[MINC-users] information loss after mincreshape

[Alex Zijdenbos]

Hi Jerome,

Although I don't think this explains what you are seeing, I suspect that
this:

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

may not do what you think it does, due to this, rather non-intuitive, bit
in the man page:

       +direction
              Flip images to give positive step value for spatial axes.
Note that the flipping of spatial axes only applies to "image dimensions".
These are the  two  fastest
              varying (non-vector) dimensions in the file. If you want to
flip a non-image dimension, you can convert it to an image dimension with
-dimsize dimname=-1 (the -1
              means don't really change the size). Check out the examples.

-- A


On Thu, May 18, 2017 at 9:30 AM, Jérôme Redouté <redoute at cermep.fr> wrote:

> 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
>>>
>>>
>>
>>
> _______________________________________________
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> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>