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

[Andrew Janke]

Hi Jörg

Unfortunately attachments aren't allowed on this list but I'm going to
take a stab at this anyhow.

On 6 September 2012 20:12, Jörg Pfannmöller
<pfannmoelj at uni-greifswald.de> wrote:
> Subsequently mydata.mnc is converted to .raw format using:
> minctoraw -short -nonormalize mydata.mnc > mydata.raw
>
> This is displayed in imageJ and seem to be correct (example image attached as number 02)
>
> If mydata.mnc is depicted using mincpik:
>
> mincpik -verbose -depth 16 -scale 40 out.mnc MIFF:- | display -
>
> a rather strange image occurs (example image attached as number 03)

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.

>Sample computations using nu_correct for the reduction of intensity in homogeneities obviously are not correct if displayed with imageJ and converted using

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.


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