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 <[email protected]>:
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, [email protected] 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')
--
.-.
=------------------------------ /v\ ----------------------------=
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Yaroslav Halchenko /( )\ ICQ#: 60653192
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