<div dir="ltr"><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small">Hi Yaroslav, <br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small"><br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif;font-size:small">Here's the complete output of the original code, error messages, and output of mvpa2.wtf(). Thanks!<br><br>Su Mei<br><br>>>> from mvpa2.tutorial_suite import *<br>>>> ds=get_raw_haxby2001_data(roi='vt')<br>>>> part=ChainNode([NFoldPartitioner(), Balancer(limit='partitions',apply_selection=True)], space='partitions')<br>>>> sl=sphere_gnbsearchlight(GNB(),part,postproc=mean_sample())<br>>>> map=sl(ds)<br>Traceback (most recent call last):<br>  File "<stdin>", line 1, in <module><br>  File "/home/user/anaconda/lib/python2.7/site-packages/mvpa2/base/learner.py", line 259, in __call__<br>    return super(Learner, self).__call__(ds)<br>  File "/home/user/anaconda/lib/python2.7/site-packages/mvpa2/base/node.py", line 121, in __call__<br>    result = self._call(ds)<br>  File "/home/user/anaconda/lib/python2.7/site-packages/mvpa2/measures/searchlight.py", line 143, in _call<br>    results = self._sl_call(dataset, roi_ids, nproc)<br>  File "/home/user/anaconda/lib/python2.7/site-packages/mvpa2/measures/adhocsearchlightbase.py", line 353, in _sl_call<br>    if not (np.all(<a href="http://p.sa">p.sa</a>[targets_sa_name].value == labels)):<br>ValueError: shape mismatch: objects cannot be broadcast to a single shape<br>>>> print mvpa2.wtf()<br>Current date:   2014-11-01 12:51<br>PyMVPA:<br> Version:       2.3.1<br> Hash:          $Format:%H$<br> Path:          /home/user/anaconda/lib/python2.7/site-packages/mvpa2/__init__.pyc<br> Version control (GIT):<br> GIT information could not be obtained due "/home/user/anaconda/lib/python2.7/site-packages/mvpa2/.. is not under GIT"<br>SYSTEM:<br> OS:            posix Linux 2.6.32-431.11.2.el6.x86_64 #1 SMP Tue Mar 25 19:59:55 UTC 2014<br> Distribution:  centos/6.5/Final<br>EXTERNALS:<br> Present:       cPickle, ctypes, good scipy.stats.rdist, good scipy.stats.rv_continuous._reduce_func(floc,fscale), good scipy.stats.rv_discrete.ppf, griddata, gzip, h5py, hdf5, ipython, liblapack.so, libsvm, libsvm verbosity control, lxml, matplotlib, mock, nibabel, nose, numpy, numpy_correct_unique, pylab, pylab plottable, scipy, skl, statsmodels, weave<br> Absent:        atlas_fsl, atlas_pymvpa, cran-energy, elasticnet, glmnet, hcluster, lars, mass, mdp, mdp ge 2.4, nipy, nipy.neurospin, numpydoc, openopt, pprocess, pywt, pywt wp reconstruct, pywt wp reconstruct fixed, reportlab, rpy2, running ipython env, sg ge 0.6.4, sg ge 0.6.5, sg_fixedcachesize, shogun, shogun.krr, shogun.lightsvm, shogun.mpd, shogun.svmocas, shogun.svrlight<br> Versions of critical externals:<br>  ctypes      : 1.1.0<br>  h5py        : 2.3.1<br>  hdf5        : 1.8.13<br>  ipython     : 2.2.0<br>  lxml        : 3.4.0<br>  matplotlib  : 1.4.0<br>  mock        : 1.0.1<br>  nibabel     : 1.3.0<br>  numpy       : 1.9.0<br>  scipy       : 0.14.0<br>  skl         : 0.15.2<br> Matplotlib backend: Qt4Agg<br>RUNTIME:<br> PyMVPA Environment Variables:<br>   PyMVPA Runtime Configuration:<br>  [general]<br>  verbose = 1<br>  <br>  [externals]<br>  have running ipython env = no<br>  have numpy = yes<br>  have scipy = yes<br>  have matplotlib = yes<br>  have h5py = yes<br>  have reportlab = no<br>  have weave = yes<br>  have good scipy.stats.rdist = yes<br>  have good scipy.stats.rv_discrete.ppf = yes<br>  have good scipy.stats.rv_continuous._reduce_func(floc,fscale) = yes<br>  have pylab = yes<br>  have lars = no<br>  have elasticnet = no<br>  have glmnet = no<br>  have skl = yes<br>  have ctypes = yes<br>  have libsvm = yes<br>  have shogun = no<br>  have openopt = no<br>  have nibabel = yes<br>  have mdp = no<br>  have mdp ge 2.4 = no<br>  have nipy = no<br>  have statsmodels = yes<br>  have pywt = no<br>  have cpickle = yes<br>  have gzip = yes<br>  have cran-energy = no<br>  have griddata = yes<br>  have nipy.neurospin = no<br>  have lxml = yes<br>  have pprocess = no<br>  have atlas_fsl = no<br>  have atlas_pymvpa = no<br>  have hcluster = no<br>  have hdf5 = yes<br>  have ipython = yes<br>  have liblapack.so = yes<br>  have libsvm verbosity control = yes<br>  have mass = no<br>  have mock = yes<br>  have nose = yes<br>  have numpy_correct_unique = yes<br>  have numpydoc = no<br>  have pylab plottable = yes<br>  have pywt wp reconstruct = no<br>  have pywt wp reconstruct fixed = no<br>  have rpy2 = no<br>  have sg ge 0.6.4 = no<br>  have sg ge 0.6.5 = no<br>  have sg_fixedcachesize = no<br>  have shogun.krr = no<br>  have shogun.lightsvm = no<br>  have shogun.mpd = no<br>  have shogun.svmocas = no<br>  have shogun.svrlight = no<br> Process Information:<br>  Name:    python<br>  State:    R (running)<br>  Tgid:    9541<br>  Pid:    9541<br>  PPid:    9335<br>  TracerPid:    0<br>  Uid:    668400015    668400015    668400015    668400015<br>  Gid:    668400015    668400015    668400015    668400015<br>  Utrace:    0<br>  FDSize:    256<br>  Groups:    668400015 668400024 668400025 668400027 668400028 <br>  VmPeak:     1813844 kB<br>  VmSize:      901476 kB<br>  VmLck:           0 kB<br>  VmHWM:     1081372 kB<br>  VmRSS:      147476 kB<br>  VmData:      205908 kB<br>  VmStk:          92 kB<br>  VmExe:           4 kB<br>  VmLib:      129200 kB<br>  VmPTE:        1464 kB<br>  VmSwap:           0 kB<br>  Threads:    9<br>  SigQ:    0/1678307<br>  SigPnd:    0000000000000000<br>  ShdPnd:    0000000000000000<br>  SigBlk:    0000000000000000<br>  SigIgn:    0000000001001004<br>  SigCgt:    0000000180010002<br>  CapInh:    0000000000000000<br>  CapPrm:    0000000000000000<br>  CapEff:    0000000000000000<br>  CapBnd:    ffffffffffffffff<br>  Cpus_allowed:    ffff,ffffffff<br>  Cpus_allowed_list:    0-47<br>  Mems_allowed:    00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000000,00000003<br>  Mems_allowed_list:    0-1<br>  voluntary_ctxt_switches:    307<br>  nonvoluntary_ctxt_switches:    69<br><br><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Oct 30, 2014 at 6:34 PM, Yaroslav Halchenko <span dir="ltr"><<a href="mailto:yoh@onerussian.com" target="_blank">yoh@onerussian.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Could you post output of<br>
<br>
print mvpa2.wtf()<br>
<br>
Embedded in your script to make sure you are using those versions<br>
<br>
On October 30, 2014 6:20:47 PM EDT, Su Mei Lee <<a href="mailto:sumeilee@gmail.com">sumeilee@gmail.com</a>> wrote:<br>
>Yaroslav Halchenko <debian@...> writes:<br>
><br>
>><br>
>><br>
>> On Sun, 04 Aug 2013, Tren Huang wrote:<br>
>><br>
>> >    Good point Yaroslav! The snippet works with numpy 1.7.0 but not<br>
>1.2.1.<br>
>><br>
>> wow -- 1.2.1, that is antique! even merely supported lucid  has<br>
>1.3.0.<br>
>> so indeed -- upgrade of numpy is very advised!<br>
>><br>
><br>
><br>
>Hi,<br>
><br>
>I ran the same code from the top of this post and got the same error<br>
>when<br>
>using ChainNode with Balancer. I updated to Numpy 1.9.0, Python 2.7.8,<br>
>PyMVPA 2.3.1 but am still getting the error so I'm not sure why the<br>
>update<br>
>didn't work for me. Help?<br>
><br>
>Thanks,<br>
>Su Mei<br>
><br>
><br>
><br>
>_______________________________________________<br>
>Pkg-ExpPsy-PyMVPA mailing list<br>
><a href="mailto:Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org">Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org</a><br>
><a href="http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa" target="_blank">http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa</a><br>
<span class="HOEnZb"><font color="#888888"><br>
--<br>
Sent from a phone which beats iPhone.<br>
</font></span></blockquote></div><br></div>