[Neuroimaging] 2D NIFTI images in nibabel

[Christopher J Markiewicz]

Paul,

Can you give us the output of:

>>> print(nib.load(nifti_file).header._structarr['dim'])

If the first number is 2, nibabel will (correctly) interpret to mean it
is to ignore dimensions 3+. If the first number is 3, then there's a bug.

That said, perhaps it is reasonable that a volumetric image should have
a minimum of three dimensions?

Chris

On 09/01/2016 05:14 AM, paul mccarthy wrote:
> Howdy all,
> 
> 
> Nibabel truncates the third dimension of a NIFTI image with dim3=1.
> 
> 
> (boo) ws189:nifti2D paulmc$ fslinfo MNI152_T1_2mm_sliceXY.nii.gz
> data_type      INT16
> dim1           91
> dim2           109
> dim3           1
> dim4           1
> datatype       4
> pixdim1        2.000000
> pixdim2        2.000000
> pixdim3        2.000000
> pixdim4        1.000000
> cal_max        8000.0000
> cal_min        3000.0000
> file_type      NIFTI-1+
> 
> 
> (boo) ws189:nifti2D paulmc$ ipython
> Python 2.7.11 (v2.7.11:6d1b6a68f775, Dec  5 2015, 12:54:16)
> Type "copyright", "credits" or "license" for more information.
> 
> IPython 5.1.0 -- An enhanced Interactive Python.
> ?         -> Introduction and overview of IPython's features.
> %quickref -> Quick reference.
> help      -> Python's own help system.
> object?   -> Details about 'object', use 'object??' for extra details.
> 
> In [1]: import nibabel as nib
> 
> In [2]: i = nib.load('MNI152_T1_2mm_sliceXY.nii.gz')
> 
> In [3]: i.shape
> Out[3]: (91, 109)
> 
> In [4]: i.header.get_zooms()
> Out[4]: (2.0, 2.0)
> 
> In [5]:
> 
> 
> Does anybody else think that this is a problem? 
> 
> Note that the dimensions for an image of e.g. size (91, 1, 91) will be
> preserved.
> 
> Cheers,
> 
> Paul
> 
> 
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-- 
Christopher J Markiewicz
Ph.D. Candidate, Quantitative Neuroscience Laboratory
Boston University