[MINC-users] mincbet

[Jon Erik Ween]

Thanks Claude

You can find some test scans at:

ftp.rotman-baycrest.on.ca/pub/Jon/testscans.cpgz

subject 14017 skull stripos nicely, 14018 does not. Both are 3T GE acquisitions.
I can't see anything particularly different about their scans. I'll try cropping
out the neck though.

Cheers

Jon

Quoting Claude LEPAGE <claude at bic.mni.mcgill.ca>:

> Hi Jon,
>
> To answer some of your questions in your recent messages...
>
> > I'm not seeing how one plots the histogram output from mincstats
> > (maybe you use another program or that?) nor how to tweak nu-correct
> > to optimize the normalization?
>
> mincstats -histo t1.txt -bins 1024 t1.mnc
> gnuplot
> gnuplot> plot "t1.txt" u 1:2 w li
> gnuplot> set grid
> gnuplot> set xrange [0:400]        (choose suitable upper limit)
> gnuplot> replot
>
> You may want to cut off the first line of t1.txt which is a very
> high voxel count for background.
>
> > If mincbet fails to converge, does it not generate a mask if you have asked
> it to?
>
> It will write out the last available mask, which may not be accurate at all.
>
> > Would anybody know why volumes from the same scanner would yield
> > vastly different mincbet results? On several scans, I wind up with
> > only half the brain masked. I've tried with and without nu_correct
> > first, though mincbet on the nu_corrected file often results in seg
> > faults. Is there any way to compare the image files to see why and how
> > they are different (I'm not sure what the critical parameters might
> > be). Any suggestions would be appreciated.
>
> In general, the masks should be similar. I have to admit though that
> mincbet is quite sensitive to data at 3 Tesla. Moreover, to obtain
> good non-uniformity correction, a good mask is needed. So there is no
> easy solution. I have been trying to improve mincbet to remove noise
> in the selection of the thresholds. It would be very useful if you
> could provide a pair of scans - one that works and one that fails -
> for testing. I could give you a better answer of the problem and
> solution. One thing you may want to try is to crop the image to
> remove the neck, something like:
>   mincreshape -start 0,0,0 -count 160,180,240  in.mnc out.mnc
> This will ensure that mincbet starts with a good centre of mass, which
> does not seem to be that easy at 3 Tesla.
>
> Claude
>
>
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