[Gate-users] Gate-users Digest, Vol 106, Issue 27
Luc SIMON
uhqd75 at gmail.com
Wed Mar 18 15:23:32 CET 2015
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 <
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> 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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> *******************************************
>
--
___________________
SIMON Luc, PhD
28, rue Pierre Barthes
31500 Toulouse
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