[pymvpa] searchlight gets stuck, issues error

[Sergey.V.Fogelson at Dartmouth.edu]

Hi,

Thanks for the quick reply.

I had upgraded to 0.4.4 when I reported this bug and whereas before it  
just got stuck at 68% (with 0.4.2), the new version actually issues  
the error I reported before. Thus, the fix via upgrade doesnt seem to  
do the trick. i will try to do the mask checking as recommended.

thanks,
Sergey.

Quoting Yaroslav Halchenko <debian at onerussian.com>:

> make sure that your mask doesn't include any voxel with 0s (i.e. you've
> masked them out prior loading with different mask).  Or just use 0.4.4
> -- that one shouldn't scale C in such cases which would avoid 'getting
> stuck'
>
> On Tue, 02 Feb 2010, Sergey.V.Fogelson at Dartmouth.edu wrote:
>
>> Hello,
>
>> Im running the searchlight algorithm on some data and it gets stuck
>> right around 68% complete.
>
>> Ive zscored and detrended the dataset before preprocessing. the
>> error that is issued says that the SVM classifier cannot converge
>> because of zero norm.
>
>> here's the code ive used to preprocess the data:
>
>> if __debug__:
>>     debug.active += ["SLC"]
>
>> attr = SampleAttributes('FFA_class_25jan10sf0')
>
>> dataset = NiftiDataset(samples='25jan10sf.nii', labels=attr.labels,
>> chunks=attr.chunks, mask = 'mask.nii')
>
>> detrend(dataset, perchunk=True, model="linear", polyord = 1)
>
>> zscore(dataset, perchunk=True,targetdtype= 'float16')
>
>> dataset = dataset.select( labels = [1,2] )
>
>> clf = LinearCSVMC()
>
>> cv = CrossValidatedTransferError(TransferError(clf), NFoldSplitter())
>> s1 = Searchlight(cv, radius=9)
>
>
>> s1_map = s1(dataset)
>> orig_s1_map = dataset.mapReverse(N.array(s1_map))
>> data_hdr = dataset.niftihdr
>> NiftiImage(orig_s1_map,header=data_hdr).save('9mmSL_SVM_tr1_facevshouse.nii.gz')
>
>
> --
>                                   .-.
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>
>
>
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