<div dir="ltr">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:<div>
<br></div><div><div>Python 2.7.6 (default, Nov 10 2013, 19:24:18) [MSC v.1500 32 bit (Intel)] on win32</div><div>Type "help", "copyright", "credits" or "license" for more information.</div>
<div>>>> from mvpa2.tutorial_suite import *</div><div>'gcc' is not recognized as an internal or external command, operable program or batch file.</div><div>c:\Python27\lib\site-packages\scipy\integrate\quadpack.py:295: UserWarning: Extremely bad integrand behavior occurs at some points of the integration interval.</div>
<div> warnings.warn(msg)</div><div>>>> ds = get_haxby2001_data()</div><div>Traceback (most recent call last):</div><div> File "<stdin>", line 1, in <module></div><div> File "c:\Python27\lib\site-packages\mvpa2\tutorial_suite.py", line 42, in get_haxby2001_data</div>
<div> ds = get_raw_haxby2001_data(roi=roi)</div><div> File "c:\Python27\lib\site-packages\mvpa2\tutorial_suite.py", line 37, in get_raw_haxby2001_data</div><div> return load_datadb_tutorial_data(path=path, roi=roi)</div>
<div> File "c:\Python27\lib\site-packages\mvpa2\misc\data_generators.py", line 380, in load_datadb_tutorial_data</div><div> mask=mask)</div><div> File "c:\Python27\lib\site-packages\mvpa2\datasets\mri.py", line 209, in fmri_dataset</div>
<div> maskimg = _load_anyimg(mask)</div><div> File "c:\Python27\lib\site-packages\mvpa2\datasets\mri.py", line 338, in _load_anyimg</div><div> data = _img2data(src)</div><div> File "c:\Python27\lib\site-packages\mvpa2\datasets\mri.py", line 60, in _img2data</div>
<div> img = nibabel.load(src)</div><div> File "c:\Python27\lib\site-packages\nibabel\loadsave.py", line 54, in load</div><div> return klass.from_filename(filename)</div><div> File "c:\Python27\lib\site-packages\nibabel\spatialimages.py", line 411, in from_filename</div>
<div> return klass.from_file_map(file_map)</div><div> File "c:\Python27\lib\site-packages\nibabel\analyze.py", line 869, in from_file_map</div><div> hdrf = hdr_fh.get_prepare_fileobj(mode='rb')</div>
<div> File "c:\Python27\lib\site-packages\nibabel\fileholders.py", line 69, in get_prepare_fileobj</div><div> obj = allopen(self.filename, *args, **kwargs)</div><div> File "c:\Python27\lib\site-packages\nibabel\volumeutils.py", line 1284, in allopen</div>
<div> return opener(fname, *args, **kwargs)</div><div> File "c:\Python27\lib\gzip.py", line 34, in open</div><div> return GzipFile(filename, mode, compresslevel)</div><div> File "c:\Python27\lib\gzip.py", line 94, in __init__</div>
<div> fileobj = self.myfileobj = __builtin__.open(filename, mode or 'rb')</div><div>IOError: [Errno 2] No such file or directory: '.\\data\\mask_vt.nii.gz'</div><div>>>></div></div><div><br></div>
<div>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?). </div>
<div><br></div><div>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...</div>
<div><br></div><div><div>Python 2.7.3 (default, Jan 2 2013, 16:53:07) </div><div>[GCC 4.7.2] on linux2</div><div>Type "help", "copyright", "credits" or "license" for more information.</div>
<div>>>> from mvpa2.tutorial_suite import *</div><div>/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</div><div>
"removed in 0.16", DeprecationWarning)</div><div>/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</div>
<div> "in 0.15", DeprecationWarning)</div></div><div><br></div><div>The next step (get_haxby2001_data()) seems to work just fine though. </div><div><br></div><div>(Note I downloaded <a href="http://neuro.debian.net/debian/vm/NeuroDebian_7.2.0_i386.ova">http://neuro.debian.net/debian/vm/NeuroDebian_7.2.0_i386.ova</a>, and I let it install all the updates after I got the machine booted up)</div>
<div><br></div><div>Cheers,</div><div>Jason</div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Sat, Dec 21, 2013 at 12:18 AM, Yaroslav Halchenko <span dir="ltr"><<a href="mailto:debian@onerussian.com" target="_blank">debian@onerussian.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">and what archive have you downloaded?<br>
<br>
please also cut/paste your error entirely, including command how you<br>
started python to import mvpa2.<br>
<div><div class="h5"><br>
On Fri, 20 Dec 2013, Jason Ozubko wrote:<br>
<br>
> Hi All,<br>
> I'm trying to get started with PyMVPA but I'm having difficulties working<br>
> through the first steps of the tutorial. �When I run get_haxby2001_data()<br>
> I get an error message saying that mask_vt.nii.gz is missing. �Is it<br>
> possible the archive I've downloaded is out of data or incomplete? �Have I<br>
> made mistakes during the install process?<br>
> Any help would be appreciated.<br>
> Thanks,<br>
> Jason<br>
<br>
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--<br>
Yaroslav O. Halchenko, Ph.D.<br>
<a href="http://neuro.debian.net" target="_blank">http://neuro.debian.net</a> <a href="http://www.pymvpa.org" target="_blank">http://www.pymvpa.org</a> <a href="http://www.fail2ban.org" target="_blank">http://www.fail2ban.org</a><br>
Senior Research Associate, Psychological and Brain Sciences Dept.<br>
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