[MINC-users] animal

[Andrew Janke]

Hi Teodor,

This looks about right to me.  Just remember that the std parameters
of nu_correct are most suited to 1.5T data.  Thus you will be best off
to modify the -distance parameter to something more appropriate. 
About the half the default value would be a good start.


Andrew

On 2/14/06, Teodor Stanescu <teodorst at cancerboard.ab.ca> wrote:
> Hi,
>
> I have 10 3T brain image datasets that I need to segment into several ROI's. I looked through the MINC-users archive and I found the following procedure (June 2004):
>
> > The procedure is as followed:
> >
> > Step 1: mritotal $arg1'_mri.mnc' $arg1'_mri_stx_lin.xfm'
> >
> > Step 2: nu_correct $arg1'_mri.mnc' $arg1'_mri_nuc.mnc'
> >
> > Step 3: mritotal -nonlinear $arg1'_mri_nuc.mnc' -transformation
> > $arg1'_mri_stx_lin.xfm' $arg1'_mri_stx_nonlin.xfm'
> >
> > Step 4a: mincresample -like
> > /avgbrain/brain/images/icbm_template_1.00mm.mnc
> > $arg1'_mri_nuc.mnc' -transformation $arg1'_mri_stx_lin.xfm'
> > $arg1'_mri_stx_nuc.mnc'
> >
> > Step 4b: classify_clean $arg1'_mri_stx_nuc.mnc'
> > $arg1'_mri_stx_classes.mnc'
> >
> > Step 5: stx_segment $arg1'_mri_stx_nonlin.xfm' $arg1'_mri_stx_lin.xfm'
> > $arg1'_mri_stx_classes.mnc' $arg1'_mri_stx_labels.mnc'
>
> Is this still the standard procedure?
>
> Thank you.
>
> Best,
>
> Teodor Stanescu
>
> PhD candidate,
> Medical Physics
> Cross Cancer Institute
> 11560 University Avenue
> Edmonton, AB, T6G 1Z2
> Phone: (780) 432-8622
> Fax: (780) 432-8615
>
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--
Andrew Janke      (a.janke at gmail.com || www.cmr.uq.edu.au/~rotor)
Canada->Montreal                                   Cell: +1 (514) 924 2012