[Rtk-users] Help Regarding FDK reconstruction

louie L ghostcz at hotmail.com
Tue Apr 19 09:29:00 EDT 2016 

It says memory allocation error. You can try to run it on your server or you can stream the pipeline. 
L

Sent from my iOS 

> Am 19.04.2016 um 15:14 schrieb AMJAD N <amjad.n.cet at gmail.com>:
> 
> Sir,
> I have changed origin for both projections and reconstructed volume. THERE IS IMPROVEMENT... Sorry for my mistake, previously I have changed only for projections.
> 
> my code modified as below
> double origin_inp[Dimension] = { -25.775, -25.275, 0 }; // for projections
> 
> // for reconstructed volume.
> origin[0] = -4.9422695280000006;
> origin[1] = -4.1357903999999994;
> origin[2] = -5.2317748560000004;
> 
> . Now I am facing another issue. My original dataset is 1500 projections. But now I could work only with 150 projections. On exceeding this it shows memory exception. "First-chance exception at 0x75DEC54F in finRecon.exe: Microsoft C++ exception: itk::MemoryAllocationError at memory location 0x002CF6E0."
> Occurs at vnl_ssc.h line 128.
> 
> My PC specification is:
> 
> Windows 7 professional
> Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz
> RAM 16.0GB
> NVIDIA GeForce GT 730  
> Dedicated video memory: 4096 MB DDR3
> 
> Thanks and Regards,
> AMJAD N
> 
> 
>> On Tue, Apr 19, 2016 at 5:22 PM, ghostcz <ghostcz at hotmail.com> wrote:
>> int dim[Dime] = { 1032, 1012,1 };
>>     double spacing_inp[Dime] = { 0.05, 0.05,0.05};
>>     double origin_inp[Dime] = { 0, 0,0};
>>  
>> This is wrong, but you said you tried with the offset right? i.e. moving the origin.
>> Then check the orientation of your raw files maybe.
>> I will try to run your code when I have some more time...
>>  
>> L
>>  
>>  
>>  
>> From: ghostcz
>> Sent: Tuesday, April 19, 2016 1:39 PM
>> To: AMJAD N ; rtk-users at public.kitware.com
>> Subject: Re: [Rtk-users] Help Regarding FDK reconstruction
>>  
>> Can you please upload the files again? The content has expired.
>>  
>> L
>>  
>> From: AMJAD N
>> Sent: Tuesday, April 19, 2016 1:24 PM
>> To: louie L ; rtk-users at public.kitware.com
>> Subject: Help Regarding FDK reconstruction
>>  
>> Sir,
>>  
>> I haven't created geometry.xml. My code and data-set are attached in the previous discussion. Also parameters for generating geometry explained in the same thread. I am working without creating geometry.xml but creating geometry in the code itself.
>>  
>> Thanks and Regards,
>>  
>> AMJAD N
>>  
>>> On Tue, Apr 19, 2016 at 3:56 PM, louie L <ghostcz at hotmail.com> wrote:
>>> Can you please send the geometry.xml?
>>>  
>>> Louie
>>> 
>>> Sent from my iOS
>>> 
>>>> Am 19.04.2016 um 12:15 schrieb AMJAD N <amjad.n.cet at gmail.com>:
>>>> 
>>>> Sir,
>>>>  
>>>> sdd and sid is measured from the experiment setup.
>>>> -0.5*spacing*(size-1) logic is applied and effect is same.
>>>>  
>>>> The parameters we know are described below. Please go through it and help me tackle this issue.
>>>>  
>>>> Number of projections: 50
>>>>  
>>>> Object size:
>>>> x = 9.924236 mm
>>>> y = 8.3048 mm
>>>> z = 10.505572mm
>>>>  
>>>> Detector panel:
>>>> flat panel : Width: 1032 px., Height: 1012 px.
>>>> Width: 51.6mm Height: 50.6mm
>>>> (Detector pixel pith: 0.05mm)
>>>>  
>>>> Source to Detector Distance = 459.154 mm
>>>> Source to object axis distance = 95.331mm
>>>>  
>>>> Direction of rotation: clock-wise
>>>>  
>>>> Angle
>>>> start: 0 degrees
>>>> increment: 7.2 degrees
>>>> total: 360 degrees
>>>>  
>>>> Thanks and Regards.
>>>> AMJADN
>>>>  
>>>>> On Tue, Apr 19, 2016 at 11:32 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr> wrote:
>>>>> Dear Amjad,
>>>>> I had a quick look at your dataset. For sure, it's a geometry problem. Do you have any information regarding the geometry? How did you obtain sdd / sid?
>>>>> Currently, I can see that you have set the projections and the volume origin to 0,0,0 which is not correct, you probably want to center them for a first test. If you want to center them, the formula to compute the origin is -0.5*spacing*(size-1) for each corrdinate.
>>>>> Simon
>>>>> 
>>>>> 
>>>>>> On 18/04/2016 08:50, AMJAD N wrote:
>>>>>> Hi, The data set is reattached below,. Someone please look into it and help me please,
>>>>>>  
>>>>>> http://filenurse.com/download/bb2827a35cc99a14feee17d2c37cdf76.html
>>>>>>  
>>>>>> Thanks in advance
>>>>>> AMJAD
>>>>>>> 
>>>>>>> Message: 1
>>>>>>> Date: Thu, 14 Apr 2016 17:21:12 +0530
>>>>>>> From: AMJAD N <amjad.n.cet at gmail.com>
>>>>>>> To: rtk-users at public.kitware.com
>>>>>>> Subject: [Rtk-users] Help Regarding FDK reconstruction
>>>>>>> Message-ID:
>>>>>>> <mailto:CAHq1iunQyc-ZGRH7o6yrMtiwqnusAPnoKzRKPnxm5bpj_3b0%2BA at mail.gmail.com>
>>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>> 
>>>>>>> Hi
>>>>>>> 
>>>>>>> I am new to RTK. and I have been looking into it for the past two weeks..I
>>>>>>> think its an amazing tool..
>>>>>>> 
>>>>>>> My problem is:
>>>>>>> 
>>>>>>> 
>>>>>>> I have a set of 50 raw CT scan projections of an industrial fin as shown
>>>>>>> (fin.jpg)
>>>>>>> I am reading it using ImageSeriesReader with RawimageIO and been have
>>>>>>> trying to reconstruct it using FDKConeBeamReconstructionFilter. Its been
>>>>>>> almost a week that I am trying this,but
>>>>>>> I could not reconstruct it correctly
>>>>>>> I tried varying my geometry, origin, spacing etc ..but still no hope
>>>>>>> 
>>>>>>> Can u please look into my program(finRecon.txt) and the current output I am
>>>>>>> getting is output_fin.mha , which is incorrect and suggest some help
>>>>>>> 
>>>>>>> The link to my dataset:
>>>>>>> 
>>>>>>> http://expirebox.com/download/b523394ea63c635d10171a69e687993b.html
>>>>>>> 
>>>>>>> raw image dimensions : 1032 *1012
>>>>>>> raw image 16 bit
>>>>>>> current spacing: 0.05 0.05 0.05
>>>>>>> origin: 0 0 0
>>>>>>> step angle 7.2 degrees
>>>>>>> 
>>>>>>> 
>>>>>>> Thanks in advance,
>>>>>>> 
>>>>>>> AMJAD
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