temp_dir, data=ds,recache=True)I get this error:
Generating new ctm file...
wm
wm
inflated
inflated
/opt/anaconda3/envs/nilearnenv/lib/python3.13/site-packages/cortex/brainctm.py:113: RuntimeWarning: invalid value encountered in cast
self.left.aux[:,1] = npz.left
/opt/anaconda3/envs/nilearnenv/lib/python3.13/site-packages/cortex/brainctm.py:114: RuntimeWarning: invalid value encountered in cast
self.right.aux[:,1] = npz.right
Exception Traceback (most recent call last)
Cell In[463], line 7
5 vertex_data = cortex.Vertex(rand_data, sub)
6 ds = cortex.Dataset(rand=vertex_data)
----> 7 cortex.webgl.make_static(outpath=temp_dir, data=ds,recache=True)
File /opt/anaconda3/envs/nilearnenv/lib/python3.13/site-packages/cortex/utils.py:40, in DocLoader.call(self, *args, **kwargs)
39 def call(self, *args, **kwargs):
---> 40 return self._load()(*args, **kwargs)
File /opt/anaconda3/envs/nilearnenv/lib/python3.13/site-packages/cortex/webgl/view.py:162, in make_static(outpath, data, recache, template, anonymize, overlays_available, overlays_visible, labels_visible, types, html_embed, copy_ctmfiles, title, layout, overlay_file, curvature_brightness, curvature_contrast, curvature_smoothness, surface_specularity, **kwargs)
153 subjects = list(package.subjects)
155 ctmargs = dict(
156 method="mg2",
157 level=9,
(...)
160 overlays_available=overlays_available,
161 )
--> 162 ctms = dict((subj, utils.get_ctmpack(subj, types, **ctmargs)) for subj in subjects)
163 package.reorder(ctms)
165 db.auxfile = None
File /opt/anaconda3/envs/nilearnenv/lib/python3.13/site-packages/cortex/webgl/view.py:162, in (.0)
153 subjects = list(package.subjects)
155 ctmargs = dict(
156 method="mg2",
157 level=9,
(...)
160 overlays_available=overlays_available,
161 )
--> 162 ctms = dict((subj, utils.get_ctmpack(subj, types, **ctmargs)) for subj in subjects)
163 package.reorder(ctms)
165 db.auxfile = None
File /opt/anaconda3/envs/nilearnenv/lib/python3.13/site-packages/cortex/utils.py:105, in get_ctmpack(subject, types, method, level, recache, decimate, external_svg, overlays_available)
103 print("Generating new ctm file...")
104 from . import brainctm
--> 105 ptmap = brainctm.make_pack(ctmfile,
106 subject,
107 types=types,
108 method=method,
109 level=level,
110 decimate=decimate,
111 external_svg=external_svg,
112 overlays_available=overlays_available)
113 return ctmfile
File /opt/anaconda3/envs/nilearnenv/lib/python3.13/site-packages/cortex/brainctm.py:292, in make_pack(outfile, subj, types, method, level, decimate, disp_layers, external_svg, overlays_available)
290 if not os.path.exists(os.path.split(outfile)[0]):
291 os.makedirs(os.path.split(outfile)[0])
--> 292 return ctm.save(os.path.splitext(outfile)[0],
293 method=method,
294 level=level,
295 external_svg=external_svg,
296 overlays_available=overlays_available)
File /opt/anaconda3/envs/nilearnenv/lib/python3.13/site-packages/cortex/brainctm.py:139, in BrainCTM.save(self, path, method, external_svg, overlays_available, **kwargs)
136 mapname = path + ".npz"
138 # Save CTM concatenation
--> 139 (lpts, _, _), lbin = self.left.save(method=method, **kwargs)
140 (rpts, _, _), rbin = self.right.save(method=method, **kwargs)
142 offsets = [0]
File /opt/anaconda3/envs/nilearnenv/lib/python3.13/site-packages/cortex/brainctm.py:237, in Hemi.save(self, **kwargs)
235 def save(self, **kwargs):
236 self.ctm.addAttrib(self.aux, 'auxdat')
--> 237 self.ctm.save(**kwargs)
238 ctm = CTMfile(self.tf.name)
239 return ctm.getMesh(), self.tf.read()
File /opt/anaconda3/envs/nilearnenv/lib/python3.13/site-packages/cortex/openctm.pyx:213, in cortex.openctm.CTMfile.save()
Exception: b'CTM_INVALID_MESH'.
I confirmed that the .gii surfaces loaded to pycrotex look visually normal in fsleyes (No NaNs; All polygons within bounds; No degenerate triangles).
Would really appreciate any insight!
Thanks in advance 🙏
Giulia