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nipy / dmriprep

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orientation uncertainties? #32

Closed akeshavan closed 5 years ago

akeshavan commented 5 years ago

@arokem : we are dropping the volumes that have > threshold outlier slices. The threshold can be defined as a number or percentation of the total number of slices. but is it safe to assume that the 2nd axis is the slice dimension? I'm thinking it's not -- is there a way with nibel to get the index of the slice dimension?

https://github.com/nipy/dmriprep/blob/master/dmriprep/run.py#L312

arokem commented 5 years ago

Yeah. I am pretty sure there are cases where this assumption would fail.

Looks like the header dim_info tuple should give us that information.

For example, I think this should work:

In [9]: img = nib.load('/Users/arokem/source/Site-SI/sub-NDARBA507GCT/dwi/sub-ND
   ...: ARBA507GCT_acq-64dir_dwi.nii.gz')                                       

In [10]: hdr = img.header                                                       

In [11]: hdr.get_dim_info()                                                     
Out[11]: (0, 1, 2)

In [12]: slice_dim = hdr.get_dim_info()[-1]

Which seems to work well in this case!

Unfortunately, this is not always preserved. For example, the data that I preprocessed through dmriprep has: 

In [13]: hdr.get_dim_info()                                                      
Out[13]: (None, None, None)

So we'll need a good fall-back strategy if that value is None (assume third dimension?). And we need to make sure we don't break it.