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<p><font size="2" face="sans-serif">No, they all have 195 volumes, but the geometry information is apparently saved differently.</font><br>
<font size="2" face="sans-serif">The output says:</font><br>
<br>
<font size="2" face="sans-serif">./sub002/BOLD/task001_run001/bold_irbadvols.nii.gz float32 [112, 112, 27, 195] 1.96x1.96x4.06x2.00 #exts: 1 sform</font><br>
<font size="2" face="sans-serif">./sub002/BOLD/task001_run001/bold_iwrbadvols.nii.gz float32 [105, 127, 105, 195] 1.50x1.50x1.50x0.00 #exts: 1</font><br>
<br>
<font size="2" face="sans-serif">while the first file could be loaded, the second one not. Could that be an issue? And in case, what would be needed?</font><br>
<font size="2" face="sans-serif">If I check the headers, it says qform_code = 1 for first file and qform_code = 4 for second one.</font><br>
<br>
<font size="2" face="sans-serif">Thanks </font><br>
<font size="2" face="sans-serif">Lydia </font><br>
<ul style="padding-left: 0pt"><font size="1" color="#595959" face="Trebuchet MS">-----------------------------------------------------------------------------------------</font><br>
<font size="1" color="#595959" face="Trebuchet MS"><b>Dr. rer. nat. Lydia Hellrung</b></font><font size="1" color="#595959" face="Trebuchet MS">, Dipl.-Inf. </font><br>
<font size="1" color="#595959" face="Trebuchet MS">University of Zurich</font><br>
<font size="1" color="#595959" face="Trebuchet MS">Department of Economics</font><br>
<font size="1" color="#595959" face="Trebuchet MS">Blümlisaplstraße 10 </font><br>
<font size="1" color="#595959" face="Trebuchet MS">8006 Zurich, Switzerland</font><br>
<font size="1" color="#595959" face="Trebuchet MS">phone: + 41 (0) 44 634 4838</font><br>
<br>
<font size="1" color="#595959" face="Trebuchet MS">e-mail:</font><font size="1" color="#595959" face="Trebuchet MS"><b> lydia.hellrung@econ.uzh.ch</b></font><br>
<font size="1" color="#595959" face="Trebuchet MS">-----------------------------------------------------------------------------------------</font></ul>
<br>
<img width="16" height="16" src="cid:1__=4EBB0BA0DFC1E2A88f9e8a93df9@lotus.uzh.ch" border="0" alt="Inactive hide details for Yaroslav Halchenko ---02/06/2017 16:42:33---On Fri, 02 Jun 2017, lydia.hellrung@econ.uzh.ch wrote: > "><font size="2" color="#424282" face="sans-serif">Yaroslav Halchenko ---02/06/2017 16:42:33---On Fri, 02 Jun 2017, lydia.hellrung@econ.uzh.ch wrote: > Dear Yaroslav,</font><br>
<br>
<font size="1" color="#5F5F5F" face="sans-serif">Von: </font><font size="1" face="sans-serif">Yaroslav Halchenko <debian@onerussian.com></font><br>
<font size="1" color="#5F5F5F" face="sans-serif">An: </font><font size="1" face="sans-serif">pkg-exppsy-pymvpa@lists.alioth.debian.org</font><br>
<font size="1" color="#5F5F5F" face="sans-serif">Datum: </font><font size="1" face="sans-serif">02/06/2017 16:42</font><br>
<font size="1" color="#5F5F5F" face="sans-serif">Betreff: </font><font size="1" face="sans-serif">Re: [pymvpa] Antwort: Re: Loading normalized data with 'get_model_bold_dataset' fails</font><br>
<font size="1" color="#5F5F5F" face="sans-serif">Gesendet von: </font><font size="1" face="sans-serif">"Pkg-ExpPsy-PyMVPA" <pkg-exppsy-pymvpa-bounces+lydia.hellrung=econ.uzh.ch@lists.alioth.debian.org></font><br>
<hr width="100%" size="2" align="left" noshade style="color:#8091A5; "><br>
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<br>
<tt><font size="2"><br>
On Fri, 02 Jun 2017, lydia.hellrung@econ.uzh.ch wrote:<br>
<br>
> Dear Yaroslav,<br>
<br>
> there is the full traceback:<br>
<br>
> /usr/lib/python2.7/dist-packages/nipy/modalities/fmri/hemodynamic_models.py:176:<br>
> RuntimeWarning: divide by zero encountered in double_scalars<br>
> min_onset) * oversampling) + 1<br>
> Traceback (most recent call last):<br>
> File "load.py2", line 31, in <module><br>
> time_attr='time_coords', condition_attr='condition')<br>
> File<br>
> "/usr/lib/python2.7/dist-packages/mvpa2/datasets/sources/openfmri.py",<br>
> line 656, in get_model_bold_dataset<br>
> 'mask', 'add_fa', 'add_sa')]))<br>
> File "/usr/lib/python2.7/dist-packages/mvpa2/datasets/eventrelated.py",<br>
> line 574, in fit_event_hrf_model<br>
> **design_kwargs)<br>
> File<br>
> "/usr/lib/python2.7/dist-packages/nipy/modalities/fmri/design_matrix.py",<br>
> line 433, in make_dmtx<br>
> paradigm, hrf_model.lower(), frametimes, fir_delays, min_onset)<br>
> File<br>
> "/usr/lib/python2.7/dist-packages/nipy/modalities/fmri/design_matrix.py",<br>
> line 200, in _convolve_regressors<br>
> min_onset=min_onset)<br>
> File<br>
> "/usr/lib/python2.7/dist-packages/nipy/modalities/fmri/hemodynamic_models.py",<br>
> line 360, in compute_regressor<br>
> exp_condition, frametimes, oversampling, min_onset)<br>
> File<br>
> "/usr/lib/python2.7/dist-packages/nipy/modalities/fmri/hemodynamic_models.py",<br>
> line 180, in _sample_condition<br>
> n_hr)<br>
> File "/usr/lib/python2.7/dist-packages/numpy/core/function_base.py",<br>
> line 76, in linspace<br>
> num = int(num)<br>
> OverflowError: cannot convert float infinity to integer<br>
<br>
could it be that some "bold" volume in your dataset has only a single<br>
volume? <br>
<br>
<br>
That would make n =1 in<br>
<br>
frametimes.max() * (1 + 1. / (n - 1))<br>
<br>
thus inf ...<br>
<br>
you can use smth like<br>
<br>
find -iname *bold*nii.gz | xargs nib-ls<br>
<br>
to quickly review all the bold volumes to have 4th dimension non-degenerate<br>
<br>
-- <br>
Yaroslav O. Halchenko<br>
Center for Open Neuroscience </font></tt><tt><font size="2"><a href="http://centerforopenneuroscience.org">http://centerforopenneuroscience.org</a></font></tt><tt><font size="2"><br>
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755<br>
Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419<br>
WWW: </font></tt><tt><font size="2"><a href="http://www.linkedin.com/in/yarik">http://www.linkedin.com/in/yarik</a></font></tt><tt><font size="2"> <br>
<br>
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