[MINC-users] retrieve coregistration

[Jérôme Redouté]

Hi,
modifying zstart effectively corrects z mismatch
unfortunately, x and y do not align files correctly and I keep a small 
mismatch
Here is an example of dataset:
https://dl.univ-lyon1.fr/iulbw8zre0
Thanks
Jerome


Le 15/09/2016 à 14:58, Robert D. Vincent a écrit :
> Hi,
>
> So the xspace and yspace values have changed slightly, but the zspace
> origin has been changed dramatically.
>
> If you do the following command:
>
> minc_modify_header -dinsert zspace:start=48.3 ratio_original.mnc
>
> Do the files line up correctly?
>
>
>
> On Thu, Sep 15, 2016 at 8:24 AM, Jérôme Redouté <redoute at cermep.fr> wrote:
>
>> Hi Robert,
>> here is the output of mincinfo
>>
>> file: CHAPO06620_F15_04_DYN_avg.mnc
>>> image: signed__ short -32768 to 32767
>>> image dimensions: xspace zspace yspace
>>>      dimension name         length         step        start
>>>      --------------         ------         ----        -----
>>>      xspace                    176          0.6        -52.8
>>>      zspace                    164    -0.601562         48.3
>>>      yspace                    208    -0.601562      63.8531
>>>
>>>
>>> file: ratio_original.mnc
>>> image: signed__ short -32000 to 32000
>>> image dimensions: zspace yspace xspace
>>>      dimension name         length         step        start
>>>      --------------         ------         ----        -----
>>>      zspace                    164    -0.601562           -0
>>>      yspace                    208     0.601562     -62.2617
>>>      xspace                    176          0.6        -52.5
>>>
>> PS: imgratio is a tool from Turku's PET center
>>
>> Jerome
>>
>>
>>
>>
>> Le 15/09/2016 à 12:23, Robert D. Vincent a écrit :
>>
>>> Hi Jérôme,
>>>
>>> I don't know the "imgratio" tool, is it possible it is changing or
>>> deleting
>>> the voxel-to-world transform? What is the output of mincinfo on the two
>>> mnc
>>> files?
>>>
>>> If the basic sampling grid hasn't changed, you should be able to use
>>> minc_modify_header to put the original voxel-to-world transform back into
>>> the ratio.mnc header.
>>>
>>>       -bert
>>>
>>> On Thu, Sep 15, 2016 at 5:59 AM, Jérôme Redouté <redoute at cermep.fr>
>>> wrote:
>>>
>>> Hi all,
>>>> I need your help concerning a coregistration loss problem during image
>>>> processing.
>>>>
>>>> I have a mnc PET 4D volume that I need to process in ECAT format.
>>>>
>>>> My processing steps are as follows:
>>>>
>>>> DYN.mnc => ecat with minctoecat
>>>>
>>>> ecat processing (imgratio) to generate a ratio image => ratio.v
>>>>
>>>> convert back to minc using ecattominc => ratio.mnc
>>>>
>>>> my problem is that ratio.mnc is not in alignment with DYN.mnc
>>>>
>>>>
>>>> How should I correct ratio.mnc header to bring this alignment back?
>>>>
>>>> Thanks for your help
>>>>
>>>> Jerome
>>>>
>>>> --
>>>> ==================================================================
>>>> 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
>>>>
>>>> _______________________________________________
>>> 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
>>
> _______________________________________________
> 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
==================================================================