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Hi, thanks for the reply. <br><br>i had already typed in import nibabel and it was accepted but when i type >>>> ds = get_haxby2001_data()<br>i get RuntimeError: Required external 'nibabel' was not found. so no change from before.<br><br>Also when i do the same in ubuntu i always get the same error as shown below<br><br> IOError: [Errno 2] No such file or directory: './data/attributes.txt'<br><br>i have also added such directory to the path so it should be able to find it.<br><br>>>> sys.path.append("/home/amit/tutorial_data/data")<br><br>thanks in advance<br><br>Amit<br><br>>>> ds = get_haxby2001_data()<br>Traceback (most recent call last):<br> File "<stdin>", line 1, in <module><br> File "/home/amit/tutorial_data/tutorial_lib.py", line 44, in get_haxby2001_data<br> ds = get_raw_haxby2001_data(roi=roi)<br> File "/home/amit/tutorial_data/tutorial_lib.py", line 39, in get_raw_haxby2001_data<br> return load_datadb_demo_blockfmri(path=path, roi=roi)<br> File "mvpa/misc/data_generators.py", line 375, in load_datadb_tutorial_data<br> attr = SampleAttributes(os.path.join(path, 'attributes.txt'))<br> File "mvpa/misc/io/base.py", line 408, in __init__<br> sep=None, dtype=dtypes)<br> File "mvpa/misc/io/base.py", line 118, in __init__<br> dtype=dtype, skiplines=skiplines)<br> File "mvpa/misc/io/base.py", line 214, in _from_file<br> file_ = open(filename, 'r')<br>IOError: [Errno 2] No such file or directory: './data/attributes.txt'<br><br>>>> mvpa.wtf()<br>Current date: 2011-03-01 14:10<br>PyMVPA:<br> Version: 0.6.0~rc1<br> Hash: feda3f526efd71a5ae34f0c1fd3d8f2334d5f412<br> Path: mvpa/__init__.py<br> Version control (GIT):<br> GIT information could not be obtained due "mvpa/.. is not under GIT"<br>SYSTEM:<br> OS: posix Linux 2.6.35-22-generic #35-Ubuntu SMP Sat Oct 16 20:45:36 UTC 2010<br> Distribution: Ubuntu/10.10/maverick<br>EXTERNALS:<br> Present: cPickle, ctypes, good scipy.stats.rdist, good scipy.stats.rv_discrete.ppf, griddata, gzip, matplotlib, mdp, mdp ge 2.4, nibabel, numpy, pylab, pylab plottable, pywt, pywt wp reconstruct, reportlab, scipy, sg ge 0.6.4, sg ge 0.6.5, sg_fixedcachesize, shogun, shogun.krr, shogun.mpd, shogun.svmocas<br> Absent: atlas_fsl, atlas_pymvpa, elasticnet, glmnet, h5py, hcluster, lars, libsvm, libsvm verbosity control, lxml, mass, nipy, nose, openopt, pprocess, pywt wp reconstruct fixed, rpy2, running ipython env, shogun.lightsvm, shogun.svrlight, skl, weave<br> Versions of critical externals:<br> shogun:full : 0.9.3_r4889_2010-05-27_20:52_<br> shogun:rev : 4889<br> reportlab : 2.4<br> shogun : 0.9.3<br> matplotlib : 0.99.3<br> scipy : 0.7.2<br> mdp : 2.6<br> numpy : 1.3.0<br> ctypes : 1.1.0<br> matplotlib : 0.99.3<br> nifti : failed to query due to "nifti is not a known dependency key."<br> numpy : 1.3.0<br> pywt : 0.2.0<br> shogun : v0.9.3_r4889_2010-05-27_20:52_<br> Matplotlib backend: TkAgg<br>RUNTIME:<br> PyMVPA Environment Variables:<br> PyMVPA Runtime Configuration:<br> [externals]<br> have griddata = yes<br> have pprocess = no<br> have good scipy.stats.rdist = yes<br> have pylab plottable = yes<br> have pywt wp reconstruct = yes<br> have h5py = no<br> have lxml = no<br> have running ipython env = no<br> have nibabel = yes<br> have sg_fixedcachesize = yes<br> have elasticnet = no<br> have shogun.mpd = yes<br> have matplotlib = yes<br> have pywt wp reconstruct fixed = no<br> have scipy = yes<br> have reportlab = yes<br> have openopt = no<br> have libsvm = no<br> have nose = no<br> have weave = no<br> have atlas_fsl = no<br> have ctypes = yes<br> have hcluster = no<br> have sg ge 0.6.4 = yes<br> have sg ge 0.6.5 = yes<br> have good scipy.stats.rv_discrete.ppf = yes<br> have libsvm verbosity control = no<br> have mdp ge 2.4 = yes<br> have shogun.svrlight = no<br> have shogun = yes<br> have shogun.svmocas = yes<br> have nipy = no<br> have glmnet = no<br> have mass = no<br> have lars = no<br> have shogun.krr = yes<br> have atlas_pymvpa = no<br> have cpickle = yes<br> have mdp = yes<br> have numpy = yes<br> have pylab = yes<br> have rpy2 = no<br> have shogun.lightsvm = no<br> have pywt = yes<br> have skl = no<br> have gzip = yes<br><br><br><br><br><br><br>> Date: Tue, 1 Mar 2011 13:38:55 -0500<br>> From: michael.hanke@gmail.com<br>> To: pkg-exppsy-pymvpa@lists.alioth.debian.org<br>> Subject: Re: [pymvpa] (no subject)<br>> <br>> Hey,<br>> <br>> On Tue, Mar 01, 2011 at 05:56:43PM +0000, Daniel Agger wrote:<br>> > <br>> > Dear pymvpa helper<br>> > <br>> > Im trying to install pymvpa and i start the tutorial, and i run into<br>> > this problem.It says nibabel not found,and it requires external<br>> > nibabel but i have nibabel in my path. so i don't what to do, please<br>> > help.<br>> <br>> It doesn't look like you have it in the path.<br>> <br>> > >>> ds = get_haxby2001_data()<br>> <br>> Can you do a<br>> <br>> import nibabel<br>> <br>> right in front of that line. I guess it doesn't work and nibabel is not<br>> available.<br>> <br>> Michael<br>> <br>> -- <br>> Michael Hanke<br>> http://mih.voxindeserto.de<br>> <br>> _______________________________________________<br>> Pkg-ExpPsy-PyMVPA mailing list<br>> Pkg-ExpPsy-PyMVPA@lists.alioth.debian.org<br>> http://lists.alioth.debian.org/mailman/listinfo/pkg-exppsy-pymvpa<br> </body>
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