[MINC-users] information loss after mincreshape

[Jérôme Redouté]

Hi all,

We are facing a new problem with mincreshape while processing dynamic 
PET data.

here is our process:

     dcm2mnc ==> dyn.mnc

     mincreshape +xdirection + ydirection +zdirection dyn.mnc tmp.mnc

we want then to reorient the image:

     param2xfm -rotations 90 0 180 dcmPET2mnc.xfm

     mincresample -transformation dcmPET2mnc.xfm tmp.mnc final.mnc -like 
template.mnc

this last step fails with the following warnings:

     "Irregular dimension in file tmp.mnc contains non-monotonic or 
repeated values"

     "substituting a step size of 1"

and the resulting file contains no data

If we don't do the mincreshape step ==>  no problem with mincresample

Any ideas?

(we are using the dev branch of Minc tools)

Thanks for your help

Jerome




Le 30/06/2016 à 16:29, Jérôme Redouté a écrit :
> Thank you!
>
> I 'm going to test it right now
>
> Best
> Jerome
>
> Le 30/06/2016 16:18, Robert D. Vincent a écrit :
>> Hi Jerome,
>>
>> I believe I have fixed the issue. After thinking about it, I believe 
>> it is
>> safe to preserve the information whenever it happens to be present, 
>> so that
>> is now the behavior of mincreshape.
>>
>> I pushed the fix to the develop branch.
>>
>>      -bert
>>
>> On Mon, Jun 27, 2016 at 8:10 AM, Jérôme Redouté <redoute at cermep.fr> 
>> wrote:
>>
>>> Hi Robert,
>>> did you find how to fix the mincreshape bug?
>>> thank you
>>> Best regards
>>>
>>> Jerome
>>>
>>> Le 15/06/2016 19:19, Robert D. Vincent a écrit :
>>>
>>>> One thing I'd like to check: is the file you're using a 
>>>> regularly-sampled
>>>> file, i.e. is there a constant time duration for each image?
>>>>
>>>>
>>>> On Wed, Jun 15, 2016 at 1:09 PM, Robert D. Vincent <
>>>> robert.d.vincent at mcgill.ca> wrote:
>>>>
>>>> Hi Jérôme,
>>>>> Thanks for the report, I've reproduced it here. It seems that 
>>>>> mincreshape
>>>>> fails to copy the time dimension properly. I will fix it as soon as
>>>>> possible.
>>>>>
>>>>>       -bert
>>>>>
>>>>> On Wed, Jun 15, 2016 at 9:53 AM, Jérôme Redouté <redoute at cermep.fr>
>>>>> wrote:
>>>>>
>>>>> Dear all,
>>>>>> I'm processing dynamic PET data acquired on Siemens Biograph mMR.
>>>>>>
>>>>>> after conversion from DICOM to MINC using dcm2mnc, I can extract 
>>>>>> frames
>>>>>> timings using:
>>>>>>
>>>>>> mincinfo -varvalue time xxx.mnc
>>>>>>
>>>>>> BUT,
>>>>>>
>>>>>> after mincreshape +xdirection +ydirection +zdirection xxx.mnc
>>>>>> xxx_res.mnc
>>>>>>
>>>>>> mincinfo -varvalue time xxx_res.mnc outputs only "0"
>>>>>>
>>>>>> any ideas about this bug?
>>>>>>
>>>>>> Thanks
>>>>>> 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
>>
>
>