[Rtk-users] Reg: CBCT 1k reconstruction error
Cyril Mory
cyril.mory at creatis.insa-lyon.fr
Wed Oct 26 16:16:20 CEST 2016
Dear Zahid,
I was able to perform a reconstruction from your header and geometry
file, using the following command lines:
rtkprojectshepploganphantom -o simulatedprojections.mha -g geo.xml
--phantomscale "128,128,128" --like Output.mhd
rtkfdk -p . -r simulatedprojections.mha -g geo.xml -o fdk.mha --hardware
cuda --dimension 1024 --spacing 0.25 --lowmem --divisions 4
The first computes projections through a Shepp & Logan phantom, with the
same size, spacing, origin, etc... as your projections, using your
geometry file geo.xml.
The second line performs the FDK reconstruction. I had to use both the
"--lowmem" and the "--divisions 4" since I have little GPU memory (3GB,
on a Geforce GTX 780). "--lowmem" loads the projections into memory by
subsets of 16. "--divisions 4" cuts the reconstructed volume into 4
parts, reconstructs them one by one, then assembles the results. Can you
run the same commands and let us know whether you still encounter the
crash you mentioned ? If it works, you can use your own projection data
in the second command line instead of "simulatedprojections.mha".
Best,
Cyril
On 10/25/2016 01:13 PM, Zahid Hasan Ansari wrote:
> Dear Sir,
>
> Please find the Header file in the attachment.
>
>
> Thanks & Regards
>
> Zahid Hasan Ansari
>
>
> ----- Original Message -----
> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr]
> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr]
> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com
> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error
>
>
>> Dear Zahid,
>>
>> We do not need the projections file, at least not for a first stage of
>> error tracking. We only need the header.
>> Try the following command line:
>>
>> rtkprojections -p . -r yourProjectionsFileName -o proj.mhd
>>
>> It should write a "proj.mhd" and a "proj.raw". The "proj.mhd" file is
>> what we need, and it is a very light text file. The "proj.raw" contains
>> the pixel values, but at the moment we do not need them. We will create
>> our own proj.raw file, filled with zeros, which should be enough to
>> track down the error you encounter.
>>
>> Looking forward to receiving your file,
>> Cyril
>>
>> On 10/25/2016 09:22 AM, Zahid Hasan Ansari wrote:
>>> Dear Sir,
>>>
>>> The single raw file of the projections is 1.4 GB and we are not
>> able to send this big file to you. Can you please suggest other alternatives
>> for this?
>>> Or can you provide us the PC configuration to solve the issue?
>>>
>>> Let me know if any other clarification is required.
>>>
>>>
>>> Thanks & Regards
>>>
>>> Zahid Hasan Ansari
>>>
>>>
>>>
>>> ----- Original Message -----
>>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr]
>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit
>> [mailto:simon.rit at creatis.insa-lyon.fr]
>>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com
>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error
>>>
>>>
>>>> Hello Zahid,
>>>>
>>>> We will need the header of your projections file, too (It is best if you
>>>> have all your projections as a single .mhd and a single .raw file, so it
>>>> should be 3-D image, and you send only the .mhd file).
>>>>
>>>> Regards,
>>>> Cyril
>>>>
>>>> On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote:
>>>>> Dear Cyril Mory,
>>>>>
>>>>>
>>>>> I have only used RTK version 1.3.0. but in the error
>>>> message it is showing RTK version 1.2.0.
>>>>> Please find the attachment of the geometry file of our
>>>> projections.
>>>>> Thanks & Regards
>>>>>
>>>>> Zahid Hasan Ansari
>>>>>
>>>>>
>>>>>
>>>>> ----- Original Message -----
>>>>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr]
>>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon
>> Rit
>>>> [mailto:simon.rit at creatis.insa-lyon.fr]
>>>>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com
>>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error
>>>>>
>>>>>
>>>>>> Dear Zahid,
>>>>>>
>>>>>> Without some more information, it's unlikely that we find the source of
>>>>>> the problem. Here are a few things you can do to help us (and therefore
>>>>>> yourself):
>>>>>> - try version 1.3.0 of RTK: there have been considerable changes in the
>>>>>> Cuda forward and back projection filters since v1.2.0, so your problem
>>>>>> might disappear just by upgrading to the new version
>>>>>> - create a small example that reproduces your problem. You can, for
>>>>>> example, simulate a geometry, simulate projections of a shepp logan
>>>>>> phantom, and reconstruct from these projections (take a look at
>>>>>> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an
>>>>>> example). And send us the script
>>>>>> - OR send us your geometry file and the header of your projections file
>>>>>> (no need to send the projection data itself, we'll create a zero-filled
>>>>>> stack of projections), and the command line that crashes
>>>>>>
>>>>>> Best regards,
>>>>>> Cyril
>>>>>>
>>>>>> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote:
>>>>>>> Dear Simon Rit,
>>>>>>>
>>>>>>> Please find the screen shot in the attachment.
>>>>>>>
>>>>>>>
>>>>>>> Thanks & Regards
>>>>>>>
>>>>>>> Zahid Hasan Ansari
>>>>>>> Senior Design Engineer
>>>>>>> Mobile No. +91-9738379729
>>>>>>>
>>>>>>> Panacea Medical Technologies Pvt. Ltd.
>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area
>> Phase
>>>> 1,
>>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA
>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial
>> Area,
>>>>>> Malur - 563130. Kolar District. INDIA.
>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url :
>>>>>> http://www.panaceamedical.com
>>>>>>> Bangalore - India.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ----- Original Message -----
>>>>>>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr]
>>>>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com]
>>>>>>> Cc: rtk-users at public.kitware.com
>> [mailto:rtk-users at public.kitware.com],
>>>>>> saimahesh.m at panaceamedical.com
>>>>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error
>>>>>>>
>>>>>>>
>>>>>>>> Dear Zahid,
>>>>>>>> There is no screenshot so I'm guessing that the problem is a CUDA
>>>> memory
>>>>>>>> error. If you use the command line tool rtkfdk, you should first make
>>>>>> sure
>>>>>>>> that you use the --lowmem option to stream the projection images. If
>> it
>>>>>> is
>>>>>>>> no sufficient, you can split your volume using the --divisions. The
>>>>>>>> corresponding C++ code can be found in rtkfdk.cxx.
>>>>>>>> Is Panacea Medical using RTK? We are happy to advertise the use of
>> RTK
>>>> on
>>>>>>>> our case studies webpage
>>>>>> <http://openrtk.org/RTK/project/casestudies.html>.
>>>>>>>> Simon
>>>>>>>>
>>>>>>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari <
>>>>>>>> zahidhasan.a at panaceamedical.com> wrote:
>>>>>>>>
>>>>>>>>>> Dear Sir\Madam,
>>>>>>>>>>
>>>>>>>>>> I am unable to do 1024x1024x1024 reconstruction
>>>> using
>>>>>> RTK
>>>>>>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot
>> of
>>>>>>>>> the
>>>>>>>>>> same.
>>>>>>>>>>
>>>>>>>>>> I am using the following items given below.
>>>>>>>>>>
>>>>>>>>>> 1. RTK - RTK version 1.3
>>>>>>>>>> 2. ITK - ITK version 4.7
>>>>>>>>>> 3. Visual Studio 2013 win 64-bit console
>> application
>>>>>>>>>> 4. GeForce GTX TITAN X GPU.
>>>>>>>>>> 5. CUDA 7.
>>>>>>>>>> 6. CMake version 3.4.3.
>>>>>>>>>> 7. Windows 7 64-bit OS.
>>>>>>>>>>
>>>>>>>>>> Please provide the solution of this and let me
>> know
>>>> if
>>>>>>>> any
>>>>>>>>>> other clarification is required.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Thanks & Regards
>>>>>>>>>>
>>>>>>>>>> Zahid Hasan Ansari
>>>>>>>>>> Senior Design Engineer
>>>>>>>>>> Mobile No. +91-9738379729
>>>>>>>>>>
>>>>>>>>>> Panacea Medical Technologies Pvt. Ltd.
>>>>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area
>>>> Phase
>>>>>>>>> 1,
>>>>>>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA
>>>>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial
>>>> Area,
>>>>>>>>>> Malur - 563130. Kolar District. INDIA.
>>>>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url :
>>>>>>>>>> http://www.panaceamedical.com
>>>>>>>>>> Bangalore - India.
>>>>>>>>> ________________________________________
>>>>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD.
>>>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area
>>>> Phase
>>>>>>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA
>>>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial
>>>> Area,
>>>>>>>>> Malur - 563130. Kolar District. INDIA.
>>>>>>>>>
>>>>>>>>> Tel : +91 80 4242 8700 / 2845 4785
>>>>>>>>> Fax : + 91 80 42428710
>>>>>>>>> Url : http://www.panaceamedical.com
>>>>>>>>> ____________________________________________________________
>>>>>>>>> ________________
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>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area
>> Phase
>>>> 1,
>>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA
>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial
>> Area,
>>>>>> Malur - 563130. Kolar District. INDIA.
>>>>>>> Tel : +91 80 4242 8700 / 2845 4785
>>>>>>> Fax : + 91 80 42428710
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>>>>> ________________________________________
>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD.
>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase
>> 1,
>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA
>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area,
>>>> Malur - 563130. Kolar District. INDIA.
>>>>> Tel : +91 80 4242 8700 / 2845 4785
>>>>> Fax : + 91 80 42428710
>>>>> Url : http://www.panaceamedical.com
>>>>>
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>>>>> PMT EMAIL DISCLAIMER:
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>>> ________________________________________
>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD.
>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1,
>> Whitefield, Bangalore - 560 066, Karnataka, INDIA
>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area,
>> Malur - 563130. Kolar District. INDIA.
>>> Tel : +91 80 4242 8700 / 2845 4785
>>> Fax : + 91 80 42428710
>>> Url : http://www.panaceamedical.com
>>>
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>>
>
> ________________________________________
> PANACEA MEDICAL TECHNOLOGIES PVT. LTD.
> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA
> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA.
>
> Tel : +91 80 4242 8700 / 2845 4785
> Fax : + 91 80 42428710
> Url : http://www.panaceamedical.com
> ____________________________________________________________________________
> PMT EMAIL DISCLAIMER:
>
> This email and any files transmitted with it are confidential and intended
> solely for the use of the individual or entity to whom they are addressed.
> If you have received this email in error please notify the system manager.
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> Finally, the recipient should check this email and any attachments for the
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