[Gate-users] Gate-users Digest, Vol 106, Issue 27
Simon Rit
simon.rit at creatis.insa-lyon.fr
Wed Mar 18 15:26:56 CET 2015
Hi,
I forgot to answer this point but vv <http://vv.creatis.insa-lyon.fr/> can
also open dicom rt doses, then you can save it in any other format.
Simon
On Wed, Mar 18, 2015 at 3:23 PM, Luc SIMON <uhqd75 at gmail.com> wrote:
> Thank you David.
> For information, I found an answer to my question. To convert (raw/mhd)
> gate output in Dicom RT Dose : SlicerRT works.
> I did not test if the output (.dcm) is well accepted by a commercial TPS,
> but I will test ASAP.
> Luc
>
>
>
> 2015-03-18 12:06 GMT+01:00 <
> gate-users-request at lists.opengatecollaboration.org>:
>
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>> Today's Topics:
>>
>> 1. Re: Exemple RT : crash (David Sarrut)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Wed, 18 Mar 2015 12:58:09 +0100
>> From: David Sarrut <David.Sarrut at creatis.insa-lyon.fr>
>> To: Simon Rit <simon.rit at creatis.insa-lyon.fr>
>> Cc: gate-users <gate-users at lists.opengatecollaboration.org>, Luc SIMON
>> <uhqd75 at gmail.com>
>> Subject: Re: [Gate-users] Exemple RT : crash
>> Message-ID:
>> <CAKTJC4C7sWULBPQ1cLhROy-53=
>> o_fAOFjTPiRxhNyuKBbK_3-Q at mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Hello,
>>
>> it is now corrected in the "develop" branch (it will be available in the
>> public repository soon https://github.com/OpenGATE/Gate ).
>>
>> thanks to the two Simons
>> David
>>
>> On Tue, Mar 17, 2015 at 5:55 PM, Simon Rit <
>> simon.rit at creatis.insa-lyon.fr>
>> wrote:
>>
>> > Hi Luc,
>> > The idea is that only the md5 checksum is in the repository and the file
>> > should be automatically downloaded from midas. Clearly, looking at the
>> file
>> > examples/CMakeLists.txt, the file is missing which is why it's not been
>> > downloaded. I'll discuss with David to correct this but in the meantime,
>> > it's available on Midas:
>> > http://midas3.kitware.com/midas/community/28
>> > Simon
>> >
>> > On Tue, Mar 17, 2015 at 4:40 PM, Luc SIMON <uhqd75 at gmail.com> wrote:
>> >
>> >> Dear Gaters,
>> >>
>> >>
>> >> Sorry for multiple questions but when downloading data used for
>> >> Example_Radiotherapy, I think a .raw file is missing : patient-4mm.raw
>> >> (Example3)
>> >>
>> >> Again on mac it is not obvious to understand what file in MD5/ is the
>> >> good .raw used for an example (see list hereafter, as it is displayed
>> using
>> >> ls command).
>> >>
>> >> But using the .md5 information it is possible to compute the size (in
>> >> bytes).
>> >>
>> >>
>> >> In Example2, patient-2mm is a 126x126x111 image of short (2 bytes) =
>> >> 3524472 bytes. In this list it is the 8th file. It is possible to
>> create a
>> >> symbolic link to this file and example2 works very well
>> >>
>> >>
>> >> In Example3, patient-4mm is a 63x93x55 image of short = 436590 bytes.
>> No
>> >> file has this size in the list.
>> >>
>> >> To summarize, can someone send me patient-4mm.raw ? (uhqd75 at gmail.com)
>> >>
>> >>
>> >> Thanks for any help
>> >>
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 4194304 16 mar 13:39
>> >> 044a158a2617c05ed8fb657a27ed23ff
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 6013 16 mar 14:14
>> >> 04f319a267d3f20a2836b342dde554fe
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 14444 16 mar 13:35
>> >> 0a63785ee8d79c3031523f20c0b7c4cc
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 4194304 16 mar 13:38
>> >> 0ecbce48f40182180e886377904c8a5b
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 4194304 16 mar 13:40
>> >> 1567a80b4d198d884be028994c0b35b2
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 17234 16 mar 14:14
>> >> 1a089668c2065750ecd32b7eb4bc07e9
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 6033 16 mar 14:14
>> >> 28f1577fc46f36527c70ca6b86009c10
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 3524472 16 mar 14:15
>> >> 2c44e3a8f824a414f0b6531ece16c528
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 32768 16 mar 14:14
>> >> 3e3549ed281ff3219949e98733ffff12
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 4194304 16 mar 13:36
>> >> 4373ca3fd7b365b6a327b4f443abac50
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 4194304 16 mar 13:39
>> >> 466062ad3402869b3fed72652ecaea76
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 4194304 16 mar 13:36
>> >> 494a61c7968269d98f8ccf35bfb0dfdd
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 4194304 16 mar 13:39
>> >> 4d2109f58e05d361e7a0e5ff6169fc58
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 4194304 16 mar 13:40
>> >> 4ec2181490f547e767f4c599791c42e3
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 4194304 16 mar 13:38
>> >> 5ca0fd75b6c76fb7cc18e782dfc14576
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 4194304 16 mar 13:38
>> >> 6277cb5a4c6e724161c8cf3595f885c1
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 4194304 16 mar 13:39
>> >> 63d5e31f2052aace22eb2b448488f462
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 202400 16 mar 14:15
>> >> 6837c84a3b563d7829cc3f0ebb3af306
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 896857 16 mar 14:14
>> >> 6bc219efcd1616741eead7ab202cc936
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 4194304 16 mar 13:37
>> >> 6e1dd112c3ff48913d55e5754ccb0510
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 4194304 16 mar 13:35
>> >> 730355e81d3c478e92b09f3764f126c4
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 741888 16 mar 14:15
>> >> 7d0f34d6f76c685996172c82ca62970f
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 31367800 16 mar 14:17
>> >> 83d961494d5b44d76fccb1922012897f
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 8192000 16 mar 14:17
>> >> 941d3cdb79120113a6330bc19882ff31
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 1024000 16 mar 14:18
>> >> 988b1744961f639cab0b2c160809b527
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 250563 16 mar 14:20
>> >> 9a0f3582f30c7eeb852f59d35f667af2
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 47507823 16 mar 13:43
>> >> 9c0989256d3b6e9b213359cd4a3b6daa
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 74624346 16 mar 14:14
>> >> a44e7bc7c3f2690a9e94e4ef4c5d3f1a
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 4096000 16 mar 14:18
>> >> a607dceeb0a8db6558814c45ae1644a0
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 4194304 16 mar 13:38
>> >> a9cd0e61d8f9f0a033b5ebb9054aebe1
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 59737 16 mar 14:14
>> >> ad591f0a5086c223402a5269b8188cd2
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 4194304 16 mar 13:37
>> >> af5b5dbef7a9aa37d1b554d2fab7bdd0
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 30781160 16 mar 14:20
>> >> baf4a6c7958099ca39965928f010e7c6
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 3524472 16 mar 14:15
>> >> beb6101f5b3daa7e16624c623759269c
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 4050 16 mar 14:14
>> >> c545ad7e01cad56e198b19994c6e72b7
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 272317 16 mar 14:15
>> >> c9263ddc7a4e21e32440480227f01a42
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 1880832 16 mar 14:20
>> >> d322322593c0961abf1eda0bbf871b63
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 4000000 16 mar 14:20
>> >> d4a8046c37d2f02c885c0a0946f68926
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 4194304 16 mar 13:37
>> >> d5a777f0731cae74ec51e94eff676385
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 4194304 16 mar 13:37
>> >> d746dd3bf5942a29c470aefff9280236
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 4194304 16 mar 13:40
>> >> dd78d8a34738054369705f879e9c4b4b
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 4194304 16 mar 13:38
>> >> ee84d77dc3ebd445548c5b0950c6558e
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 4194304 16 mar 13:36
>> >> ef43ddc95ae120b5d05eb09cb9371e2a
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 226795 16 mar 14:14
>> >> f7fe754b3cc066c664c5b408166d93e9
>> >>
>> >> -rw-r--r-- 1 lucsimon admin 3407872 16 mar 14:15
>> >> f942d5a94d90ccfaa2bbc5823b790c44
>> >>
>> >> 2015-03-16 8:33 GMT+01:00 David Sarrut <
>> David.Sarrut at creatis.insa-lyon.fr
>> >> >:
>> >>
>> >>> Hello Luc,
>> >>>
>> >>> did the file patient-2mm.raw exists ? An image is stored with 2 files
>> :
>> >>> A.mhd (the header) and A.raw (the pixel data).
>> >>>
>> >>> If not, in cmake, set GATE_DOWNLOAD_EXAMPLES_DATA to ON to download
>> the
>> >>> data
>> >>>
>> >>> welcome back to Gate ;)
>> >>> David
>> >>>
>> >>> On Thu, Mar 12, 2015 at 10:46 PM, Luc SIMON <uhqd75 at gmail.com> wrote:
>> >>>
>> >>>> Dear Gaters
>> >>>>
>> >>>> It is a real pleasure to me to come back here after a 12 years
>> break. I
>> >>>> worked previously in Lausanne at the very beginning of Gate v1...
>> >>>> I am going to use Gate again for new purposes, in particular in RT.
>> >>>> Well... a lot to learn with all these new features.
>> >>>> I start with a newbee question, but if someone can help...
>> >>>>
>> >>>> I installed GATE V7 on a mac book Yosemite 10.10.2
>> >>>> my configuration is at the end of this email, hereafter.
>> >>>>
>> >>>> Well It half works.
>> >>>> I execute some exemples of Geant4 and GATE with success
>> >>>> (PETcylindrilcal is ok with visualization !!)
>> >>>> But I try to execute Radiotherapy examples and it doesn't work.
>> >>>>
>> >>>> I tried example_Radiotherapy/example2/mac/main-NPV1.mac
>> >>>>
>> >>>> and it doesnt work.
>> >>>> The following command :
>> >>>>
>> >>>> Idle> /control/execute mac/start.mac
>> >>>>
>> >>>> gives :
>> >>>>
>> >>>> [Core-0] Initialization of geometry
>> >>>>
>> >>>> MetaImage: Read: Cannot open data file
>> >>>>
>> >>>> GateMHDImage.cc (l.185): MHD File cannot be read:
>> data/patient-2mm.mhd
>> >>>>
>> >>>>
>> >>>> I checked the rwx rights of the file patient-2mm.mhd
>> >>>>
>> >>>> and it is ok (rwxrwxrwx)
>> >>>>
>> >>>>
>> >>>> Can someone has the same problem ?
>> >>>>
>> >>>> I must add that I changed
>> >>>>
>> >>>> #/vis/open OGLIQt
>> >>>> to
>> >>>>
>> >>>> /vis/open OGLSX
>> >>>>
>> >>>> because it didn't work with OGLIQt
>> >>>>
>> >>>> Thank you
>> >>>>
>> >>>>
>> >>>>
>> >>>>
>> >>>>
>> >>>>
>> >>>> config :
>> >>>>
>> >>>> CMAKE 3.1.3
>> >>>>
>> >>>> xcode 6.1.1
>> >>>>
>> >>>> xquartz 2.7.7
>> >>>>
>> >>>> cmake 2.8.12.2
>> >>>>
>> >>>> CLHEP 2.1.3.1
>> >>>>
>> >>>> root v5.34.26
>> >>>>
>> >>>> GEANT4.9.6p04
>> >>>>
>> >>>> GATE v7.0
>> >>>>
>> >>>> --
>> >>>> ___________________
>> >>>>
>> >>>> SIMON Luc, PhD
>> >>>> 28, rue Pierre Barthes
>> >>>> 31500 Toulouse
>> >>>>
>> >>>> _______________________________________________
>> >>>> Gate-users mailing list
>> >>>> Gate-users at lists.opengatecollaboration.org
>> >>>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>> >>>>
>> >>>
>> >>>
>> >>>
>> >>> --
>> >>> David Sarrut, Phd
>> >>> Directeur de recherche CNRS
>> >>> CREATIS, UMR CNRS 5220, Inserm U 1044
>> >>> Centre de lutte contre le cancer L?on B?rard
>> >>> 28 rue La?nnec, 69373 Lyon cedex 08
>> >>> Tel : 04 78 78 51 51 / 06 74 72 05 42
>> >>> http://www.creatis.insa-lyon.fr/~dsarrut
>> >>> _________________________________
>> >>> "2 + 2 = 5, for extremely large values of 2"
>> >>> _________________________________
>> >>>
>> >>
>> >>
>> >>
>> >> --
>> >> ___________________
>> >>
>> >> SIMON Luc, PhD
>> >> IUCT-Oncopole / CRCT Team 15
>> >>
>> >>
>> >> _______________________________________________
>> >> Gate-users mailing list
>> >> Gate-users at lists.opengatecollaboration.org
>> >> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>> >>
>> >
>> >
>> > _______________________________________________
>> > Gate-users mailing list
>> > Gate-users at lists.opengatecollaboration.org
>> > http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>> >
>>
>>
>>
>> --
>> David Sarrut, Phd
>> Directeur de recherche CNRS
>> CREATIS, UMR CNRS 5220, Inserm U 1044
>> Centre de lutte contre le cancer L?on B?rard
>> 28 rue La?nnec, 69373 Lyon cedex 08
>> Tel : 04 78 78 51 51 / 06 74 72 05 42
>> http://www.creatis.insa-lyon.fr/~dsarrut
>> _________________________________
>> "2 + 2 = 5, for extremely large values of 2"
>> _________________________________
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>> End of Gate-users Digest, Vol 106, Issue 27
>> *******************************************
>>
>
>
>
> --
> ___________________
>
> SIMON Luc, PhD
> 28, rue Pierre Barthes
> 31500 Toulouse
>
> _______________________________________________
> Gate-users mailing list
> Gate-users at lists.opengatecollaboration.org
> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>
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