[MINC-users] MINC-users Digest, Vol 58, Issue 5

Thu May 13 10:17:32 EDT 2010

Hi Paul

I might have a small perl script for doing the dynamic blurring of pet
scans, if you are interested ill send it to you and you could use some
of that for your csh script.

 best regards Anders

On Wed, May 12, 2010 at 6:00 PM,  <minc-users-request at bic.mni.mcgill.ca> wrote:
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> Today's Topics:
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>   1.  mincblur removes data:time variable (Paul GRAVEL)
>   2. Re: mincblur removes data:time variable (Andrew Janke)
>   3. Re: mincblur removes data:time variable (Anthonin Reilhac)
>   4. Re: mincblur removes data:time variable (Paul GRAVEL)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 12 May 2010 11:26:49 -0400 (EDT)
> From: Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
> Subject: [MINC-users]  mincblur removes data:time variable
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Cc: Paul Gravel - McGill Account <paul.gravel2 at mail.mcgill.ca>
> Message-ID:
>        <Pine.LNX.4.64.1005121121210.9617 at grumio.bic.mni.mcgill.ca>
> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>
> Dear All,
>
> I am looking into having a csh script to blur a dynamic PET scan. To
> accomplish this, I extract each frame using mincreshape, then blur them
> using mincblur, then finally concatenate (over the time dimension) the
> blurred frames into a blurred dynamic PET. However, it seems that mincblur
> removes the data:time variable, thus resulting in a concatenated blurred
> dynamic PET without the proper frame start time information.
> Is there a work around to get the proper time values reinserted in this
> blurred PET scan file?
>
> Many thanks again!
>
> Paul
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 13 May 2010 01:43:51 +1000
> From: Andrew Janke <a.janke at gmail.com>
> Subject: Re: [MINC-users] mincblur removes data:time variable
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Message-ID:
>        <AANLkTimR9N2NkcDu-KdvshmAqXtLXI16sxsYDba3NS6D at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Paul,
>
>> I am looking into having a csh script to blur a dynamic PET scan. To
>> accomplish this, I extract each frame using mincreshape, then blur them
>> using mincblur, then finally concatenate (over the time dimension) the
>> blurred frames into a blurred dynamic PET. However, it seems that mincblur
>> removes the data:time variable, thus resulting in a concatenated blurred
>> dynamic PET without the proper frame start time information.
>> Is there a work around to get the proper time values reinserted in this
>> blurred PET scan file?
>
> I can only suggest that you first extract the values and then when you
> put everything back together (with mincconcat) that you use the
> -coordlist option with your extracted time points.
>
>
> --
> Andrew Janke
> (a.janke at gmail.com || http://a.janke.googlepages.com/)
> Canberra->Australia    +61 (402) 700 883
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 12 May 2010 11:48:43 -0400
> From: Anthonin Reilhac <anthonin at biospective.com>
> Subject: Re: [MINC-users] mincblur removes data:time variable
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Message-ID:
>        <AANLkTikEvK0zuszYO6FiITit0tDzZv4qtUvC0F_WrM-5 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Paul,
>
>
>
> I can only suggest that you first extract the values and then when you
>> put everything back together (with mincconcat) that you use the
>> -coordlist option with your extracted time points.
>>
>>
>> This is what I usually do as well.
> I had the same issue with the do_PET_realignement script in which I had to
> work on individual frames and concatenate them back in a single dynamic PET
> volume.
>
>
> Anthonin
>
>> --
>> Andrew Janke
>> (a.janke at gmail.com || http://a.janke.googlepages.com/)
>> Canberra->Australia    +61 (402) 700 883
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 12 May 2010 11:54:05 -0400 (EDT)
> From: Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
> Subject: Re: [MINC-users] mincblur removes data:time variable
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Message-ID:
>        <Pine.LNX.4.64.1005121153460.17382 at grumio.bic.mni.mcgill.ca>
> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>
> Thanks Anthonin and Andrew!
>
> I will give it a try!
>
> Best,
>
> Paul
>
>
> On Wed, 12 May 2010, Anthonin Reilhac wrote:
>
>> Hi Paul,
>>
>>
>>
>> I can only suggest that you first extract the values and then when you
>>> put everything back together (with mincconcat) that you use the
>>> -coordlist option with your extracted time points.
>>>
>>>
>>> This is what I usually do as well.
>> I had the same issue with the do_PET_realignement script in which I had to
>> work on individual frames and concatenate them back in a single dynamic PET
>> volume.
>>
>>
>> Anthonin
>>
>>> --
>>> Andrew Janke
>>> (a.janke at gmail.com || http://a.janke.googlepages.com/)
>>> Canberra->Australia    +61 (402) 700 883
>>> _______________________________________________
>>> 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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>
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> End of MINC-users Digest, Vol 58, Issue 5
> *****************************************
>

-- 
Anders Bertil Rodell M.Sc. C.S. PhD.
Aarhus PET Centre, Aarhus University Hospital,
Norrebrogade 44, 8000 Aarhus C,
phone work:   +45 89 49 40 97
mobile phone: +45 61 70 85 30
email: rodell at pet.auh.dk