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FNNDSC / med2image

Converts medical images to more displayable formats, e.g. NIfTI to jpg.
MIT License
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some dcm files do not work #1

Open NicolasRannou opened 9 years ago

NicolasRannou commented 9 years ago

in chris/data:

cd data/VWFA_13_02-1691/2015.03.11-033Y-INVESTIGATORS_Kanwisher_Active-3003/

Mon Mar 23 04:23:36 2015 chris med2image.py[20777]: Converting DICOM image.
Mon Mar 23 04:23:36 2015 chris med2image.py[20777]: PatientName:                                VWFA_13_02
Mon Mar 23 04:23:36 2015 chris med2image.py[20777]: PatientAge:                                 033Y
Mon Mar 23 04:23:36 2015 chris med2image.py[20777]: PatientSex:                                 M
Mon Mar 23 04:23:36 2015 chris med2image.py[20777]: PatientID:                                  VWFA_13_02
Mon Mar 23 04:23:36 2015 chris med2image.py[20777]: SeriesDescription:                          DIFFUSION_HighRes_60dir_ColorFA
Mon Mar 23 04:23:36 2015 chris med2image.py[20777]: ProtocolName:                               DIFFUSION_HighRes_60dir
Mon Mar 23 04:23:36 2015 chris med2image.py[20777]: Converting middle slice in DICOM series:    32
Mon Mar 23 04:23:36 2015 chris med2image.py[20777]: Outputfile = ./0046-1.3.12.2.1107.5.2.32.35115.201503111041251465434043.jpg
Traceback (most recent call last):
  File "/neuro/users/chris//arch/scripts/med2image.py", line 568, in <module>
    C_convert.run()
  File "/neuro/users/chris//arch/scripts/med2image.py", line 263, in run
    self.slice_save(str_outputFile)
  File "/neuro/users/chris//arch/scripts/med2image.py", line 204, in slice_save
    pylab.imsave(astr_outputFile, self._Mnp_2Dslice, cmap = cm.Greys_r)
  File "/usr/lib/pymodules/python2.7/matplotlib/pyplot.py", line 2182, in imsave
    return _imsave(*args, **kwargs)
  File "/usr/lib/pymodules/python2.7/matplotlib/image.py", line 1302, in imsave
    fig.savefig(fname, dpi=dpi, format=format, transparent=True)
  File "/usr/lib/pymodules/python2.7/matplotlib/figure.py", line 1421, in savefig
    self.canvas.print_figure(*args, **kwargs)
  File "/usr/lib/pymodules/python2.7/matplotlib/backend_bases.py", line 2220, in print_figure
    **kwargs)
  File "/usr/lib/pymodules/python2.7/matplotlib/backend_bases.py", line 2008, in print_jpg
    buf, size = agg.print_to_buffer()
  File "/usr/lib/pymodules/python2.7/matplotlib/backends/backend_agg.py", line 524, in print_to_buffer
    FigureCanvasAgg.draw(self)
  File "/usr/lib/pymodules/python2.7/matplotlib/backends/backend_agg.py", line 451, in draw
    self.figure.draw(self.renderer)
  File "/usr/lib/pymodules/python2.7/matplotlib/artist.py", line 55, in draw_wrapper
    draw(artist, renderer, *args, **kwargs)
  File "/usr/lib/pymodules/python2.7/matplotlib/figure.py", line 1034, in draw
    func(*args)
  File "/usr/lib/pymodules/python2.7/matplotlib/artist.py", line 55, in draw_wrapper
    draw(artist, renderer, *args, **kwargs)
  File "/usr/lib/pymodules/python2.7/matplotlib/image.py", line 1030, in draw
    im = self.make_image(renderer.get_image_magnification())
  File "/usr/lib/pymodules/python2.7/matplotlib/image.py", line 999, in make_image
    x = self.to_rgba(self._A, bytes=True)
  File "/usr/lib/pymodules/python2.7/matplotlib/cm.py", line 248, in to_rgba
    raise ValueError("third dimension must be 3 or 4")
ValueError: third dimension must be 3 or 4