[MINC-users] retrieve coregistration
Robert D. Vincent
robert.d.vincent at mcgill.ca
Wed Sep 21 07:19:26 EDT 2016
Hi,
It was enclosed in the email... Here it is again (I am cc'ing you directly
in case the mailing list software filtered out the enclosure).
-bert
On Wed, Sep 21, 2016 at 5:14 AM, Jérôme Redouté <redoute at cermep.fr> wrote:
> Thank you Robert!
> just can't finfd you python scipt ;)
> Best
> Jerome
>
>
> Le 20/09/2016 à 17:37, Robert D. Vincent a écrit :
>
>> Hi Jérôme,
>>
>> Thank you for the files. So I tried just converting your original file to
>> ecat using minctoecat, and then converting it back with ecat to minc:
>>
>> minctoecat CHAPO06620_F15_04_DYN_avg.mnc test.v
>> ecattominc test.v test.mnc
>>
>> The resulting test.mnc has reordered dimensions, but the two MINC volumes
>> align properly. So it does seem as though there is an issue with the
>> imgratio tool, it is somehow changing the voxel-to-world transform in an
>> unexpected way.
>>
>> I wrote a little Python 3 script that fixes this - it's enclosed (and
>> poorly tested at this point, so be careful).
>>
>> Here's a link to the ratio file with the corrected transform:
>>
>> https://www.dropbox.com/s/nwe7r2cqaik97vw/ratio_fixed.mnc?dl=0
>>
>> The corrected file looks fairly good when overlaid on the original in
>> Display, so hopefully imgratio isn't changing the underlying sampling of
>> the data, but rather it is only failing to properly preserve the
>> transform.
>>
>> -bert
>>
>>
>> On Fri, Sep 16, 2016 at 4:58 AM, Jérôme Redouté <redoute at cermep.fr>
>> wrote:
>>
>> 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
>>> ==================================================================
>>>
>>>
>>> _______________________________________________
>>> 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
>
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