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Why can't I segment my T1w data?

See original GitHub issue

Issue Description

import ants
import numpy as np
in_brain = '/Users/derekpisner/Downloads/tuning_derivatives/BIDS/sub-25637/ses-1/anat/

sub-25637_desc-preproc_T1w.nii.gz'

img = ants.image_read(in_brain)
mask = ants.get_mask(img)

In [30]: img                                                                                                                     
Out[30]: 
ANTsImage (LPI)
	 Pixel Type : float (float32)
	 Components : 1
	 Dimensions : (12948672768602079266, 140735019887547, 0)
	 Spacing    : (0.0, 28.3333, 0.0)
	 Origin     : (71.2519, 130.012, -114.7487)
	 Direction  : [-1.  0.  0.  0. -1.  0.  0.  0.  1.]

In [30]: img_seg = ants.atropos(a=img, i='kmeans[3]', x=mask)
AttributeError                            Traceback (most recent call last)
<ipython-input-28-8990f5c3164a> in <module>
     10         'x': mymask
     11     }
---> 12     for k, v in kwargs.items():
     13         myargs[k] = v
     14 
AttributeError: 'NoneType' object has no attribute 'items'

Is this because it’s 3d?

Here’s the file: https://drive.google.com/file/d/1OuDofzvWa8ZtSnB0xseO0EezTWhwgsul/view?usp=sharing @dPys

Issue Analytics

  • State:closed
  • Created 2 years ago
  • Comments:8 (4 by maintainers)

github_iconTop GitHub Comments

1reaction
ntustisoncommented, Jul 24, 2020

It’s probably because you have a spacing of 0 in two of three dimensions.

0reactions
dPyscommented, Jul 24, 2020

@stnava – that worked. Thanks to both of you! Will close now and if I experience any further issues, I’ll reopen a new issue.

@dPys ;

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