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

[Paul GRAVEL]

Thanks all who replied to this email!

I actually implemented Andrew's and Anthonin's recommendations, and it 
does work. Nevertheless, thanks Anders and Jim for sharing your scripts!

Best,

Paul


On Thu, 13 May 2010, Anders Rodell wrote:

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