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3D DWI files produce are not marked as invalid, but fail VOLUME_COUNT_MISMATCH #1858
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We may need both.
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I would like to see this resolved. While @effigies noted a kludge to describe the data as 4D, this causes subsequent scripts to assume that images have different dimensions. Consider comparing two NIfTI files (e.g. from our new
In this case, one can correct this with |
I understand that the current spec requires this, but I don't think that it makes much sense to require b-values and b-vectors to accompany TRACE/ADC images, or even to implicitly assume that they have a b-value and b-vector associated with them (even 0). I understand that these fall under the definition of "raw" data, because they are produced by the computer that is attached to the scanner, but I think that we need a different tack for these files. Would it make sense to implement "ADC"/"TRACE" suffixes for these files? |
Has a decision been made about this, even if not already part of the specs, and/or coded into validator ? I also think requiring bval/bvec files for these images is silly, so if we are still unsure, perhaps we can leave these as 3D without the proposed hack and place them in .bidsignore. |
No, there hasn't been a decision and I just saw another post that reminded me of this. How about I just make an issue on the spec where we can vote about whether ADC/TRACE volumes should be |
Please note that this would still not cover the case of a b=0 with just one volume. We could require Alternative, one more b0 suffix could do, but I don't particularly like this option. |
Please vote on ADC/TRACE here: bids-standard/bids-specification#1723
I'm okay with this; this would be a simple patch to the validator, and any added text to the spec would be clarification, not a change. If there are alternatives that others would like to consider for B0 volumes then we can make a voting issue, but if not, let's just do the straightforward thing. |
Creating a fake DWI volume with shape
(5, 5, 5, 1)
, bval of0
and bvec of0\n0\n0\n
is valid. If I change the shape to(5, 5, 5)
, then I get the following error:We have a couple options here:
I don't have a strong sense of which would be the simplest or most maintainable. Schema checks would be easy to write in either case, so I would prefer to go with what makes the most sense from the perspective of understanding a dataset.
cc @neurolabusc
xref https://neurostars.org/t/question-regarding-validation-of-dwi-data/27542
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