Package: python3-nibabel
Version: 2.1.0-1
There is something a bit odd with DICOM plugin, here is what I get:
% nib-dicomfs -v -v -v -v /tmp/raw /tmp/foo
...
matched: (<bound method _Series.nifti_size of <nibabel.dft._Series
object at 0x7f4b11e4a910>>, <bound method _Series.as_nifti of
<nibabel.dft._Series object at 0x7f4b11e4a910>>)
open
/1.3.12.2.1107.5.2.30.26321.30000017030713461021800000007/20170307_122808.515000/3/3.nii
path:/1.3.12.2.1107.5.2.30.26321.30000017030713461021800000007/20170307_122808.515000/3/3.nii
part:1.3.12.2.1107.5.2.30.26321.30000017030713461021800000007
path:/1.3.12.2.1107.5.2.30.26321.30000017030713461021800000007/20170307_122808.515000/3/3.nii
part:20170307_122808.515000
path:/1.3.12.2.1107.5.2.30.26321.30000017030713461021800000007/20170307_122808.515000/3/3.nii
part:3
path:/1.3.12.2.1107.5.2.30.26321.30000017030713461021800000007/20170307_122808.515000/3/3.nii
part:3.nii
return
reading 1/13
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/fuse.py", line 362, in __call__
return apply(self.func, args, kw)
File "/usr/lib/python2.7/dist-packages/fuse.py", line 778, in wrap
res = fun(*a, **kw)
File "/usr/bin/nib-dicomfs", line 156, in open
self.fhs[i] = matched_path[1]()
File "/usr/lib/python2.7/dist-packages/nibabel/dft.py", line 173, in as_nifti
data[i, :, :] = d.pixel_array
File "/usr/lib/python2.7/dist-packages/dicom/dataset.py", line 417,
in pixel_array
return self._get_pixel_array()
File "/usr/lib/python2.7/dist-packages/dicom/dataset.py", line 399,
in _get_pixel_array
raise NotImplementedError("Pixel Data is compressed in a format
pydicom does not yet handle. Cannot return array")
NotImplementedError: Pixel Data is compressed in a format pydicom does
not yet handle. Cannot return array
getattr /
return root
However input is simply:
$ gdcminfo /tmp/raw
filename: /tmp/raw/MR0001.dcm
MediaStorage is 1.2.840.10008.5.1.4.1.1.4 [MR Image Storage]
TransferSyntax is 1.2.840.10008.1.2.1 [Explicit VR Little Endian]
NumberOfDimensions: 2
Dimensions: (1024,1024,1)
SamplesPerPixel :1
BitsAllocated :16
BitsStored :12
HighBit :11
PixelRepresentation:0
ScalarType found :UINT16
PhotometricInterpretation: MONOCHROME2
PlanarConfiguration: 0
TransferSyntax: 1.2.840.10008.1.2.1
Origin: (-969.322,-995.593,55.9534)
Spacing: (1.875,1.875,2.5)
DirectionCosines: (1,0,0,0,1,0)
Rescale Intercept/Slope: (0,1)
Orientation Label: AXIAL
filename: /tmp/raw/MR0005.dcm
MediaStorage is 1.2.840.10008.5.1.4.1.1.4 [MR Image Storage]
TransferSyntax is 1.2.840.10008.1.2.1 [Explicit VR Little Endian]
NumberOfDimensions: 2
Dimensions: (1024,1024,1)
SamplesPerPixel :1
BitsAllocated :16
BitsStored :12
HighBit :11
PixelRepresentation:0
ScalarType found :UINT16
PhotometricInterpretation: MONOCHROME2
PlanarConfiguration: 0
TransferSyntax: 1.2.840.10008.1.2.1
Origin: (-969.322,-995.593,55.9534)
Spacing: (1.875,1.875,2.5)
DirectionCosines: (1,0,0,0,1,0)
Rescale Intercept/Slope: (0,1)
Orientation Label: AXIAL
filename: /tmp/raw/MR0010.dcm
MediaStorage is 1.2.840.10008.5.1.4.1.1.4 [MR Image Storage]
TransferSyntax is 1.2.840.10008.1.2.1 [Explicit VR Little Endian]
NumberOfDimensions: 2
Dimensions: (1024,1024,1)
SamplesPerPixel :1
BitsAllocated :16
BitsStored :12
HighBit :11
PixelRepresentation:0
ScalarType found :UINT16
PhotometricInterpretation: MONOCHROME2
PlanarConfiguration: 0
TransferSyntax: 1.2.840.10008.1.2.1
Origin: (-969.322,-995.593,55.9534)
Spacing: (1.875,1.875,2.5)
DirectionCosines: (1,0,0,0,1,0)
Rescale Intercept/Slope: (0,1)
Orientation Label: AXIAL
filename: /tmp/raw/MR0008.dcm
MediaStorage is 1.2.840.10008.5.1.4.1.1.4 [MR Image Storage]
TransferSyntax is 1.2.840.10008.1.2.1 [Explicit VR Little Endian]
NumberOfDimensions: 2
Dimensions: (1024,1024,1)
SamplesPerPixel :1
BitsAllocated :16
BitsStored :12
HighBit :11
PixelRepresentation:0
ScalarType found :UINT16
PhotometricInterpretation: MONOCHROME2
PlanarConfiguration: 0
TransferSyntax: 1.2.840.10008.1.2.1
Origin: (-969.322,-995.593,55.9534)
Spacing: (1.875,1.875,2.5)
DirectionCosines: (1,0,0,0,1,0)
Rescale Intercept/Slope: (0,1)
Orientation Label: AXIAL
filename: /tmp/raw/MR0006.dcm
MediaStorage is 1.2.840.10008.5.1.4.1.1.4 [MR Image Storage]
TransferSyntax is 1.2.840.10008.1.2.1 [Explicit VR Little Endian]
NumberOfDimensions: 2
Dimensions: (1024,1024,1)
SamplesPerPixel :1
BitsAllocated :16
BitsStored :12
HighBit :11
PixelRepresentation:0
ScalarType found :UINT16
PhotometricInterpretation: MONOCHROME2
PlanarConfiguration: 0
TransferSyntax: 1.2.840.10008.1.2.1
Origin: (-969.322,-995.593,55.9534)
Spacing: (1.875,1.875,2.5)
DirectionCosines: (1,0,0,0,1,0)
Rescale Intercept/Slope: (0,1)
Orientation Label: AXIAL
filename: /tmp/raw/MR0009.dcm
MediaStorage is 1.2.840.10008.5.1.4.1.1.4 [MR Image Storage]
TransferSyntax is 1.2.840.10008.1.2.1 [Explicit VR Little Endian]
NumberOfDimensions: 2
Dimensions: (1024,1024,1)
SamplesPerPixel :1
BitsAllocated :16
BitsStored :12
HighBit :11
PixelRepresentation:0
ScalarType found :UINT16
PhotometricInterpretation: MONOCHROME2
PlanarConfiguration: 0
TransferSyntax: 1.2.840.10008.1.2.1
Origin: (-969.322,-995.593,55.9534)
Spacing: (1.875,1.875,2.5)
DirectionCosines: (1,0,0,0,1,0)
Rescale Intercept/Slope: (0,1)
Orientation Label: AXIAL
filename: /tmp/raw/MR0012.dcm
MediaStorage is 1.2.840.10008.5.1.4.1.1.4 [MR Image Storage]
TransferSyntax is 1.2.840.10008.1.2.1 [Explicit VR Little Endian]
NumberOfDimensions: 2
Dimensions: (1024,1024,1)
SamplesPerPixel :1
BitsAllocated :16
BitsStored :12
HighBit :11
PixelRepresentation:0
ScalarType found :UINT16
PhotometricInterpretation: MONOCHROME2
PlanarConfiguration: 0
TransferSyntax: 1.2.840.10008.1.2.1
Origin: (-969.322,-995.593,55.9534)
Spacing: (1.875,1.875,2.5)
DirectionCosines: (1,0,0,0,1,0)
Rescale Intercept/Slope: (0,1)
Orientation Label: AXIAL
filename: /tmp/raw/MR0003.dcm
MediaStorage is 1.2.840.10008.5.1.4.1.1.4 [MR Image Storage]
TransferSyntax is 1.2.840.10008.1.2.1 [Explicit VR Little Endian]
NumberOfDimensions: 2
Dimensions: (1024,1024,1)
SamplesPerPixel :1
BitsAllocated :16
BitsStored :12
HighBit :11
PixelRepresentation:0
ScalarType found :UINT16
PhotometricInterpretation: MONOCHROME2
PlanarConfiguration: 0
TransferSyntax: 1.2.840.10008.1.2.1
Origin: (-969.322,-995.593,55.9534)
Spacing: (1.875,1.875,2.5)
DirectionCosines: (1,0,0,0,1,0)
Rescale Intercept/Slope: (0,1)
Orientation Label: AXIAL
filename: /tmp/raw/MR0007.dcm
MediaStorage is 1.2.840.10008.5.1.4.1.1.4 [MR Image Storage]
TransferSyntax is 1.2.840.10008.1.2.1 [Explicit VR Little Endian]
NumberOfDimensions: 2
Dimensions: (1024,1024,1)
SamplesPerPixel :1
BitsAllocated :16
BitsStored :12
HighBit :11
PixelRepresentation:0
ScalarType found :UINT16
PhotometricInterpretation: MONOCHROME2
PlanarConfiguration: 0
TransferSyntax: 1.2.840.10008.1.2.1
Origin: (-969.322,-995.593,55.9534)
Spacing: (1.875,1.875,2.5)
DirectionCosines: (1,0,0,0,1,0)
Rescale Intercept/Slope: (0,1)
Orientation Label: AXIAL
filename: /tmp/raw/MR0013.dcm
MediaStorage is 1.2.840.10008.5.1.4.1.1.4 [MR Image Storage]
TransferSyntax is 1.2.840.10008.1.2.1 [Explicit VR Little Endian]
NumberOfDimensions: 2
Dimensions: (1024,1024,1)
SamplesPerPixel :1
BitsAllocated :16
BitsStored :12
HighBit :11
PixelRepresentation:0
ScalarType found :UINT16
PhotometricInterpretation: MONOCHROME2
PlanarConfiguration: 0
TransferSyntax: 1.2.840.10008.1.2.1
Origin: (-969.322,-995.593,55.9534)
Spacing: (1.875,1.875,2.5)
DirectionCosines: (1,0,0,0,1,0)
Rescale Intercept/Slope: (0,1)
Orientation Label: AXIAL
filename: /tmp/raw/MR0002.dcm
MediaStorage is 1.2.840.10008.5.1.4.1.1.4 [MR Image Storage]
TransferSyntax is 1.2.840.10008.1.2.1 [Explicit VR Little Endian]
NumberOfDimensions: 2
Dimensions: (1024,1024,1)
SamplesPerPixel :1
BitsAllocated :16
BitsStored :12
HighBit :11
PixelRepresentation:0
ScalarType found :UINT16
PhotometricInterpretation: MONOCHROME2
PlanarConfiguration: 0
TransferSyntax: 1.2.840.10008.1.2.1
Origin: (-969.322,-995.593,55.9534)
Spacing: (1.875,1.875,2.5)
DirectionCosines: (1,0,0,0,1,0)
Rescale Intercept/Slope: (0,1)
Orientation Label: AXIAL
filename: /tmp/raw/MR0011.dcm
MediaStorage is 1.2.840.10008.5.1.4.1.1.4 [MR Image Storage]
TransferSyntax is 1.2.840.10008.1.2.1 [Explicit VR Little Endian]
NumberOfDimensions: 2
Dimensions: (1024,1024,1)
SamplesPerPixel :1
BitsAllocated :16
BitsStored :12
HighBit :11
PixelRepresentation:0
ScalarType found :UINT16
PhotometricInterpretation: MONOCHROME2
PlanarConfiguration: 0
TransferSyntax: 1.2.840.10008.1.2.1
Origin: (-969.322,-995.593,55.9534)
Spacing: (1.875,1.875,2.5)
DirectionCosines: (1,0,0,0,1,0)
Rescale Intercept/Slope: (0,1)
Orientation Label: AXIAL
filename: /tmp/raw/MR0004.dcm
MediaStorage is 1.2.840.10008.5.1.4.1.1.4 [MR Image Storage]
TransferSyntax is 1.2.840.10008.1.2.1 [Explicit VR Little Endian]
NumberOfDimensions: 2
Dimensions: (1024,1024,1)
SamplesPerPixel :1
BitsAllocated :16
BitsStored :12
HighBit :11
PixelRepresentation:0
ScalarType found :UINT16
PhotometricInterpretation: MONOCHROME2
PlanarConfiguration: 0
TransferSyntax: 1.2.840.10008.1.2.1
Origin: (-969.322,-995.593,55.9534)
Spacing: (1.875,1.875,2.5)
DirectionCosines: (1,0,0,0,1,0)
Rescale Intercept/Slope: (0,1)
Orientation Label: AXIAL
