[MINC-users] information loss after mincreshape

Thu May 18 10:28:02 EDT 2017

Thank you Alex,

Ok, it's still a bit obscure for me:

If I understand, one of the 3 dimensions is a non-image dimension?

Does it mean that it can only have 2 "image dimensions"?

I don't really understand what you mean by "the 2 fastest varying". How 
can I identify the "non image dimension"

thank you

Jerome

Le 18/05/2017 à 15:38, Alex Zijdenbos a écrit :
> 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
>>>>
>>>>
>>>
>> _______________________________________________
>> 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
>