12:03:09 #startmeeting Fedora Medical SIG 2013-09-03 12:03:09 Meeting started Tue Sep 3 12:03:09 2013 UTC. The chair is FranciscoD. Information about MeetBot at http://wiki.debian.org/MeetBot. 12:03:09 Useful Commands: #action #agreed #halp #info #idea #link #topic. 12:03:19 #meetingname Fedora Medical 2013-09-03 12:03:19 The meeting name has been set to 'fedora_medical_2013-09-03' 12:03:27 #chair sebp SSlater sjodogne 12:03:27 Current chairs: FranciscoD SSlater sebp sjodogne 12:03:30 #topic Init process 12:03:34 .fasinfo ankursinha 12:03:36 FranciscoD: User: ankursinha, Name: Ankur Sinha, email: sanjay.ankur@gmail.com, Creation: 2008-05-28, IRC Nick: FranciscoD, Timezone: Australia/Sydney, Locale: en, GPG key ID: 0xE629112D, Status: active 12:03:39 FranciscoD: Unapproved Groups: marketing 12:03:42 FranciscoD: Approved Groups: elections cla_fedora cla_done ambassadors fedorabugs freemedia sysadmin sysadmin-ask packager @gitfedora-tour cla_fpca 12:03:56 * FranciscoD thinks just .fas would do.. 12:04:40 sebp: SSlater sjodogne : could you please identify yourselves for the logs? 12:04:46 Mario just mailed, he should be here momentarily 12:05:33 .fasinfo sebp 12:05:34 sebp: User: sebp, Name: None, email: sebp@k-d-w.org, Creation: 2007-09-10, IRC Nick: None, Timezone: None, Locale: None, GPG key ID: None, Status: active 12:05:37 sebp: Approved Groups: packager cla_done cla_fpca cla_fedora fedorabugs 12:05:45 .fasinfo sjodogne 12:05:46 sjodogne: User: sjodogne, Name: Sebastien Jodogne, email: s.jodogne@gmail.com, Creation: 2012-12-10, IRC Nick: , Timezone: Europe/Brussels, Locale: en, GPG key ID: , Status: active 12:05:49 sjodogne: Approved Groups: fedorabugs packager cla_done cla_fpca 12:06:00 .fasinfo sslater 12:06:01 SSlater: User: sslater, Name: Simon Slater, email: pyevet@aapt.net.au, Creation: 2008-12-07, IRC Nick: None, Timezone: UTC, Locale: C, GPG key ID: None, Status: inactive 12:06:04 SSlater: Approved Groups: cla_fedora 12:06:19 #topic Current status 12:06:40 I think this provides the most up to date status of the packages that we have already included, and ones that are in progress: 12:06:43 https://bugzilla.redhat.com/show_bug.cgi?id=673841 12:07:12 The fedora-medical trac is where we started with this initially. I'm not sure if it's quite up to date though 12:07:15 https://fedorahosted.org/fedora-medical/report/6 12:07:36 #info Track tickets need to be updated to reflect current state of packages 12:07:57 Here's the link for imaging software: 12:07:59 http://fedoraproject.org/wiki/Medical_Imaging 12:08:07 Practitioner workflows: http://fedoraproject.org/wiki/Practitioner_workflow 12:08:27 I think the most important ones here were freemedforms and freediams, which are already packaged 12:09:14 Ginko CAD X still needs to be packaged: I dropped the review due to shortage of time: https://bugzilla.redhat.com/show_bug.cgi?id=726201 12:09:33 The package "orthanc" is not listed on Bugzilla, nor on Trac. Should I add a dependency on case 673841? 12:09:52 sjodogne: if it's a medical package, sure :) 12:10:22 I'll wait a few minutes. So you folks can take a look at the links I've posted 12:11:43 #topic contributors' update 12:12:02 sebp: SSlater sjodogne : are you working on anything fedora medical related yet? 12:12:06 .fasinfo mrceresa 12:12:07 FranciscoD: User: mrceresa, Name: None, email: mrceresa@gmail.com, Creation: 2009-11-17, IRC Nick: None, Timezone: None, Locale: None, GPG key ID: None, Status: active 12:12:08 Hi! 12:12:10 FranciscoD: Approved Groups: cla_fedora cla_done packager fedorabugs cla_fpca 12:12:22 FranciscoD: I'm trying to help out packaging ITK 12:12:41 #info sebp working on ITK 12:12:46 Hi everybody, I've just got in 12:12:56 did I miss something? 12:13:00 mrceresa: A little: http://meetbot.fedoraproject.org/fedora-meeting/2013-09-03/fedora_medical_2013-09-03.2013-09-03-12.03.log.txt 12:13:23 Take a minute to go through it, and you can have the floor to add everything that I missed :) 12:13:26 FranciscoD: I'm the main developper of orthanc, a lightweight PACS, and I've packaged it for Fedora 12:13:26 #chair mrceresa 12:13:26 Current chairs: FranciscoD SSlater mrceresa sebp sjodogne 12:13:55 #info sjodogne Developer of orthanc, a lightweight PACS: already packaged for Fedora 12:14:24 FranciscoD: I'm more observing from the wings at the moment, a little thing called time. 12:14:26 Yes no need to add orthanc as a dep, we've already got it in :) 12:14:36 SSlater: no worries 12:14:46 mrceresa: I suggested he add it so we can just follow the tracking bug 12:15:10 aah okay! 12:15:12 that way it stays the one place we refer to, since the trac and the wiki are slightly more difficult to follow 12:15:38 FranciscoD: I have just added the dependency in Bugzilla 12:16:46 mrceresa: for one I think we need to update the trac tickets to reflect the state of packages? 12:17:58 I'm not a big fan of having the information in many different places... I'd say, let's decide on one single point and stick with it,otherwise a lot of sync work 12:18:13 mrceresa: ++. What do you propose? 12:18:38 I think susmit had setup the trac for gsoc basically. It hasnt been used since 12:18:42 I personally like the wiki most because you can have tables :) but trac is good too if you prefer 12:18:53 ah okay 12:19:13 mrceresa: I wouldnt mind the trac, since it'll come in handy when we finally do have a spin 12:19:22 (for feedback, and for feature requests etc) 12:19:29 well i'm happy with the wiki, I'd just reorganize the pages somehow 12:19:38 ah okay 12:19:50 let's stay with trac if it's more useful 12:20:04 just had no use case for it right now :) 12:20:10 mrceresa: I'll see if I can find time to update all the trac tickets sometime this week. 12:20:27 #task FranciscoD update fedora medical trac tickets to reflect current state of packages 12:20:59 that would be great! 12:21:31 mrceresa: when we finally do have a spin, what packages do you think we need to include? 12:21:47 (We could prioritize packaging those software) 12:22:02 I mean, we aren't going to ship them *all*, are we? 12:22:20 Well, I think it will depend on what we use the spin for. For me is research and processing of medical images 12:22:43 PIMS packages would be a good starting point. 12:22:50 which basically means itk and derived, ginkocad,orthanc and FEM code and modeler 12:23:05 but probably there are other use cases 12:23:09 what is PIMS? 12:23:25 http://en.wikipedia.org/wiki/Project_management_information_system ? 12:23:29 * FranciscoD didn't know either :P 12:23:45 SSlater: ^ 12:23:51 For me, thigns like gnumed, freemed forms, open emr etc 12:24:08 Practice Information Management Systems 12:24:14 for me same as mrceresa 12:24:21 Ok. What I hear is that we need to identify use cases. Is that right? 12:24:37 We can either have small subspins for each use case 12:24:38 OR 12:24:44 A *big* spin that includes it all 12:25:13 mrceresa_: keep refreshing this if you lose connectivity: http://meetbot.fedoraproject.org/fedora-meeting/2013-09-03/fedora_medical_2013-09-03.2013-09-03-12.03.log.txt 12:25:13 How much makes a spin too big? 12:25:36 SSlater: well, ideally a spin should stay about 1G if we want to have a live environment 12:25:44 the installer dvd can be much bigger 12:25:53 (4Gs) 12:26:19 Wouldn't 3DSlicer be an interesting candidate too? 12:26:36 sjodogne: http://www.slicer.org/ ? 12:26:42 Sure, only it's difficult to packages 12:26:56 FranciscoD: yes, this one 12:27:14 but now that itk is in we can try it. Anybody volunteerings for a review? 12:27:14 sjodogne: you can open a ticket here so we at least remember it https://fedorahosted.org/fedora-medical/newticket 12:27:20 :) 12:27:29 #task sjodogne open ticket for 3D slicer 12:27:46 I think there are at least 2 use cases here: 12:28:06 a pratictioner who need management tools + dicom 12:28:23 mrceresa_: The official package of 3D Slicer indeed quite heavyweight (200MB), perhaps not suited to a spin 12:28:30 mrceresa_: use #info so it shows up in the logs please ;) 12:28:56 * FranciscoD has an idea but will let mrceresa_ finish 12:29:14 sorry this is my first irc chat :( 12:29:53 #info: I was saying a use case for pratictioners with dicom software + management ones 12:30:29 #info: plus a second one aimed to medical image research with orthanc, itk and derived and software to make a segmentation 12:30:48 what do you think about it? (I'll read how to use irc in the meantime) 12:30:54 mrceresa_: how about we ship 2 spins: one for each use case 12:31:13 these will be live images, that you can also install off, just like the different spins 12:31:33 I think this makes perfect sense, one targeting developers and the other W74KBRoq@L 12:31:37 pratictioners 12:31:40 Sure, I like the idea 12:31:44 and, if required, we can later also create an installer image (non live) which will have both these combined? 12:32:02 Sounds good. 12:32:19 +1 for me 12:32:20 Should we discuss these two spins then? 12:32:35 #topic Spin 1: dicom + management 12:32:48 what packages do you think need to be included here? 12:32:53 Please use #info 12:33:35 #task FranciscoD open a trac ticket also, so that folks who didn't make it to the meeting can comment and make suggestions 12:33:40 #info: orthanc, ginkocad 12:33:59 #info freemedforms/freediams 12:34:08 (I think they'll come in handy?) 12:34:22 sure! 12:34:33 SSlater: how are freemedforms and openemr different? They are both EMR softwares, are they not? 12:34:49 It might make sense to only include one EMR software? 12:34:52 * FranciscoD doesn't know 12:35:27 One of the good things about freemedforms is the drug compatibility database. 12:36:17 I think openemr and gnumed are more for day to day practice workflow. 12:36:55 SSlater: so, freemedforms is two part, right: the EMR, and freediams which is the drug related software 12:37:11 So I believe. 12:37:28 SSlater: so, would openemr/gnumed be preferred over the freemedforms EMR? 12:37:39 "default EMR"? 12:38:03 Depends on how important drug interactions are to you. 12:38:09 hrm 12:38:32 lets include them all for the moment. We can always cut them down if our spin becomes too bulky.. 12:38:43 With new graduates or patients seeing many different practitioners, interactions would be very important. 12:38:50 #info gnumed, openemr 12:39:14 SSlater: Aye. We might have to fine grain our use cases further in the future. 12:39:25 mrceresa_: any other software? We have kind of a huge list on the trac 12:39:39 https://fedorahosted.org/fedora-medical/report/6 12:40:01 basically the others i see seems more tailored to research 12:40:08 let me see better 12:40:50 Ah, OK. We could start with these for the time being then. 12:41:50 well ginkocad depends on gdcm and itk so they would be put into by deps 12:42:07 Yep 12:42:08 also dcmtk I thinkwould be pulled in by orthanc 12:42:19 which might make sense here 12:42:30 yes, you're right, orthanc depends on dcmtk 12:42:51 because a practictioner wants to see CT images or share with a collegue 12:43:00 ++ 12:43:14 the command-line tools of dcmtk (especially dcm2xml) could also be useful for people dealing with DICOM in the medical practice 12:43:50 #info the command-line tools of dcmtk (especially dcm2xml) could also be useful for people dealing with DICOM in the medical practic 12:44:03 in the same spirit, what about ImageJ, for the quick preview of DICOM? 12:44:26 sjodogne: is it packaged alreadY? 12:44:39 what about aeskulap? 12:44:41 I don't know... Mario? 12:44:49 yep but beware it's missing all the plugins 12:44:51 "A full open source replacement for commercially available DICOM viewers" 12:44:57 #info: trac contains a bug report about Fiji https://fedorahosted.org/fedora-medical/ticket/17 12:45:01 I mean imagej 12:45:14 sebp: i think it had licensing issues. 12:45:38 I might be wrong, but I think ImageJ is the most widely used DICOM viewer in hospitals 12:45:44 sebp: yep: https://fedorahosted.org/fedora-medical/ticket/17#comment:3 12:45:45 FranciscoD: ah okay, because of the addtional plugins compared to ImageJ 12:46:26 sjodogne: I see imagej is already in the repositories 12:47:28 sjodogne: it sounds like a general purpose image too from the description in yum info imagej 12:47:53 #info imagej will pull in java 12:48:34 FranciscoD: yes, but it features good DICOM support (including 16bpp), it is well known by medical physicists and medical engineers 12:48:35 at least it's well documented 12:49:41 #info imagej 12:50:03 lets start with these for spin1 then. We can modify the package list any time 12:50:12 What about the second spin? 12:50:14 Fiji is tagged as "wontfix" 12:50:23 sjodogne: licensing issues. Unsuitable for Fedora 12:51:21 for the second spin, I think we should distinguish the case of brain imaging 12:51:39 there are a lot of specific tools for this field of research 12:51:58 #topic Spin 2 Medical Image research 12:52:09 sjodogne: all yours, what packages do you propose? :) 12:52:24 * FranciscoD is interested in brain imaging 12:52:47 well, I am not active on brain imaging personnally, my interest is rather on radiotherapy and nuclear medicine ;) 12:53:05 heh, any packages related to those? 12:53:17 I'm guessing you folks want all the imaging packages of spin 1 in here anyway 12:53:40 #chair mrceresa 12:53:40 Current chairs: FranciscoD SSlater mrceresa sebp sjodogne 12:53:59 yes, spin 2 clearly depends on spin 1 12:54:14 maybe we can use groups 12:54:26 mrceresa: rpm groups? they are obsolete 12:54:28 Now we only use comps 12:54:45 which have also been restructured in F19. I still need to see how the new version works 12:54:51 perhaps including 3D Slicer in spin 2 would make a lot of sense, plus ITK/VTK development packages 12:55:10 #info 3D slicer, ITK/VTK devel packages 12:55:23 #info 3D slicer will need to be packaged first 12:55:23 also something to make segmentations 12:55:30 #info itk-snap 12:55:43 ++ 12:55:53 #info seg3d2 12:56:19 the problem with seg3d2 is that I was unable to convice upstream to take patches 12:56:26 mrceresa: at all? 12:56:33 what are these patches related to? 12:56:45 they just want it to be built against fixed version of libs 12:56:56 which is of course impossible to do infedora 12:57:01 mrceresa: less maintenance burden for them eh? 12:57:06 it works perfectly 12:57:25 and i use it daily to do the segmentations 12:57:34 mrceresa: are the patches too many to carry locally in Fedora? 12:57:45 #info octave 12:58:17 no, actually, but I fear it will diverge 12:58:50 however every year or so they actualize the bundled libs 12:59:18 mrceresa: that's a tough one then.. 12:59:23 so it might only be the case to host them in fedora for a while and then revert them when upstream finally upgrades 12:59:44 mrceresa: yeah, that's a little extra work, but we can manage it I guess 12:59:50 mrceresa: is it packaged already, or is it under review? 12:59:53 I'll thinkabout it again, but definitively seg3d2 is very useful 13:00:07 I have a working spe 13:00:13 but it's not polished :) 13:00:19 heh 13:00:21 no worries 13:00:31 #info seg3d2 needs to be packaged 13:00:35 any more? 13:00:42 #task mrceresa start a review of seg3d2 13:00:45 Or we could move up to other details 13:00:54 #task mrceresa add seg3d2 to trac as a ticket 13:00:55 ;) 13:01:03 side-note: there is a real need for an open-source visualization tool for PET/CT 13:01:16 as well as for viewing DICOM-RT-STRUCT 13:01:30 did you try ginkocad? 13:01:38 sjodogne: do you mean such a tool needs to be developed, or do you have a tool in mind we could package? 13:02:33 mrceresa: To my best knowledge, DICOM-RT is not supported by ginkocad, and it is rather unstable on my Ubuntu box (perhaps this is just a local problem) 13:02:59 FranciscoD: My point is that it should be developed 13:03:29 a quick google for "open source dicom rt" gives some links 13:03:41 3D Slicer and medInria fulfill the needs, but they are very complex 13:03:46 http://www.offis.de/en/competence_center/ict_for_smart_grids/publications/publications_in_detail.html?user_offis_pi1%5Baction%5D=detail&user_offis_pi1%5Brecord%5D=11167&cHash=3c3b69faf561ecb26522a230db5547e3 13:03:57 http://code.google.com/p/dicompyler/ 13:04:20 sjodogne: dicomplyer also mentions PET/MR in it's feature list 13:05:20 the first link seems to just be a paper. I can't find the tool.. 13:05:27 meh 13:05:28 sjodogne: maybe you can try one and tell us which one would you like to be packaged? 13:05:56 mrceresa: do we have pydicom in the repos? I don't think so? 13:06:16 yes, dicompyler is really great tool, but 3D visualization is not its goal 13:06:21 I think not 13:06:59 mrceresa: it isnt 13:07:04 #info pydicom isn't in the repos 13:07:16 #info dicomplyer needs to be packaged 13:07:30 I think that's enough tools for the second spin to get started with? 13:07:44 what about brain imaging? 13:08:13 you mean registration or MRI? 13:08:19 both ;) 13:08:30 I don't think we have anything packaged yet 13:08:41 jejejeje 13:08:46 #info elastix 13:08:55 which is for registration 13:09:01 also there is 13:09:05 plastimatch is another candidate 13:09:05 #info ants 13:09:34 #info plastimatch 13:09:35 well, Debian Med can bring a lot of ideas: http://debian-med.alioth.debian.org/tasks/imaging 13:09:47 #info plastimatch needs to be packaged 13:10:25 that's quite a few tools 13:10:41 yes there are way too many for a spin 13:11:01 yep, maybe it's wise to stop here for now :) 13:11:19 Once I put up the trac tickets maybe we can pick a few from there for later, as extra options 13:11:20 we got some work, didn't we? 13:11:27 ;) 13:11:30 Quite a lot of work actually ;) 13:11:35 #topic other details 13:11:44 First: what DE do we base the spin on? 13:11:55 gnome/kde/mate/xfce/lxde? 13:11:58 gnome! 13:12:06 :) 13:12:13 +1 for gnome here :) 13:12:22 mrceresa: you sure? I use gnome, but it's slightly heavy and has trouble with older hardware 13:12:26 (by gnome I mean gnome3) 13:12:27 ...but xfce could be cool. 13:12:42 I normally use KDE. 13:13:06 I lean towards xfce, which is the lightest, and most "windows style" 13:13:13 you know, panels, start menu etc 13:13:23 gnome has a slight learning curve IMO 13:13:23 FranciscoD: I generally find KDE much more heavyweight than Gnome, but this is quite a mather of personal preference 13:13:41 sjodogne: aye, it's really difficult to decide a DE that'll work for everyone 13:13:47 What background is the target audience? 13:13:57 I fear that XFCE is too close to metal for a medical audience 13:14:00 SSlater: the two use cases, who ever comes under it 13:14:16 FranciscoD: yeah, maybe it's true, but I have a powerful pc at work :) I'm cool with either kde or gnome 13:14:35 the question really is: what DE do we select so *most* people from the two use cases can test out the live media 13:14:38 I think practicioner are using windows and macs 13:14:50 we don't need to worry about the dvd, we can include multiple DEs there 13:14:53 so i'd say kde or gnome3 13:15:15 some more esoteric choice could drive people away 13:15:38 okay, lets base it on gnome for the time being 13:15:59 that's a barebones gnome 13:16:16 no extraneous applications at all, no libreoffice etc 13:16:17 gnome2 or gnome3? 13:16:26 gnome3 is what I'm talking about 13:16:33 gnome2 doesnt exist in fedora, it's now MATE 13:16:36 +1 for me 13:16:55 +1 13:16:57 +1 13:17:05 #info Use gnome as default DE for spins 13:17:15 Now, we need someone who can build these spins 13:17:15 so 13:17:21 I havent' used Gnome for a while. Will windows users catch on easily? 13:17:42 SSlater: should be fine, they even have a "how to use gnome" thing that runs the first time you log in 13:17:43 SSlater: I have some fears about gnome3, which looks more like Windows 8 13:17:44 well... 13:17:49 Kde might be a challenge. 13:18:02 it's sort of why I was going for XFCE ;) 13:18:08 it's closest to windows 13:18:17 or the "traditional desktop" if you will 13:18:24 FranciscoD: Yes, I would favor XFCE 13:18:43 (sorry for changing my point of view ;) ) 13:18:46 there is also gnome3 with the "classic" feal 13:18:49 I only played with xfce a few years ago. 13:19:01 sebp: thats just gnome3 with extensions. I wouldn't suggest that one 13:19:14 if the extensions dont keep up with gnome updates, classic mode breaks 13:19:31 if someone wants a classic desktop, they should just use MATE 13:19:36 FranciscoD: I know, but it's closer to what windows users except than the regular version 13:19:37 okay, I think there is no real problem here, the user can change it later and we would always let someone discontent 13:19:57 just let's choose one and go on :) 13:20:06 mrceresa: aye, should we pick XFCE then? as the simplest DE? 13:20:09 #undo 13:20:09 Removing item from minutes: 13:20:31 Keep it simple for a start. 13:20:34 It's only to give them a demo. They can always install a DE of choice later 13:20:43 Okay. XFCE it is then. 13:20:51 #info Base spins on XFCE 13:20:59 okay 13:21:02 Now, we really need to get more folks involved 13:21:12 We cannot manage all this work by ourselves 13:21:17 #info Spin handler required 13:21:22 #info more package maintainers required 13:21:38 Please remember that you can get new folks into packaging by letting them co-maintain your packages 13:21:52 I think I could get a collegue involved 13:22:07 #info If anyone wants to co-maintain my packages, they're more than welcome to get in touch with me 13:22:31 SSlater: knwo anything about creating fedora spins :P? 13:22:33 sebp: ^? 13:22:45 I was trying to hide. 13:22:57 I saw you hiding ;) 13:22:58 jajajaja 13:23:10 I did attend a fedora-classroom event a while back. 13:23:11 no, never tried 13:23:32 sebp: SSlater : how about you look into it, and let us know how it works? 13:23:36 Maybe a wiki page 13:23:36 But for the next few months I am stretched pretty thin. 13:23:46 ah, time contraints :/ 13:24:04 AFAIC, I am already very busy with the development and the packaging of orthanc 13:24:07 I'll see if I can get in touch with one of the spin maintainers and ask them to write us a wiki page 13:24:08 How can you package up more time for me? 13:24:18 SSlater: we can't :( 13:24:33 FranciscoD: some material or pointers to get started would be very welcome 13:24:48 #task FranciscoD get in touch with design team spin wrangler and request a post on how the spin is made 13:25:06 sebp: Not really sure. I know you need to use a kickstart file etc. I thinki I have a link somewhere. A moment 13:25:28 Knowing time neded for commitments for maintaining would be useful. 13:25:56 sebp: http://spins.fedoraproject.org/support -> end of the page has a few links 13:26:05 Ta. 13:26:11 SSlater: well, for spins, it's mostly a one time task where you figure out how its done 13:26:29 once that happens, it's all about running the same commands again to generate an updated media 13:26:46 Guys, I've to got back to work. Sorry! 13:26:46 Also, this is only until we don't have an official fedora spin, at which point, the task will be automated by infra 13:26:54 mrceresa: no worries, we're almost done here. 13:27:05 mrceresa: if you can, please do write a blog post that'll hit planet fedora? 13:27:29 We could target F21 for an official spin 13:27:45 okay! I'll check the logs later on! Thanks to everybody for staying 13:27:51 1 year away. 13:28:05 sure, I'll send an email to you later 13:28:07 SSlater: yeah, but we'll have to propose it before the feature freeze happens 13:28:12 so it isn't actually a year 13:28:17 bye! 13:28:20 it's about a month after f20 is released 13:28:28 (as far as I remember) 13:28:40 the unofficial spin can go out any time though 13:28:52 @f20release 13:29:00 ah, not fixed yet 13:29:12 I think we've coverd most of what we intended to 13:29:14 #topic Open floor 13:29:26 Please bring up anything else you'd like to, and I'll close the meeting up 13:29:51 #task sebp SSlater sjodogne FranciscoD : catch hold of any new volunteers who'd like to help and get them started 13:29:56 Anything else anyone? 13:30:40 Okay. Ending the meeting in 5 13:30:41 4 13:30:43 3 13:30:46 2 13:30:49 1 13:30:52 #endmeeting