[MINC-users] mincresample -like problem

[Robert D. Vincent]

Hi Jerome,

I'm not sure. Those warnings may not be telling us anything important. Does
the output of mincresample look good?

Can you send the output of mincheader for TEP_sum.mnc?

    -bert

On Wed, Jun 7, 2017 at 10:51 AM, Jérôme Redouté <redoute at cermep.fr> wrote:

> Hi all,
>
> here is the problem we are facing with:
>
> 1. dcm2mnc DICOM to TEP_DYN.mnc
>
> 2. mincaverage  -avgdim time TEP_DYN.mnc TEP_sum.mnc
>
> 3. mnc2nii TEP_sum.mnc TEP_sum.nii
>
> 3. we use SPM to coregister TEP_sum.nii with MRI, segment MRI and then
> push ATLAS.nii in TEP_sum space
>
> 4. at this point: ATLAS.nii and TEP_sum.nii are well coregistred when
> checking with register
>
> 5. nii2mnc -byte ATLAS.nii ATLAS.mnc
>
> 6. then we need to resample ATLAS.mnc:
>
>     mincresample -verbose -nearest_neighbour -byte -like TEP_sum.mnc
> ATLAS.mnc ATLAS_Res.mnc
>
> the problem is at this step:
>
> we get warnings:
>
> WARN: Irregular dimension in file TEP_sum.mnc contains non-monotonic or
>> repeated values.
>> WARN: Something is wrong with the irregular dimension in file TEP_sum.mnc.
>>       Substituting a step size of 1.0.
>> WARN: Irregular dimension in file EP_sum.mnc contains non-monotonic or
>> repeated values.
>> WARN: Something is wrong with the irregular dimension in file EP_sum.mnc.
>>       Substituting a step size of 1.0.
>> WARN: Irregular dimension in file EP_sum.mnc contains non-monotonic or
>> repeated values.
>> WARN: Something is wrong with the irregular dimension in file EP_sum.mnc.
>>       Substituting a step size of 1.0.
>>
> and the resulting ATLAS_Res.mnc is not coregistred with TEP_sum.mnc
>
> Any ideas n what is wrong with our reference image?
>
> thank you
>
> Jerome
>
>
>
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