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<p><font size="2" face="sans-serif">Okay, this seems to be an issue. Thanks a lot! </font><br>
<font size="2" face="sans-serif">Funnily, the pixdim4 was set to 1 and not to zero, but still after I set it to 2 in the header, at least I came beyond this error.</font><br>
<font size="2" face="sans-serif">Unfortunately, I end up with another error message now, still while loading. It says:</font><br>
<br>
<font size="2" face="sans-serif">Traceback (most recent call last):</font><br>
<font size="2" face="sans-serif"> File "load.py2", line 31, in <module></font><br>
<font size="2" face="sans-serif"> time_attr='time_coords', condition_attr='condition')</font><br>
<font size="2" face="sans-serif"> File "/usr/lib/python2.7/dist-packages/mvpa2/datasets/sources/openfmri.py", line 656, in get_model_bold_dataset</font><br>
<font size="2" face="sans-serif"> 'mask', 'add_fa', 'add_sa')]))</font><br>
<font size="2" face="sans-serif"> File "/usr/lib/python2.7/dist-packages/mvpa2/datasets/eventrelated.py", line 587, in fit_event_hrf_model</font><br>
<font size="2" face="sans-serif"> model_params = glm(ds)</font><br>
<font size="2" face="sans-serif"> File "/usr/lib/python2.7/dist-packages/mvpa2/base/learner.py", line 258, in __call__</font><br>
<font size="2" face="sans-serif"> return super(Learner, self).__call__(ds)</font><br>
<font size="2" face="sans-serif"> File "/usr/lib/python2.7/dist-packages/mvpa2/base/node.py", line 137, in __call__</font><br>
<font size="2" face="sans-serif"> result = self._call(ds, **(_call_kwargs or self._get_call_kwargs(ds)))</font><br>
<font size="2" face="sans-serif"> File "/usr/lib/python2.7/dist-packages/mvpa2/mappers/base.py", line 291, in _call</font><br>
<font size="2" face="sans-serif"> return self.forward(ds)</font><br>
<font size="2" face="sans-serif"> File "/usr/lib/python2.7/dist-packages/mvpa2/mappers/base.py", line 215, in forward</font><br>
<font size="2" face="sans-serif"> return self._forward_dataset(data)</font><br>
<font size="2" face="sans-serif"> File "/usr/lib/python2.7/dist-packages/mvpa2/mappers/glm/__init__.py", line 126, in _forward_dataset</font><br>
<font size="2" face="sans-serif"> model, out = self._fit_model(ds, X, reg_names)</font><br>
<font size="2" face="sans-serif"> File "/usr/lib/python2.7/dist-packages/mvpa2/mappers/glm/nipy_glm.py", line 49, in _fit_model</font><br>
<font size="2" face="sans-serif"> glm.fit(ds.samples, **self.glmfit_kwargs)</font><br>
<font size="2" face="sans-serif"> File "/usr/lib/python2.7/dist-packages/nipy/modalities/fmri/glm.py", line 123, in fit</font><br>
<font size="2" face="sans-serif"> ols_result = OLSModel(self.X).fit(Y)</font><br>
<font size="2" face="sans-serif"> File "/usr/lib/python2.7/dist-packages/nipy/algorithms/statistics/models/regression.py", line 301, in fit</font><br>
<font size="2" face="sans-serif"> dispersion = np.sum(wresid ** 2, 0) / (self.wdesign.shape[0] -</font><br>
<font size="2" face="sans-serif">MemoryError</font><br>
<br>
<br>
<font size="2" face="sans-serif">What could still be missing?</font><br>
<font size="2" face="sans-serif">Thank you</font><br>
<font size="2" face="sans-serif">Lydia </font><br>
<br>
<font size="2" face="sans-serif">P.S: Yes, I',m always just loading one of the two flavor files (and compatible mask), but since it worked with the 'irbadvols', I just wanted to show you the difference for these two in the output. </font><br>
<br>
<br>
<br>
<img width="16" height="16" src="cid:1__=4EBB0BA0DFC874938f9e8a93df9@lotus.uzh.ch" border="0" alt="Inactive hide details for Yaroslav Halchenko ---02/06/2017 17:21:42---On Fri, 02 Jun 2017, lydia.hellrung@econ.uzh.ch wrote: > "><font size="2" color="#424282" face="sans-serif">Yaroslav Halchenko ---02/06/2017 17:21:42---On Fri, 02 Jun 2017, lydia.hellrung@econ.uzh.ch wrote: > No, they all have 195 volumes, but the g</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 17:21</font><br>
<font size="1" color="#5F5F5F" face="sans-serif">Betreff: </font><font size="1" face="sans-serif">Re: [pymvpa] Antwort: Re: 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>
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<tt><font size="2"><br>
On Fri, 02 Jun 2017, lydia.hellrung@econ.uzh.ch wrote:<br>
<br>
> No, they all have 195 volumes, but the geometry information is apparently<br>
> saved differently.<br>
> The output says:<br>
<br>
> ./sub002/BOLD/task001_run001/bold_irbadvols.nii.gz float32 [112, 112,<br>
> 27, 195] 1.96x1.96x4.06x2.00 #exts: 1 sform<br>
> ./sub002/BOLD/task001_run001/bold_iwrbadvols.nii.gz float32 [105, 127,<br>
> 105, 195] 1.50x1.50x1.50x0.00 #exts: 1<br>
<br>
> while the first file could be loaded, the second one not. Could that be an<br>
> issue? And in case, what would be needed?<br>
<br>
well -- you are saying flavor='iwrbadvols' so only that one should be<br>
loaded, and I guess the 'brain.nii.gz' mask is of the 'compatible'<br>
dimensionality I guess. otherwise I would have expected it to fail<br>
earlier.<br>
<br>
But the above shows the "culprit" -- 1.50x1.50x1.50x0.00 so your TR<br>
there is set to 0 sec... so time indices are degenerate and I guess<br>
that played out somewhere (may be compressed everything into a single<br>
sample or smth like that)<br>
<br>
You could fix it via a quick python code using nibabel or using<br>
nifti_tool ... --help gives<br>
<br>
e.g. modifying nifti_1_header fields:<br>
-mod_field descrip 'toga, toga, toga'<br>
-mod_field qoffset_x 19.4 -mod_field qoffset_z -11<br>
-mod_field pixdim '1 0.9375 0.9375 1.2 1 1 1 1'<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>
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