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Hi Jenna, I'm sorry you're having these issues! Let's see if we can figure this out. Best, |
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Hello,
First, thank you so much for HALFpipe! It is such an amazing tool.
I've successfully run one subject through HALFpipe v1.2.2 on our HPC. I went to QC their data but when I opened the index.html file in the browser no content appeared. It seems that all the necessary figures and js files were created. However, in the err.txt file I did get the following warning:
[2023-11-11 00:33:11,0996] [py.warnings ] [WARNING ] /usr/local/miniconda/lib/python3.10/site-packages/nilearn/plotting/displays/_axes.py:71: UserWarning: No contour levels were found within the data range. \u2502 im = getattr(ax, type)(data_2d.copy(), \u2502 Stack (most recent call last): \u2502 File "<string>", line 1, in <module> \u2502 File "/usr/local/miniconda/lib/python3.10/multiprocessing/forkserver.py", line 274, in main \u2502 code = _serve_one(child_r, fds, \u2502 File "/usr/local/miniconda/lib/python3.10/multiprocessing/forkserver.py", line 313, in _serve_one \u2502 code = spawn._main(child_r, parent_sentinel) \u2502 File "/usr/local/miniconda/lib/python3.10/multiprocessing/spawn.py", line 129, in _main \u2502 return self._bootstrap(parent_sentinel) \u2502 File "/usr/local/miniconda/lib/python3.10/multiprocessing/process.py", line 315, in _bootstrap \u2502 self.run() \u2502 File "/usr/local/miniconda/lib/python3.10/multiprocessing/process.py", line 108, in run \u2502 self._target(*self._args, **self._kwargs) \u2502 File "/usr/local/miniconda/lib/python3.10/concurrent/futures/process.py", line 243, in _process_worker \u2502 r = call_item.fn(*call_item.args, **call_item.kwargs) \u2502 File "/usr/local/miniconda/lib/python3.10/site-packages/halfpipe/plugins/multiproc.py", line 72, in run_node \u2502 result["result"] = node.run(updatehash=updatehash) \u2502 File "/usr/local/miniconda/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 524, in run \u2502 result = self._run_interface(execute=True) \u2502 File "/usr/local/miniconda/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 642, in _run_interface \u2502 return self._run_command(execute) \u2502 File "/usr/local/miniconda/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 719, in _run_command \u2502 result = self._interface.run(cwd=outdir, ignore_exception=True) \u2502 File "/usr/local/miniconda/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 399, in run \u2502 runtime = self._post_run_hook(runtime) \u2502 File "/usr/local/miniconda/lib/python3.10/site-packages/nipype/interfaces/mixins/reporting.py", line 50, in _post_run_hook \u2502 self._generate_report() \u2502 File "/usr/local/miniconda/lib/python3.10/site-packages/niworkflows/interfaces/masks.py", line 340, in _generate_report \u2502 plot_segs( \u2502 File "/usr/local/miniconda/lib/python3.10/site-packages/niworkflows/viz/utils.py", line 252, in plot_segs \u2502 svg = _plot_anat_with_contours( \u2502 File "/usr/local/miniconda/lib/python3.10/site-packages/niworkflows/viz/utils.py", line 288, in _plot_anat_with_contours \u2502 display.add_contours(segs[i], levels=levels[i], **plot_params) \u2502 File "/usr/local/miniconda/lib/python3.10/site-packages/nilearn/plotting/displays/_slicers.py", line 315, in add_contours \u2502 self._map_show(img, type='contour', threshold=threshold, **kwargs) \u2502 File "/usr/local/miniconda/lib/python3.10/site-packages/nilearn/plotting/displays/_slicers.py", line 403, in _map_show \u2502 im = display_ax.draw_2d(data_2d, data_bounds, bounding_box, \u2502 File "/usr/local/miniconda/lib/python3.10/site-packages/nilearn/plotting/displays/_axes.py", line 71, in draw_2d \u2502 im = getattr(ax, type)(data_2d.copy(), \u2502 File "/usr/local/miniconda/lib/python3.10/site-packages/matplotlib/__init__.py", line 1412, in inner \u2502 return func(ax, *map(sanitize_sequence, args), **kwargs) \u2502 File "/usr/local/miniconda/lib/python3.10/site-packages/matplotlib/axes/_axes.py", line 6301, in contour \u2502 contours = mcontour.QuadContourSet(self, *args, **kwargs) \u2502 File "/usr/local/miniconda/lib/python3.10/site-packages/matplotlib/contour.py", line 812, in __init__ \u2502 kwargs = self._process_args(*args, **kwargs) \u2502 File "/usr/local/miniconda/lib/python3.10/site-packages/matplotlib/contour.py", line 1441, in _process_args \u2502 x, y, z = self._contour_args(args, kwargs) \u2502 File "/usr/local/miniconda/lib/python3.10/site-packages/matplotlib/contour.py", line 1492, in _contour_args \u2502 self._process_contour_level_args(args) \u2502 File "/usr/local/miniconda/lib/python3.10/site-packages/matplotlib/contour.py", line 1187, in _process_contour_level_args \u2502 _api.warn_external( \u2502 File "/usr/local/miniconda/lib/python3.10/site-packages/matplotlib/_api/__init__.py", line 299, in warn_external \u2502 warnings.warn(message, category, stacklevel) \u2502 File "/usr/local/miniconda/lib/python3.10/warnings.py", line 109, in _showwarnmsg \u2502 sw(msg.message, msg.category, msg.filename, msg.lineno, \u2502 File "/usr/local/miniconda/lib/python3.10/site-packages/halfpipe/logging/base.py", line 35, in showwarning \u2514\u2500 logger.warning(f"{s}", stack_info=True)
Do you have any suggestions as to what I can do to be able to view the QC report?
Thank you in advance,
Jenna
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