From simon.rit at creatis.insa-lyon.fr  Thu Jan  5 11:57:32 2017
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Thu, 5 Jan 2017 17:57:32 +0100
Subject: [Rtk-users] Type of CudaDataManager::m_BufferSize
In-Reply-To: <CAH+sHrXgomFue2HERP=9Yy9nHDoSCXPD7TvsjjvOfP8UGdatRw@mail.gmail.com>
References: <CAH+sHrXgomFue2HERP=9Yy9nHDoSCXPD7TvsjjvOfP8UGdatRw@mail.gmail.com>
Message-ID: <CAF0oig0Z4E=28egmDuZ9SRLbv-Z3TXFS-XbUm5+3GuqiUcdUpQ@mail.gmail.com>

Hi,
I have modified it, check that this is enough:
https://github.com/SimonRit/RTK/commit/ef23a0668a70c8a874eb2e2718e5f30b41f27f14
Thinking about this, I think it fixes one issue encountered by the user
louie <ghostcz at hotmail.com> with large images (that I discussed with him
during the training last June). Maybe he could confirm if he still follows
the project...
Thanks again,
Simon

On Thu, Dec 15, 2016 at 12:15 PM, Chao Wu <wuchao04 at gmail.com> wrote:

> Hi all,
>
> In utilities\ITKCudaCommon\include\itkCudaDataManager.h the type
> of CudaDataManager::m_BufferSize is unsigned int, which prevents
> buffering >4GB image data in CUDA memory. In the same file, the type
> of GPUMemPointer::m_BufferSize is size_t which looks more proper.
>
> Is there any special reason for this unsigned int type? I am going to
> change the type from unsigned int to size_t and test what will happen, but
> if anyone already have the experience please let me know. Many thanks.
>
> Best regards,
> Chao
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>
>
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From ghostcz at hotmail.com  Thu Jan  5 12:00:49 2017
From: ghostcz at hotmail.com (louie L)
Date: Thu, 5 Jan 2017 17:00:49 +0000
Subject: [Rtk-users] Type of CudaDataManager::m_BufferSize
In-Reply-To: <CAF0oig0Z4E=28egmDuZ9SRLbv-Z3TXFS-XbUm5+3GuqiUcdUpQ@mail.gmail.com>
References: <CAH+sHrXgomFue2HERP=9Yy9nHDoSCXPD7TvsjjvOfP8UGdatRw@mail.gmail.com>,
 <CAF0oig0Z4E=28egmDuZ9SRLbv-Z3TXFS-XbUm5+3GuqiUcdUpQ@mail.gmail.com>
Message-ID: <AMSPR05MB0685993F1BBFC642B97BED6B1600@AMSPR05MB068.eurprd05.prod.outlook.com>

Exactly. I changed this when I was his message a few weeks back in my own copy.
Thank you.
Maybe I will spend some time in the next few month to do some optimizations of the cuda part.

Best regards,
Louie

Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

From: Simon Rit<mailto:simon.rit at creatis.insa-lyon.fr>
Sent: Thursday, January 5, 2017 17:58
To: Chao Wu<mailto:wuchao04 at gmail.com>
Cc: rtk-users at public.kitware.com<mailto:Rtk-users at public.kitware.com>
Subject: Re: [Rtk-users] Type of CudaDataManager::m_BufferSize

Hi,
I have modified it, check that this is enough:
https://github.com/SimonRit/RTK/commit/ef23a0668a70c8a874eb2e2718e5f30b41f27f14
Thinking about this, I think it fixes one issue encountered by the user louie <ghostcz at hotmail.com<mailto:ghostcz at hotmail.com>> with large images (that I discussed with him during the training last June). Maybe he could confirm if he still follows the project...
Thanks again,
Simon

On Thu, Dec 15, 2016 at 12:15 PM, Chao Wu <wuchao04 at gmail.com<mailto:wuchao04 at gmail.com>> wrote:
Hi all,

In utilities\ITKCudaCommon\include\itkCudaDataManager.h the type of CudaDataManager::m_BufferSize is unsigned int, which prevents buffering >4GB image data in CUDA memory. In the same file, the type of GPUMemPointer::m_BufferSize is size_t which looks more proper.

Is there any special reason for this unsigned int type? I am going to change the type from unsigned int to size_t and test what will happen, but if anyone already have the experience please let me know. Many thanks.

Best regards,
Chao

_______________________________________________
Rtk-users mailing list
Rtk-users at public.kitware.com<mailto:Rtk-users at public.kitware.com>
http://public.kitware.com/mailman/listinfo/rtk-users


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From wuchao04 at gmail.com  Thu Jan  5 13:10:03 2017
From: wuchao04 at gmail.com (Chao Wu)
Date: Thu, 5 Jan 2017 19:10:03 +0100
Subject: [Rtk-users] Type of CudaDataManager::m_BufferSize
In-Reply-To: <CAF0oig0Z4E=28egmDuZ9SRLbv-Z3TXFS-XbUm5+3GuqiUcdUpQ@mail.gmail.com>
References: <CAH+sHrXgomFue2HERP=9Yy9nHDoSCXPD7TvsjjvOfP8UGdatRw@mail.gmail.com>
 <CAF0oig0Z4E=28egmDuZ9SRLbv-Z3TXFS-XbUm5+3GuqiUcdUpQ@mail.gmail.com>
Message-ID: <CAH+sHrWP8coJ080DfS8knTF=vHobfHpEX8eqfqHoLihazw+BGg@mail.gmail.com>

Thanks. The changes are identical to the ones I made in my own testing
version. It works well without any problems in the past few weeks.

Regards, Chao
Sent from Huawei Nexus 6P

2017?1?5? ??5:57?"Simon Rit" <simon.rit at creatis.insa-lyon.fr>???

> Hi,
> I have modified it, check that this is enough:
> https://github.com/SimonRit/RTK/commit/ef23a0668a70c8a874eb2e2718e5f3
> 0b41f27f14
> Thinking about this, I think it fixes one issue encountered by the user
> louie <ghostcz at hotmail.com> with large images (that I discussed with him
> during the training last June). Maybe he could confirm if he still follows
> the project...
> Thanks again,
> Simon
>
> On Thu, Dec 15, 2016 at 12:15 PM, Chao Wu <wuchao04 at gmail.com> wrote:
>
>> Hi all,
>>
>> In utilities\ITKCudaCommon\include\itkCudaDataManager.h the type
>> of CudaDataManager::m_BufferSize is unsigned int, which prevents
>> buffering >4GB image data in CUDA memory. In the same file, the type
>> of GPUMemPointer::m_BufferSize is size_t which looks more proper.
>>
>> Is there any special reason for this unsigned int type? I am going to
>> change the type from unsigned int to size_t and test what will happen, but
>> if anyone already have the experience please let me know. Many thanks.
>>
>> Best regards,
>> Chao
>>
>> _______________________________________________
>> Rtk-users mailing list
>> Rtk-users at public.kitware.com
>> http://public.kitware.com/mailman/listinfo/rtk-users
>>
>>
>
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From simon.rit at creatis.insa-lyon.fr  Fri Jan  6 05:33:25 2017
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Fri, 6 Jan 2017 11:33:25 +0100
Subject: [Rtk-users] RTK training - April 10 2017
Message-ID: <CAF0oig0Y3rdFAhsFYxLWf3cvwW5r+7ocKP7KsQhZx1gUEjNDSw@mail.gmail.com>

Dear RTK users,
We will organize a new training session on April 10 2017 in Lyon, from 9:30
am to 5:30 pm. Like last time, we organize it ourselves (although Kitware
kindly advertises it, see this link <http://www.kitware.fr/browse/152>) so
it's *free* and you can just send me an email if you want to participate.
The training is for both users and developers. We are happy to answer any
question that you might have and we are looking forward to this new
training session.
I'm looking forward to meet you at the training,
Simon
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From simon.rit at creatis.insa-lyon.fr  Sun Jan 15 04:23:37 2017
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Sun, 15 Jan 2017 10:23:37 +0100
Subject: [Rtk-users] Bug tracker
Message-ID: <CAF0oig2mSvRLyAno=P-=2uVPOm7wo4tc3-ykpPhzcUxrU3fgvg@mail.gmail.com>

Dear all,
I have changed the link http://bug.openrtk.org to the GitHub bug tracker.
It makes more sense to use this one than the old bug tracker
<http://kingkong.grid.creatis.insa-lyon.fr:9002/projects/rtk>, that I might
close soon.
Simon
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From a.makarova.ru at ieee.org  Mon Jan 23 20:16:03 2017
From: a.makarova.ru at ieee.org (Anastasia Makarova)
Date: Tue, 24 Jan 2017 10:16:03 +0900
Subject: [Rtk-users] RTK for PET
Message-ID: <CADi-QtB3dcSZyFzT0Z7TKQmC3+mTzyZ1BJ3=c-dyBJP9SAxe1g@mail.gmail.com>

Dear RTK Users,

I am new to RTK, but have some experience with ITK and VTK toolkits. Could
you, please advise me if RTK can be used for PET reconstruction?

Thank you for your time,
Makarova
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From cyril.mory at creatis.insa-lyon.fr  Tue Jan 24 11:37:26 2017
From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory)
Date: Tue, 24 Jan 2017 17:37:26 +0100
Subject: [Rtk-users] RTK for PET
In-Reply-To: <CADi-QtB3dcSZyFzT0Z7TKQmC3+mTzyZ1BJ3=c-dyBJP9SAxe1g@mail.gmail.com>
References: <CADi-QtB3dcSZyFzT0Z7TKQmC3+mTzyZ1BJ3=c-dyBJP9SAxe1g@mail.gmail.com>
Message-ID: <ea3700fe-cb73-b6cc-aa3f-8c70be798643@creatis.insa-lyon.fr>

Hi Anastasia,

RTK currently doesn't provide the tools required for PET reconstruction. 
You could probably use it to avoid re-implementing things like forward 
and back projection, but it would still take a significant development 
effort to make it able to reconstruct clinical PET data.

Best regards,
Cyril

On 01/24/2017 02:16 AM, Anastasia Makarova wrote:
> Dear RTK Users,
>
> I am new to RTK, but have some experience with ITK and VTK toolkits. 
> Could you, please advise me if RTK can be used for PET reconstruction?
>
> Thank you for your time,
> Makarova
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users

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From a.makarova.ru at ieee.org  Tue Jan 24 19:59:53 2017
From: a.makarova.ru at ieee.org (Anastasia Makarova)
Date: Wed, 25 Jan 2017 09:59:53 +0900
Subject: [Rtk-users] RTK for PET
Message-ID: <CADi-QtCQm4brf-4zU-9bE9JAAtHnsooOacTu2giQ1-8d_60BDA@mail.gmail.com>

Dear Cyril,

Thank you for the comprehensive answer.

Anastasia

On Wed, Jan 25, 2017 at 1:37 AM, Cyril Mory <cyril.mory at creatis.insa-lyon.fr
> wrote:

> Hi Anastasia,
>
> RTK currently doesn't provide the tools required for PET reconstruction.
> You could probably use it to avoid re-implementing things like forward and
> back projection, but it would still take a significant development effort
> to make it able to reconstruct clinical PET data.
>
> Best regards,
> Cyril
>
>
> On 01/24/2017 02:16 AM, Anastasia Makarova wrote:
>
> Dear RTK Users,
>
> I am new to RTK, but have some experience with ITK and VTK toolkits. Could
> you, please advise me if RTK can be used for PET reconstruction?
>
> Thank you for your time,
> Makarova
>
>
> _______________________________________________
> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users
>
>
>
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From yuzhang at echopixeltech.com  Fri Jan 27 11:37:12 2017
From: yuzhang at echopixeltech.com (Yu Zhang)
Date: Fri, 27 Jan 2017 11:37:12 -0500
Subject: [Rtk-users] Issue with Cuda filter
Message-ID: <CAGuDUtLa1Su=wy8tqWh-6KWVWunuzwEPi0Scs1YAUXhpmQmGZQ@mail.gmail.com>

Hi Simon,

May I ask you a question about how to use the following filters:
CudaForwardProjectionImageFilter is similar to
JosephForwardProjectionImageFilter

I was able to get satisfied results using
JosephForwardProjectionImageFilter,
However, when I switch to CudaForwardProjectionImageFilter, the output is
all zero.
I run the test of those filters, which turns out to be successful. But I am
not aware of
any config parameters to check whether CUDA is actually working or not.
The version I am using is rtk 1.3.0, but it is the same as previous version
from github.

Best regards,
Yu Zhang
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From simon.rit at creatis.insa-lyon.fr  Sun Jan 29 15:33:36 2017
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Sun, 29 Jan 2017 21:33:36 +0100
Subject: [Rtk-users] Issue with Cuda filter
In-Reply-To: <CAGuDUtLa1Su=wy8tqWh-6KWVWunuzwEPi0Scs1YAUXhpmQmGZQ@mail.gmail.com>
References: <CAGuDUtLa1Su=wy8tqWh-6KWVWunuzwEPi0Scs1YAUXhpmQmGZQ@mail.gmail.com>
Message-ID: <CAF0oig1oOfrxxXqHveCOkq4u4YpWA+j0hSfsXROJxOQ=oVg1qQ@mail.gmail.com>

Hi,
The two algorithms differ: Cuda uses trilinear interpolation where
Joseph uses bilinear interpolation in the slices of the main
direction. Other than that, you should get very similar results
(visually) from the same input images and geometry.
Don't hesitate to share the dataset if you'd like us to test it. I'm
not sure what you mean by "any config parameters to check whether CUDA
is actually working or not. "? But looking at the output and checking
that the result looks good is definitely the first step.
Best regards,
Simon

On Fri, Jan 27, 2017 at 5:37 PM, Yu Zhang <yuzhang at echopixeltech.com> wrote:
> Hi Simon,
>
> May I ask you a question about how to use the following filters:
> CudaForwardProjectionImageFilter is similar to
> JosephForwardProjectionImageFilter
>
> I was able to get satisfied results using
> JosephForwardProjectionImageFilter,
> However, when I switch to CudaForwardProjectionImageFilter, the output is
> all zero.
> I run the test of those filters, which turns out to be successful. But I am
> not aware of
> any config parameters to check whether CUDA is actually working or not.
> The version I am using is rtk 1.3.0, but it is the same as previous version
> from github.
>
> Best regards,
> Yu Zhang
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>

From simon.rit at creatis.insa-lyon.fr  Sun Jan 29 15:38:32 2017
From: simon.rit at creatis.insa-lyon.fr (Simon Rit)
Date: Sun, 29 Jan 2017 21:38:32 +0100
Subject: [Rtk-users] Installing SimpleRTK on 64-bit windows
In-Reply-To: <64068DCC8BB0D44EB99B225FFE5580894054F421@RMPMBX02.rmpuhn.ca>
References: <64068DCC8BB0D44EB99B225FFE5580894054F421@RMPMBX02.rmpuhn.ca>
Message-ID: <CAF0oig05=4Zne=8CQrHfp1mqyDFLpwj0GkBi4gV9E6Rrprhhig@mail.gmail.com>

Hi Daniel,
Please use the mailing list. There might be better users than me to
answer your question (particularly this one!).
I'm not an expert in Python and Windows but it seems that it's not
looking for the module in the install directory of the SimpleRTK
module. Have you set PYTHONPATH to look at the install directory of
SimpleRTK? Have you set the correct python include and libraries in
the compilation of RTK?
Kind regards,
Simon

On Fri, Jan 27, 2017 at 9:03 PM, Markel, Daniel
<daniel.markel at rmp.uhn.ca> wrote:
> Hi Simon,
>
>
>
>                   I?m trying to install simpleRTK  on my laptop running
> windows 7 64-bit and having great difficulty. I managed to build ITK
> properly and create a 64-bit build of RTK with simpleRTK without any errors
> using visual studio 2015. I?m also running anaconda which has Python 3.5.1
> built in. However after building it and installing using the ?python
> PythonPackages/setup.py install? command in the command prompt I?m still
> unable to use simpleRTK in python. I?m running the test code placed in the
> openRTK wiki installation page. I keep getting similar if not the same error
> that it is unable to find the _SimpleRTK module. It?s looking in the
> simpleRTK folder that gets installed into  I?m assuming this has to be the
> result of an incorrect installation but I can?t find anything online telling
> me what I did wrong. I?ve tried rebuilding with several different versions
> of swig (the default included version as well as the most up to date and
> several others) but keep coming back to the same error. Would you know how
> to fix this to get a proper installation or should I be trying on a
> different setup? Any help would be much appreciated.
>
>
>
> Thanks,
>
>
>
> -Daniel
>
>
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