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Merge pull request #561 from rmarkello/brikhead
NF: Functionality for reading AFNI BRIK/HEAD
2 parents 636d5d2 + c5f0ecf commit 4c2bca7

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+1310
-5
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‎nibabel/brikhead.py

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‎nibabel/imageclasses.py

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@@ -9,6 +9,7 @@
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''' Define supported image classes and names '''
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from .analyze import AnalyzeImage
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from .brikhead import AFNIImage
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from .cifti2 import Cifti2Image
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from .freesurfer import MGHImage
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from .gifti import GiftiImage
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Cifti2Image, Nifti2Image, # Cifti2 before Nifti2
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Spm2AnalyzeImage, Spm99AnalyzeImage, AnalyzeImage,
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Minc1Image, Minc2Image, MGHImage,
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PARRECImage, GiftiImage]
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PARRECImage, GiftiImage, AFNIImage]
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# DEPRECATED: mapping of names to classes and class functionality
@@ -88,7 +89,12 @@ def __getitem__(self, *args, **kwargs):
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'ext': '.par',
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'has_affine': True,
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'makeable': False,
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'rw': False})
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'rw': False},
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afni={'class': AFNIImage,
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'ext': '.brik',
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'has_affine': True,
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'makeable': False,
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'rw': False})
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class ExtMapRecoder(Recoder):
@@ -107,14 +113,15 @@ def __getitem__(self, *args, **kwargs):
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('mgh', '.mgh'),
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('mgz', '.mgz'),
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('par', '.par'),
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('brik', '.brik')
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))
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# Image classes known to require spatial axes to be first in index ordering.
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# When adding an image class, consider whether the new class should be listed
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# here.
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KNOWN_SPATIAL_FIRST = (Nifti1Pair, Nifti1Image, Nifti2Pair, Nifti2Image,
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Spm2AnalyzeImage, Spm99AnalyzeImage, AnalyzeImage,
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MGHImage, PARRECImage)
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MGHImage, PARRECImage, AFNIImage)
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def spatial_axes_first(img):

‎nibabel/tests/data/bad_attribute+orig.HEAD

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type = string-attribute
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name = DATASET_NAME
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count = 5
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'none~
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type = string-attribute
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name = TYPESTRING
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count = 15
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'3DIM_HEAD_ANAT~
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type = string-attribute
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name = IDCODE_STRING
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count = 27
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'AFN_-zxZ0OyZs8eEtm9syGBNdA~
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type = string-attribute
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name = IDCODE_DATE
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count = 25
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'Sun Oct 1 21:13:09 2017~
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type = integer-attribute
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name = SCENE_DATA
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count = 8
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0 2 0 -999 -999
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-999 -999 -999
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type = string-attribute
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name = LABEL_1
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count = 5
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'none~
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type = string-attribute
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name = LABEL_2
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count = 5
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'none~
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type = integer-attribute
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name = ORIENT_SPECIFIC
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count = 3
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0 3 4
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type = float-attribute
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name = ORIGIN
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count = 3
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-49.5 -82.312 -52.3511
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type = float-attribute
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name = DELTA
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count = 3
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3 3 3
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type = float-attribute
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name = IJK_TO_DICOM
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count = 12
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3 0 0 -49.5 0
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3 0 -82.312 0 0
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3 -52.3511
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type = float-attribute
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name = IJK_TO_DICOM_REAL
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count = 12
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3 0 0 -49.5 0
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3 0 -82.312 0 0
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3 -52.3511
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type = float-attribute
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name = BRICK_STATS
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count = 6
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0 13722 0 10051 0
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type = integer-attribute
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name = TAXIS_NUMS
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count = 8
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3 25 77002 -999 -999
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-999 -999 -999
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type = float-attribute
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name = TAXIS_FLOATS
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count = 8
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0 3 0 -52.3511 3
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-999999 -999999 -999999
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type = float-attribute
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name = TAXIS_OFFSETS
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count = 25
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0.3260869 1.826087 0.3913043 1.891304 0.4565217
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1.956521 0.5217391 2.021739 0.5869564 2.086956
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0.6521738 2.152174 0.7173912 2.217391 0.7826086
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2.282609 0.8478259 2.347826 0.9130433 2.413044
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0.9782607 2.478261 1.043478 2.543479 1.108696
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type = integer-attribute
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name = DATASET_RANK
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count = 8
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3 3 0 0 0
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0 0 0
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type = integer-attribute
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name = DATASET_DIMENSIONS
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count = 5
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type = integer-attribute
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name = BRICK_TYPES
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count = 3
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1 1 1
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type = float-attribute
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name = BRICK_FLOAT_FACS
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count = 3
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0 0 0
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type = string-attribute
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name = TEMPLATE_SPACE
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count = 5
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'ORIG~
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type = integer-attribute
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name = INT_CMAP
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count = 1
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0
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type = integer-attribute
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name = BYTEORDER_STRING
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count = 10
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'LSB_FIRST~
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type = string-attribute
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name = BRICK_LABS
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count = 9
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'#0~#1~#2~

‎nibabel/tests/data/bad_datatype+orig.HEAD

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type = string-attribute
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name = DATASET_NAME
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count = 5
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'none~
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type = string-attribute
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name = TYPESTRING
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count = 15
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'3DIM_HEAD_ANAT~
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type = string-attribute
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name = IDCODE_STRING
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count = 27
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'AFN_-zxZ0OyZs8eEtm9syGBNdA~
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type = string-attribute
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name = IDCODE_DATE
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count = 25
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'Sun Oct 1 21:13:09 2017~
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type = integer-attribute
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name = SCENE_DATA
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count = 8
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0 2 0 -999 -999
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-999 -999 -999
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type = string-attribute
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name = LABEL_1
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count = 5
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'none~
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type = string-attribute
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name = LABEL_2
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count = 5
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'none~
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type = integer-attribute
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name = ORIENT_SPECIFIC
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count = 3
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0 3 4
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type = float-attribute
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name = ORIGIN
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count = 3
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type = float-attribute
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name = DELTA
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count = 3
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3 3 3
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type = float-attribute
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name = IJK_TO_DICOM
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count = 12
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3 0 0 -49.5 0
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3 0 -82.312 0 0
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3 -52.3511
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type = float-attribute
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name = IJK_TO_DICOM_REAL
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count = 12
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3 0 0 -49.5 0
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3 0 -82.312 0 0
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3 -52.3511
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type = float-attribute
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name = BRICK_STATS
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count = 6
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0 13722 0 10051 0
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type = integer-attribute
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name = TAXIS_NUMS
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count = 8
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3 25 77002 -999 -999
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-999 -999 -999
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type = float-attribute
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name = TAXIS_FLOATS
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count = 8
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0 3 0 -52.3511 3
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-999999 -999999 -999999
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type = float-attribute
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name = TAXIS_OFFSETS
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count = 25
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0.3260869 1.826087 0.3913043 1.891304 0.4565217
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1.956521 0.5217391 2.021739 0.5869564 2.086956
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0.6521738 2.152174 0.7173912 2.217391 0.7826086
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2.282609 0.8478259 2.347826 0.9130433 2.413044
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0.9782607 2.478261 1.043478 2.543479 1.108696
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type = integer-attribute
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name = DATASET_RANK
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count = 8
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3 3 0 0 0
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0 0 0
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type = integer-attribute
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name = DATASET_DIMENSIONS
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count = 5
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33 41 25 0 0
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type = integer-attribute
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name = BRICK_TYPES
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count = 3
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1 3 5
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type = float-attribute
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name = BRICK_FLOAT_FACS
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count = 3
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0 0 0
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type = string-attribute
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name = TEMPLATE_SPACE
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count = 5
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'ORIG~
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type = integer-attribute
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name = INT_CMAP
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count = 1
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0
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type = string-attribute
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name = BYTEORDER_STRING
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count = 10
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'LSB_FIRST~
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type = string-attribute
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name = BRICK_LABS
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count = 9
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'#0~#1~#2~

‎nibabel/tests/data/example4d+orig.BRIK.gz

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