[MINC-users] minctracc/masking bug?

[Vladimir S. FONOV]

What is the procedure that you are using for flipping the grid file ?

The way how I am doing it in my symmetric model building script (
https://github.com/vfonov/build_average_model )  :

nlfit_s $input $model $tempdir/left_nl.xfm -source_mask $input_mask
-target_mask $model_mask -level $level

nlfit_s $input_flip $model $tempdir/right_nl.xfm -source_mask
$input_flip_mask -target_mask $model_mask \
     -level $level -work_dir $tempdir

xfm_normalize.pl $tempdir/left_nl.xfm $tempdir/output_left.xfm -like
$model --step $level

xfmconcat $flip $tempdir/right_nl.xfm $flip $tempdir/right_nl_flip.xfm

#make nonlinear only
xfm_normalize.pl $tempdir/right_nl_flip.xfm
$tempdir/output_right_flip.xfm -like $model --step $level

#average left and right flipped
xfmavg $tempdir/output_left.xfm $tempdir/output_right_flip.xfm $output

On Tue, May 21, 2013 at 12:07 AM, Alex Zijdenbos <zijdenbos at gmail.com> wrote:
> Thanks, Claude - looking at your suggestions (and at the minctracc
> source code). In the mean time, I performed some phenomenological
> experiments that I thought would be interesting to share. Here's what
> I did:
>
> - take 100 subjects, already in linear template (stx) space
> - register these with an nlfit*-like process, up to 4mm grid step
> size, to a symmetric template+mask
> - flip the subject image and its mask about x=0, repeat the registration
> - flip the resampled image and the grid from the registration again about x=0
> - calculate the magnitude of the difference between the 'normal' and
> '2xflipped' grid (per subject)
>
> - average the 'normal' and '2xflipped' grid files across subjects
> - calculate the magnitude of the difference between the average
> 'normal' and average '2xflipped' grid files
>
> In the end, what I am left with is the asymmetry in the deformation
> field(s) due solely to the registration process; if minctracc were
> unbiased, these difference images would be 0. This image:
>
> https://dl.dropboxusercontent.com/u/5709165/def_diff_mag.jpeg
>
> shows the average of the non-linearly registered images over these 100
> subjects; and the magnitude of the difference of the average
> deformation estimated 'normally' and '2xflipped'. Note that the in
> these population averages, the maximum deformation magnitude is 2.86;
> in individual subjects, the max magnitude of the deformation
> difference is typically in the 10-20 range. In other words, the
> asymmetry in the estimated deformation field purely caused by the
> methodology, can be as high as 20mm.
>
> I'd be very happy if somebody could run a similar experiment, if
> anything on a single subject; just to confirm that I didn't do
> anything fundamentally wrong somewhere (which would be great).
>
> -- A
>
>
>
>
>
> On Fri, May 10, 2013 at 2:00 PM, Claude LEPAGE <claude at bic.mni.mcgill.ca> wrote:
>> Alex,
>>
>>> So far the only explanation I can think of, is that the optimizer
>>> follows a particular/fixed trajectory through the parameter space,
>>> implicitly generating an "expansion force" in a particular direction
>>> that can go unchecked given the right set of circumstances (a
>>> particular mask being one of them). Anyways, still testing different
>>> parameters, will report on what I find.
>>
>> Can you do only 1 iteration of minctracc? Is symmetry preserved?
>> Try this 1 iteration with and without smoothing (set smoothing weight
>> to zero). Still symmetric?
>>
>> Your suggestion above sounds like the result could be influenced by
>> the order of the loops. This is a common mistake in numerical analysis.
>> For example:
>>    vec[i] = some_function( vec[i-1], vec[i], vec[i+1] );
>> When you process vec[i+1], the value of its previous neighbour has
>> changed, so running the loop forward/backward gives a different answer.
>> You can check the code for something like this (good luck).
>>
>> Have you tried minctracc 0.99.3? Have you tried mincreshape to change
>> the x,y,z ordering? I doubt this will have an impact on the results.
>>
>> Claude
>>
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
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>>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
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-- 
Best regards,

 Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com