[MINC-users] Conversion to MINC and visual inspection of the MINC-file

[Andrew Janke]

>> My guess is that you don't want a scale of 40 here, you probably want
>> to use a -width option instead.  The problem is that a lot of the minc
>> tools have a few constants hard-coded in there for "human head" sized
>> data so working with little voxels will occasionally cause grief.
>
> That should be considered a bug to be identified and fixed - do you know where that's still the case? We run everything at native resolution (i.e. voxel sizes between 5 and 200 micron isotropic) and haven't been bitten by that in a while with the exception of some ITK algorithms.

I don't disagree. Thus the suggestion of using -width over -scale.

>> For a start you are going to have to specify a -distance parameter to
>> nu_correct to suit your data. This will depend on field strength. One
>> of the common approaches when working with mouse data is to simple
>> scale it all to "human" size. Typically this is about a scale of 30.
>
> Eek - we really shouldn't have to do that. Step sizes should accurately reflect the acquired data. For what it's worth, we use these nu_correct parameters on mouse brain MRIs (we keep it constant regardless of whether we use ex or in-vivo data, so voxel sizes ranging from 30 to 125 micron isotropic):

Again, completely agree. But there are a number of defaults in
nu_correct that need to be changed (thanks for posting what you use).
In the first instance to see if things will "just work" I will usually
scale data to head size, test and then if all is good go back and redo
things.  Perhaps I should change my ways.

Still, this sounds like we now have something to do when I'm in
Toronto in a weeks time...



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