[MINC-users] mincresample -like problem

[Robert D. Vincent]

Hi Jerome,

Irregular dimensions in MINC are used to represent situations like a PET
acquisition with irregularly-spaced sample points in time. Irregular
dimensions are represented with a vector of sample points, in some places
the code checks that the sample points are valid (monotonically increasing,
with no repeated values). We should see errors only if there is something
wrong with the original DICOM.

Most spatial dimensions in MRI and PET are regular, meaning that they can
be expressed with just a pair of values that represent a start and step.

In the file header you sent, the spatial dimensions are marked as
irregular, but they have the correct attributes to be treated as regular.

     -bert

On Thu, Jun 8, 2017 at 8:17 AM, Jérôme Redouté <redoute at cermep.fr> wrote:

> Hi,
> Thank you Robert,
>
> this seems to fix the problem, but I had to also modify yspace and xspace
> in the same way because these WARN subsisted:
>
> WARN: Irregular dimension in file /home/redoute/protocoles/TEP/S
>> PORTIVES/DATA/BENSU/BENSU_DPN_DYN_37F_sum.mnc contains non-monotonic or
>> repeated values.
>> WARN: Something is wrong with the irregular dimension in file
>> /home/redoute/protocoles/TEP/SPORTIVES/DATA/BENSU/BENSU_DPN_
>> DYN_37F_sum.mnc.
>>       Substituting a step size of 1.0.
>> WARN: Irregular dimension in file /home/redoute/protocoles/TEP/S
>> PORTIVES/DATA/BENSU/BENSU_DPN_DYN_37F_sum.mnc contains non-monotonic or
>> repeated values.
>> WARN: Something is wrong with the irregular dimension in file
>> /home/redoute/protocoles/TEP/SPORTIVES/DATA/BENSU/BENSU_DPN_
>> DYN_37F_sum.mnc.
>>       Substituting a step size of 1.0.
>>
>
>
> few questions then:
>
> the problem is also present in the PET_DYN.mnc that comes from dcm2mnc
> conversion (can't use it for the -like option)
>
> do I need to also correct the DYN file ?
> What are the consequences of such a correction? (don't know exactly what
> is the meaning of this "regular" option...
>
> Thank you again for your precious help
>
> Jerome
>
>
>
>
>
>
> Le 07/06/2017 à 18:10, Robert D. Vincent a écrit :
>
>> HI Jerome,
>>
>> The version of mincaverage you are using is creating a strange, possibly
>> incorrect output file.
>>
>> Please try the following with the output of mincaverage:
>>
>> minc_modify_header -sinsert zspace:spacing=regular infile.mnc outfile.mnc
>>
>> and use the output of this command as the input to the -like option of
>> mincresample.
>>
>>      -bert
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>
>
> --
> ==================================================================
> Jérôme Redouté
> Ph.D. - Ingénieur de Recherche - Université Claude Bernard - Lyon1
> CERMEP - Imagerie du vivant
> 59 Bd Pinel. 69677 Bron - FRANCE
> tel : 33 (0)4 72 68 86 18 (bureau)
> tel : 33 (0)4 72 68 86 00 (standard)
> fax : 33 (0)4 72 68 86 10
> ==================================================================
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>