No, they all have 195 volumes, but the geometry information is apparently saved differently. The output says:
./sub002/BOLD/task001_run001/bold_irbadvols.nii.gz float32 [112, 112, 27, 195] 1.96x1.96x4.06x2.00 #exts: 1 sform ./sub002/BOLD/task001_run001/bold_iwrbadvols.nii.gz float32 [105, 127, 105, 195] 1.50x1.50x1.50x0.00 #exts: 1 while the first file could be loaded, the second one not. Could that be an issue? And in case, what would be needed? If I check the headers, it says qform_code = 1 for first file and qform_code = 4 for second one. Thanks Lydia ----------------------------------------------------------------------------------------- Dr. rer. nat. Lydia Hellrung, Dipl.-Inf. University of Zurich Department of Economics Blümlisaplstraße 10 8006 Zurich, Switzerland phone: + 41 (0) 44 634 4838 e-mail: lydia.hellr...@econ.uzh.ch ----------------------------------------------------------------------------------------- Von: Yaroslav Halchenko <deb...@onerussian.com> An: pkg-exppsy-pymvpa@lists.alioth.debian.org Datum: 02/06/2017 16:42 Betreff: Re: [pymvpa] Antwort: Re: Loading normalized data with 'get_model_bold_dataset' fails Gesendet von: "Pkg-ExpPsy-PyMVPA" <pkg-exppsy-pymvpa-bounces +lydia.hellrung=econ.uzh...@lists.alioth.debian.org> On Fri, 02 Jun 2017, lydia.hellr...@econ.uzh.ch wrote: > Dear Yaroslav, > there is the full traceback: > > /usr/lib/python2.7/dist-packages/nipy/modalities/fmri/hemodynamic_models.py:176: > RuntimeWarning: divide by zero encountered in double_scalars > min_onset) * oversampling) + 1 > Traceback (most recent call last): > File "load.py2", line 31, in <module> > time_attr='time_coords', condition_attr='condition') > File > "/usr/lib/python2.7/dist-packages/mvpa2/datasets/sources/openfmri.py", > line 656, in get_model_bold_dataset > 'mask', 'add_fa', 'add_sa')])) > File "/usr/lib/python2.7/dist-packages/mvpa2/datasets/eventrelated.py", > line 574, in fit_event_hrf_model > **design_kwargs) > File > "/usr/lib/python2.7/dist-packages/nipy/modalities/fmri/design_matrix.py", > line 433, in make_dmtx > paradigm, hrf_model.lower(), frametimes, fir_delays, min_onset) > File > "/usr/lib/python2.7/dist-packages/nipy/modalities/fmri/design_matrix.py", > line 200, in _convolve_regressors > min_onset=min_onset) > File > "/usr/lib/python2.7/dist-packages/nipy/modalities/fmri/hemodynamic_models.py", > line 360, in compute_regressor > exp_condition, frametimes, oversampling, min_onset) > File > "/usr/lib/python2.7/dist-packages/nipy/modalities/fmri/hemodynamic_models.py", > line 180, in _sample_condition > n_hr) > File "/usr/lib/python2.7/dist-packages/numpy/core/function_base.py", > line 76, in linspace > num = int(num) > OverflowError: cannot convert float infinity to integer could it be that some "bold" volume in your dataset has only a single volume? That would make n =1 in frametimes.max() * (1 + 1. / (n - 1)) thus inf ... you can use smth like find -iname *bold*nii.gz | xargs nib-ls to quickly review all the bold volumes to have 4th dimension non-degenerate -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik _______________________________________________ Pkg-ExpPsy-PyMVPA mailing list Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa
_______________________________________________ Pkg-ExpPsy-PyMVPA mailing list Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa