Hi guys,
I am trying to adapt the jupyter notebook written by Chris on my data:
at the stage of modelgen for the level1 stats with FSL FEAT I get this Error:
190204-19:53:49,130 nipype.workflow INFO:
[Node] Setting-up “d0a98d67288f6564381b8944704bf770” in “/Users/dima/Desktop/odormixture/jupyter/nipype_mem/nipype-interfaces-fsl-model-FEATModel/d0a98d67288f6564381b8944704bf770”.
190204-19:53:49,142 nipype.workflow INFO:
[Node] Running “d0a98d67288f6564381b8944704bf770” (“nipype.interfaces.fsl.model.FEATModel”), a CommandLine Interface with command:
feat_model run0
190204-19:53:49,355 nipype.interface INFO:
stdout 2019-02-04T19:53:49.354427:
190204-19:53:49,358 nipype.interface INFO:
stdout 2019-02-04T19:53:49.354427:error: pinv(): svd failed
190204-19:53:49,359 nipype.interface INFO:
stdout 2019-02-04T19:53:49.354427:
190204-19:53:49,361 nipype.interface INFO:
stderr 2019-02-04T19:53:49.361079:libc++abi.dylib: terminating with uncaught exception of type std::runtime_error: pinv(): svd failed
190204-19:53:49,461 nipype.workflow WARNING:
[Node] Error on “d0a98d67288f6564381b8944704bf770” (/Users/dima/Desktop/odormixture/jupyter/nipype_mem/nipype-interfaces-fsl-model-FEATModel/d0a98d67288f6564381b8944704bf770)
RuntimeError Traceback (most recent call last)
in ()
1 modelgen = mem.cache(fsl.model.FEATModel)
2 modelgen_results = modelgen(fsf_file=level1design_results.outputs.fsf_files,
----> 3 ev_files=level1design_results.outputs.ev_files)
4 modelgen_results.outputs
~/anaconda3/lib/python3.7/site-packages/nipype/caching/memory.py in call(self, **kwargs)
79 cwd = os.getcwd()
80 try:
—> 81 out = node.run()
82 finally:
83 # node.run() changes to the node directory - if something goes
~/anaconda3/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py in run(self, updatehash)
469
470 try:
–> 471 result = self._run_interface(execute=True)
472 except Exception:
473 logger.warning(’[Node] Error on “%s” (%s)’, self.fullname, outdir)
~/anaconda3/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py in _run_interface(self, execute, updatehash)
553 self._update_hash()
554 return self._load_results()
–> 555 return self._run_command(execute)
556
557 def _load_results(self):
~/anaconda3/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py in _run_command(self, execute, copyfiles)
633 logger.info(message)
634 try:
–> 635 result = self._interface.run(cwd=outdir)
636 except Exception as msg:
637 result.runtime.stderr = ‘%s\n\n%s’.format(
~/anaconda3/lib/python3.7/site-packages/nipype/interfaces/base/core.py in run(self, cwd, ignore_exception, **inputs)
520 try:
521 runtime = self._pre_run_hook(runtime)
–> 522 runtime = self._run_interface(runtime)
523 runtime = self._post_run_hook(runtime)
524 outputs = self.aggregate_outputs(runtime)
~/anaconda3/lib/python3.7/site-packages/nipype/interfaces/base/core.py in _run_interface(self, runtime, correct_return_codes)
1036 if runtime.returncode is None or
1037 runtime.returncode not in correct_return_codes:
-> 1038 self.raise_exception(runtime)
1039
1040 return runtime
~/anaconda3/lib/python3.7/site-packages/nipype/interfaces/base/core.py in raise_exception(self, runtime)
973 (‘Command:\n{cmdline}\nStandard output:\n{stdout}\n’
974 ‘Standard error:\n{stderr}\nReturn code: {returncode}’
–> 975 ).format(**runtime.dictcopy()))
976
977 def _get_environ(self):
RuntimeError: Command:
feat_model run0
Standard output:
error: pinv(): svd failed
Standard error:
libc++abi.dylib: terminating with uncaught exception of type std::runtime_error: pinv(): svd failed
Return code: -6
Does anybody has any ideas what is the reason?
Best,
Dima