[pymvpa] get_haxby2001_data() missing mask_vt.nii.gz

Sun Dec 22 17:48:38 UTC 2013

Thanks for the reply Yaroslav. I am trying to setup py-mvpa on a Windows 7
machine. I downloaded and installed pymvpa2-2.2.0.win32-py2.7.exe, from the
Unofficial Windows binaries collection of Christoph Gohlke. I'm trying to
follow the getting started tutorial (Part 1: Gentle Start).  Here's what I
get on my Windows 7 machine:

Python 2.7.6 (default, Nov 10 2013, 19:24:18) [MSC v.1500 32 bit (Intel)]
on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> from mvpa2.tutorial_suite import *
'gcc' is not recognized as an internal or external command, operable
program or batch file.
c:\Python27\lib\site-packages\scipy\integrate\quadpack.py:295: UserWarning:
Extremely bad integrand behavior occurs at some points of the integration
interval.
  warnings.warn(msg)
>>> ds = get_haxby2001_data()
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "c:\Python27\lib\site-packages\mvpa2\tutorial_suite.py", line 42, in
get_haxby2001_data
    ds = get_raw_haxby2001_data(roi=roi)
  File "c:\Python27\lib\site-packages\mvpa2\tutorial_suite.py", line 37, in
get_raw_haxby2001_data
    return load_datadb_tutorial_data(path=path, roi=roi)
  File "c:\Python27\lib\site-packages\mvpa2\misc\data_generators.py", line
380, in load_datadb_tutorial_data
    mask=mask)
  File "c:\Python27\lib\site-packages\mvpa2\datasets\mri.py", line 209, in
fmri_dataset
    maskimg = _load_anyimg(mask)
  File "c:\Python27\lib\site-packages\mvpa2\datasets\mri.py", line 338, in
_load_anyimg
    data = _img2data(src)
  File "c:\Python27\lib\site-packages\mvpa2\datasets\mri.py", line 60, in
_img2data
    img = nibabel.load(src)
  File "c:\Python27\lib\site-packages\nibabel\loadsave.py", line 54, in load
    return klass.from_filename(filename)
  File "c:\Python27\lib\site-packages\nibabel\spatialimages.py", line 411,
in from_filename
    return klass.from_file_map(file_map)
  File "c:\Python27\lib\site-packages\nibabel\analyze.py", line 869, in
from_file_map
    hdrf = hdr_fh.get_prepare_fileobj(mode='rb')
  File "c:\Python27\lib\site-packages\nibabel\fileholders.py", line 69, in
get_prepare_fileobj
    obj = allopen(self.filename, *args, **kwargs)
  File "c:\Python27\lib\site-packages\nibabel\volumeutils.py", line 1284,
in allopen
    return opener(fname, *args, **kwargs)
  File "c:\Python27\lib\gzip.py", line 34, in open
    return GzipFile(filename, mode, compresslevel)
  File "c:\Python27\lib\gzip.py", line 94, in __init__
    fileobj = self.myfileobj = __builtin__.open(filename, mode or 'rb')
IOError: [Errno 2] No such file or directory: '.\\data\\mask_vt.nii.gz'
>>>

I am pretty certain the gcc step means I missed a step in installing a
component, but the get_haxby command is failing from missing files (I am
unable to find a mask_vt.nii.gz file anywhere, I suppose maybe they weren't
packaged in the unofficial binaries properly?).

Given these troubles getting things working in Windows 7, I've tried out
the NeuroDebian virtual machine (which is actually a terrific concept) and
I think I have it working.  Although I'll just say that I do get some
warnings when I try the first step in the Debian virtual machine...

Python 2.7.3 (default, Jan  2 2013, 16:53:07)
[GCC 4.7.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from mvpa2.tutorial_suite import *
/usr/lib/python2.7/dist-packages/sklearn/pls.py:7: DeprecationWarning: This
module has been moved to cross_decomposition and will be removed in 0.16
  "removed in 0.16", DeprecationWarning)
/usr/lib/python2.7/dist-packages/sklearn/linear_model/coordinate_descent.py:553:
DeprecationWarning: rho was renamed to l1_ratio and will be removed in 0.15
  "in 0.15", DeprecationWarning)

The next step (get_haxby2001_data()) seems to work just fine though.

(Note I downloaded
http://neuro.debian.net/debian/vm/NeuroDebian_7.2.0_i386.ova, and I let it
install all the updates after I got the machine booted up)

Cheers,
Jason

On Sat, Dec 21, 2013 at 12:18 AM, Yaroslav Halchenko
<debian at onerussian.com>wrote:

> and what archive have you downloaded?
>
> please also cut/paste your error entirely, including command how you
> started python to import mvpa2.
>
> On Fri, 20 Dec 2013, Jason Ozubko wrote:
>
> >    Hi All,
> >    I'm trying to get started with PyMVPA but I'm having difficulties
> working
> >    through the first steps of the tutorial. �When I run
> get_haxby2001_data()
> >    I get an error message saying that mask_vt.nii.gz is missing. �Is it
> >    possible the archive I've downloaded is out of data or incomplete?
> �Have I
> >    made mistakes during the install process?
> >    Any help would be appreciated.
> >    Thanks,
> >    Jason
>
> > _______________________________________________
> > Pkg-ExpPsy-PyMVPA mailing list
> > Pkg-ExpPsy-PyMVPA at lists.alioth.debian.org
> >
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa
>
>
> --
> Yaroslav O. Halchenko, Ph.D.
> http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org
> Senior Research Associate,     Psychological and Brain Sciences Dept.
> 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
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