Okay, this seems to be an issue. Thanks a lot! 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. Unfortunately, I end up with another error message now, still while loading. It says:
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 587, in fit_event_hrf_model model_params = glm(ds) File "/usr/lib/python2.7/dist-packages/mvpa2/base/learner.py", line 258, in __call__ return super(Learner, self).__call__(ds) File "/usr/lib/python2.7/dist-packages/mvpa2/base/node.py", line 137, in __call__ result = self._call(ds, **(_call_kwargs or self._get_call_kwargs(ds))) File "/usr/lib/python2.7/dist-packages/mvpa2/mappers/base.py", line 291, in _call return self.forward(ds) File "/usr/lib/python2.7/dist-packages/mvpa2/mappers/base.py", line 215, in forward return self._forward_dataset(data) File "/usr/lib/python2.7/dist-packages/mvpa2/mappers/glm/__init__.py", line 126, in _forward_dataset model, out = self._fit_model(ds, X, reg_names) File "/usr/lib/python2.7/dist-packages/mvpa2/mappers/glm/nipy_glm.py", line 49, in _fit_model glm.fit(ds.samples, **self.glmfit_kwargs) File "/usr/lib/python2.7/dist-packages/nipy/modalities/fmri/glm.py", line 123, in fit ols_result = OLSModel(self.X).fit(Y) File "/usr/lib/python2.7/dist-packages/nipy/algorithms/statistics/models/regression.py", line 301, in fit dispersion = np.sum(wresid ** 2, 0) / (self.wdesign.shape[0] - MemoryError What could still be missing? Thank you Lydia 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. Von: Yaroslav Halchenko <deb...@onerussian.com> An: pkg-exppsy-pymvpa@lists.alioth.debian.org Datum: 02/06/2017 17:21 Betreff: Re: [pymvpa] Antwort: Re: 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: > 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? well -- you are saying flavor='iwrbadvols' so only that one should be loaded, and I guess the 'brain.nii.gz' mask is of the 'compatible' dimensionality I guess. otherwise I would have expected it to fail earlier. But the above shows the "culprit" -- 1.50x1.50x1.50x0.00 so your TR there is set to 0 sec... so time indices are degenerate and I guess that played out somewhere (may be compressed everything into a single sample or smth like that) You could fix it via a quick python code using nibabel or using nifti_tool ... --help gives e.g. modifying nifti_1_header fields: -mod_field descrip 'toga, toga, toga' -mod_field qoffset_x 19.4 -mod_field qoffset_z -11 -mod_field pixdim '1 0.9375 0.9375 1.2 1 1 1 1' -- 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
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