[pymvpa] Antwort: Re: Antwort: Re: Antwort: Re: Loading normalized data with 'get_model_bold_dataset' fails

Fri Jun 2 16:51:35 UTC 2017

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 <debian at onerussian.com>
An:	pkg-exppsy-pymvpa at 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.ch at lists.alioth.debian.org>

On Fri, 02 Jun 2017, lydia.hellrung at 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

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