[MINC-users] minctracc error

[Andrew Janke]

Hi Anthonin,

On Sat, Feb 20, 2010 at 09:22, Anthonin Reilhac
<anthonin at biospective.com> wrote:
> I am currently experiencing issues with minctracc which crashes and outputs
> this error:
> *Error in /usr/local/bic/bin/minctracc in file init_params.c, line 593
> Cannot calculate the COG or COV of volume 1.*

minctracc really doesn't do all that well with non 3D data as only a
small out of plane registration is needed to send things haywire. You
can fiddle with the weights parameters but it still won't help you
that much.   My suggestions would be to make the problem "more 3D".
The easiest way to do this is to turn each of your 2D slices into a
thick 3D "cylinder" as such:

(assuming 1mm voxels)

# First fake  3D block:
mincconcat -concat_dimension zspace slice.mnc slice.mnc slice.mnc
slice.mnc slice.mnc slice.mnc slice.mnc slice.mnc -step 1 -start 0
block.mnc

# then add a few blank slices top and bottom and blur the edges
volpad -distance 4 -smooth -smooth_distance 2 block.mnc padded.mnc

Then run minctracc on your resulting padded volumes.  I would set the
out of plane rotations weights to 0:

   minctracc -w_rotations 0 0 0.0174533 ...

Once you have recovered a transformation you can then apply this to
the original volumes and hope all goes well. :)

volpad can be found here:

   http://mavis.anu.edu.au/scripts/



--
Andrew Janke
(a.janke at gmail.com || http://a.janke.googlepages.com/)
Canberra->Australia    +61 (402) 700 883