[Neuroimaging] PAR/REC scaling in nibabel

[Gregory Lee]

Hi Mike,

Yes, the default is 'dv'.  The documentation could be updated to make this
clearer.

p.s.
Depending on the data you have, one other thing to watch out for is the
strict_sort flag.  I recommend always setting strict_sort=True, but it is
False by default for reasons of backwards compatibility.  It won't matter
for simple 3D structural scans or standard fMRI timeseries data, but for
anything with additional dimensions (such as echoes, ASL tagging labels,
etc) it prevents things from potentially getting mis-sorted.  It doesn't
hurt to always have it on by default.



On Fri, Aug 18, 2017 at 1:18 AM, Mike Jarrett <mike.jarrett at ubc.ca> wrote:

> Hello experts!
>
> After some trial and error, I've discovered that (at least in the cases
> I've checked), the default action of nib.parrec.load('file.PAR') is to
> scale the rec image to "display values".
>
> In other words,
> > nib.parrec.load('file.PAR').get_data()
> returns the same values as
> > nib.parrec.load('file.PAR',scaling='dv').get_data()
>
> Is this the intended behaviour? The docs don't seem to explicitly say that
> scaling='dv' is the default, only that setting the scaling value is
> optional. I had naively expected that not setting a preferred scaling would
> return the raw unscaled values.
>
> Could anyone shed light on this for me? I now know I can just set
> scaling='fp' to get floating point values, but it would put my mind at ease
> if someone could confirm that I'm looking at this correctly.
>
> Thanks!
>
> Mike Jarrett
>
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