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@JohnGriffiths
Last active September 23, 2016 13:19
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Dipy hcp dsi reconstruction error

====================================

I'm getting an error with dipy DSI reconstruction on HCP WU-MINN data.

It's a bit of a mystery as I've definitely got successful reconstructions using dipy with code very similar to this. But now I am getting the error below every time.

All the files are included in this gist to reproduce the error, apart from the DWI data (too big); that was simply data.nii.gz from subject 100307.

The error:

In [5]: run track_dipy_hcp_test.py


0dit-`/alexandra/mcintosh_lab/john/Software/miniconda2/envs/_ipython2.4b/lib/python2.7/site-packages/dipy/reconst/dsi.py:173: RuntimeWarning: invalid value encountered in divide
  Pr /= Pr.sum()
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
/alexandra/mcintosh_lab/john/Data/dipy_hcp_test_gist/track_dipy_hcp_test.py in <module>()
     93                              relative_peak_threshold=.5,
     94                              min_separation_angle=25,
---> 95                              parallel=False) # True
     96 
     97 # get generalized fractional anisotropy (GFA)

/alexandra/mcintosh_lab/john/Software/miniconda2/envs/_ipython2.4b/lib/python2.7/site-packages/dipy/direction/peaks.pyc in peaks_from_model(model, data, sphere, relative_peak_threshold, min_separation_angle, mask, return_odf, return_sh, gfa_thr, normalize_peaks, sh_order, sh_basis_type, npeaks, B, invB, parallel, nbr_processes)
    453         direction, pk, ind = peak_directions(odf, sphere,
    454                                              relative_peak_threshold,
--> 455                                              min_separation_angle)
    456 
    457         # Calculate peak metrics

/alexandra/mcintosh_lab/john/Software/miniconda2/envs/_ipython2.4b/lib/python2.7/site-packages/dipy/direction/peaks.pyc in peak_directions(odf, sphere, relative_peak_threshold, min_separation_angle, minmax_norm)
    128 
    129     """
--> 130     values, indices = local_maxima(odf, sphere.edges)
    131 
    132     # If there is only one peak return

/alexandra/mcintosh_lab/john/Software/miniconda2/envs/_ipython2.4b/lib/python2.7/site-packages/dipy/reconst/recspeed.so in dipy.reconst.recspeed.local_maxima (dipy/reconst/recspeed.c:4598)()

ValueError: odf can not have nans
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