{"action":"created","issue":{"url":"https://api.github.com/repos/neurospin/pypreprocess/issues/37","labels_url":"https://api.github.com/repos/neurospin/pypreprocess/issues/37/labels{/name}","comments_url":"https://api.github.com/repos/neurospin/pypreprocess/issues/37/comments","events_url":"https://api.github.com/repos/neurospin/pypreprocess/issues/37/events","html_url":"https://github.com/neurospin/pypreprocess/issues/37","id":22894427,"number":37,"title":"do-report breaks due to an attempt to display a 4D fMRI image","user":{"login":"bthirion","id":234454,"avatar_url":"https://avatars.githubusercontent.com/u/234454?v=3","gravatar_id":"","url":"https://api.github.com/users/bthirion","html_url":"https://github.com/bthirion","followers_url":"https://api.github.com/users/bthirion/followers","following_url":"https://api.github.com/users/bthirion/following{/other_user}","gists_url":"https://api.github.com/users/bthirion/gists{/gist_id}","starred_url":"https://api.github.com/users/bthirion/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bthirion/subscriptions","organizations_url":"https://api.github.com/users/bthirion/orgs","repos_url":"https://api.github.com/users/bthirion/repos","events_url":"https://api.github.com/users/bthirion/events{/privacy}","received_events_url":"https://api.github.com/users/bthirion/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2013-11-19T08:11:01Z","updated_at":"2015-03-30T13:12:28Z","closed_at":null,"body":"Maybe you shuold coregister also the mean functional image created by realign and use it for display ?\r\nThanks !\r\n\r\n\r\n\r\n--------------------------------------------------------------------------\r\nValueError                                Traceback (most recent call last)\r\n/usr/lib/python2.7/dist-packages/IPython/utils/py3compat.pyc in execfile(fname, *where)\r\n    173             else:\r\n    174                 filename = fname\r\n--> 175             __builtin__.execfile(filename, *where)\r\n\r\n/volatile/thirion/mygit/mathematicians/do_preprocessing.py in <module>()\r\n     45         do_subject_preproc(preproc_dict, concat=False, do_coreg=True,\r\n     46                            do_stc=False, do_cv_tc=True, do_realign=True,\r\n---> 47                            do_report=True)\r\n\r\n/home/bt206016/.local/lib/python2.7/site-packages/pypreprocess/purepython_preproc_utils.pyc in do_subject_preproc(subject_data, verbose, do_caching, do_stc, interleaved, slice_order, do_realign, do_coreg, coreg_func_to_anat, do_cv_tc, fwhm, write_output_images, concat, do_report, parent_results_gallery, shutdown_reloaders)\r\n    297             # generate coreg QA thumbs\r\n\r\n    298             subject_data.generate_coregistration_thumbnails(\r\n--> 299                 coreg_func_to_anat=coreg_func_to_anat)\r\n    300 \r\n    301         # garbage collection\r\n\r\n\r\n/home/bt206016/.local/lib/python2.7/site-packages/pypreprocess/subject_data.pyc in generate_coregistration_thumbnails(self, coreg_func_to_anat, log, comment)\r\n    420             else None,\r\n    421             results_gallery=self.results_gallery,\r\n--> 422             comment=comment\r\n    423             )\r\n    424 \r\n\r\n/home/bt206016/.local/lib/python2.7/site-packages/pypreprocess/reporting/preproc_reporter.pyc in generate_coregistration_thumbnails(target, source, output_dir, execution_log_html_filename, results_gallery, comment)\r\n    551         output_dir,\r\n    552         execution_log_html_filename=execution_log_html_filename,\r\n--> 553         results_gallery=results_gallery,\r\n    554         )\r\n    555 \r\n\r\n/home/bt206016/.local/lib/python2.7/site-packages/pypreprocess/reporting/preproc_reporter.pyc in generate_registration_thumbnails(target, source, procedure_name, output_dir, execution_log_html_filename, results_gallery)\r\n    417         title=\"Outline of %s on %s\" % (\r\n    418             target[1],\r\n--> 419             source[1],\r\n    420             ))\r\n    421 \r\n\r\n/home/bt206016/.local/lib/python2.7/site-packages/joblib-0.6.5-py2.7.egg/joblib/memory.pyc in __call__(self, *args, **kwargs)\r\n    169                           'directory %s'\r\n    170                         % (name, argument_hash, output_dir))\r\n--> 171             return self.call(*args, **kwargs)\r\n    172         else:\r\n    173             try:\r\n\r\n/home/bt206016/.local/lib/python2.7/site-packages/joblib-0.6.5-py2.7.egg/joblib/memory.pyc in call(self, *args, **kwargs)\r\n    321         if self._verbose:\r\n    322             print self.format_call(*args, **kwargs)\r\n--> 323         output = self.func(*args, **kwargs)\r\n    324         self._persist_output(output, output_dir)\r\n    325         duration = time.time() - start_time\r\n\r\n/home/bt206016/.local/lib/python2.7/site-packages/pypreprocess/reporting/check_preprocessing.pyc in plot_registration(reference_img, coregistered_img, title, cut_coords, slicer, cmap, output_filename)\r\n    249     # plot the coregistered image\r\n\r\n    250     if hasattr(coregistered_img, '__len__'):\r\n--> 251         coregistered_img = load_specific_vol(coregistered_img, 0)[0]\r\n    252     # XXX else i'm assuming a nifi object ;)\r\n\r\n    253     coregistered_data = coregistered_img.get_data()\r\n\r\n/home/bt206016/.local/lib/python2.7/site-packages/pypreprocess/io_utils.pyc in load_specific_vol(vols, t, strict)\r\n     91     if isinstance(vols, list):\r\n     92         n_scans = len(vols)\r\n---> 93         vol = load_vol(vols[t])\r\n     94     elif is_niimg(vols) or isinstance(vols, basestring):\r\n     95         _vols = nibabel.load(vols) if isinstance(vols, basestring) else vols\r\n\r\n/home/bt206016/.local/lib/python2.7/site-packages/pypreprocess/io_utils.pyc in load_vol(x)\r\n     66         else:\r\n     67             raise ValueError(\r\n---> 68                 \"Each volume must be 3D; got shape %s\" % str(vol.shape))\r\n     69     elif len(vol.shape) != 3:\r\n     70             raise ValueError(\r\n\r\nValueError: Each volume must be 3D; got shape (128, 128, 80, 185)\r\n\r\nIn [2]: %debug\r\n> /home/bt206016/.local/lib/python2.7/site-packages/pypreprocess/io_utils.py(68)load_vol()\r\n     67             raise ValueError(\r\n---> 68                 \"Each volume must be 3D; got shape %s\" % str(vol.shape))\r\n     69     elif len(vol.shape) != 3:\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/neurospin/pypreprocess/issues/comments/87672028","html_url":"https://github.com/neurospin/pypreprocess/issues/37#issuecomment-87672028","issue_url":"https://api.github.com/repos/neurospin/pypreprocess/issues/37","id":87672028,"user":{"login":"dohmatob","id":634068,"avatar_url":"https://avatars.githubusercontent.com/u/634068?v=3","gravatar_id":"","url":"https://api.github.com/users/dohmatob","html_url":"https://github.com/dohmatob","followers_url":"https://api.github.com/users/dohmatob/followers","following_url":"https://api.github.com/users/dohmatob/following{/other_user}","gists_url":"https://api.github.com/users/dohmatob/gists{/gist_id}","starred_url":"https://api.github.com/users/dohmatob/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dohmatob/subscriptions","organizations_url":"https://api.github.com/users/dohmatob/orgs","repos_url":"https://api.github.com/users/dohmatob/repos","events_url":"https://api.github.com/users/dohmatob/events{/privacy}","received_events_url":"https://api.github.com/users/dohmatob/received_events","type":"User","site_admin":false},"created_at":"2015-03-30T13:12:28Z","updated_at":"2015-03-30T13:12:28Z","body":"I can't reproduce this. Do you still observe the bug. Otherwise I'll just close the issue."}}