Fixes/misc #63
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Fixes/misc #63
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* BF: copytree now copies files from directories instead of just soft linking them
| This is probably not related to this update, but more likely to ipython 0.10.1. When I run fsl_feeds_tutorial with "ipcluster local -n 3" I get: DEBUG:workflow:level1.firstlevel.modelfit.level1design session_info level1.firstlevel.modelfit.modelspec session_info DEBUG:workflow:setting node input: session_info->[{'regress': [], 'cond': [{'duration': [30.0], 'onset': [0.0, 60.0, 120.0, 180.0, 240.0, 300.0, 360.0, 420.0, 480.0], 'name': 'Visual'}, {'duration': [45.0], 'onset': [0.0, 90.0, 180.0, 270.0, 360.0, 450.0], 'name': 'Auditory'}], 'hpf': 100.0, 'scans': '/media/data/nipype_examples/fsl_feeds/workingdir/level1/firstlevel/preproc/highpass/mapflow/_highpass0/fmri_dtype_mcf_mask_smooth_mask_intnorm_hpf.nii.gz'}] DEBUG:workflow:setting nodelevel input session_info = [{'regress': [], 'cond': [{'duration': [30.0], 'onset': [0.0, 60.0, 120.0, 180.0, 240.0, 300.0, 360.0, 420.0, 480.0], 'name': 'Visual'}, {'duration': [45.0], 'onset': [0.0, 90.0, 180.0, 270.0, 360.0, 450.0], 'name': 'Auditory'}], 'hpf': 100.0, 'scans': '/media/data/nipype_examples/fsl_feeds/workingdir/level1/firstlevel/preproc/highpass/mapflow/_highpass0/fmri_dtype_mcf_mask_smooth_mask_intnorm_hpf.nii.gz'}] DEBUG:workflow:Clearing id: 23 INFO:workflow:Submitting 1 jobs INFO:workflow:Executing: level1design ID: 31 H:d682ea96b7a1b56b09f4bfad6888bb01 ERROR:workflow:['Node level1design failed to run on host filo-dtc.'] DEBUG:workflow:creating pickleable graph INFO:workflow:Saving crash info to /media/data/nipype_examples/fsl_feeds/crashdumps/crash-20101109-184949-filo-level1design.npz INFO:workflow:Traceback (most recent call last): File "", line 2, in File "nipype/pipeline/engine.py", line 1055, in run self._run_interface(execute=True, cwd=outdir) File "nipype/pipeline/engine.py", line 1079, in _run_interface self._result = self._run_command(execute, cwd) File "nipype/pipeline/engine.py", line 1099, in _run_command result = self._interface.run() File "nipype/interfaces/base.py", line 750, in run runtime = self._run_interface(runtime) File "nipype/interfaces/fsl/model.py", line 250, in _run_interface fsf_header = load_template('feat_header_l1.tcl') File "nipype/interfaces/base.py", line 61, in load_template template_file = open(full_fname) IOError: [Errno 2] No such file or directory: 'nipype/interfaces/script_templates/feat_header_l1.tcl' DEBUG:workflow:Clearing id: 24 INFO:workflow:*********************************** ERROR:workflow:could not run node: level1.firstlevel.modelfit.level1design INFO:workflow:crashfile: /media/data/nipype_examples/fsl_feeds/crashdumps/crash-20101109-184949-filo-level1design.npz DEBUG:workflow:The following dependent nodes were not run DEBUG:workflow:level1design DEBUG:workflow:modelgen DEBUG:workflow:modelestimate DEBUG:workflow:conestimate DEBUG:workflow:datasink DEBUG:workflow:l2model DEBUG:workflow:flameo DEBUG:workflow:copemerge DEBUG:workflow:varcopemerge INFO:workflow:*********************************** Everything works smoothly in the sequential (non-parallel) mode. |
| works fine for me in parallel on my mac. can you make sure you have no other ipengine running and restart ipcluster. ipcluster needs to be restarted everytime the nipype installation is changed. |
| could not replicate - merging |
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python 2.5, copytree fix