From najmeh.khalilimahani at mcgill.ca Mon Oct 5 16:16:55 2015 From: najmeh.khalilimahani at mcgill.ca (Najmeh Khalili-Mahani, Dr) Date: Mon, 5 Oct 2015 16:16:55 -0400 Subject: [Loris-dev] Circumventing PACS and avoiding firewalls: how to configure image uploader? Message-ID: Hi, # background: # We need LORIS to circumvent the PACS system and set a link # between a data host (where the scanner images are stored--from a GE scanner) # and the LORIS image uploader. LORIS 15 is installed on CentOS, and is # accessible from a browser. We are at the stage of configuration of paths. Our system administrator is asking "What port does Loris listen to for incoming DICOM image transfers? I haven?t seen it among the configuration settings in the Admin pages. I?ll have to make sure that the firewall is permitting that traffic through to the server. " Much thanks for any advice. Naj -------------- next part -------------- An HTML attachment was scrubbed... URL: From waveflux at gmail.com Thu Oct 8 11:29:47 2015 From: waveflux at gmail.com (Tom Beaudry) Date: Thu, 8 Oct 2015 11:29:47 -0400 Subject: [Loris-dev] deleting test data Message-ID: Hi Everyone, I am back from my paternal leave today and am deleting all of the test / demo data on my LORIS instance so the real data entry can start! I used this script: /var/www/loris/tools/delete_candidate.php to successfully delete 10 of 15 entries. For the remaining 5 of them, the candidates still show up in my access profile - although when I click on them, aside from their visit label, they have no instruments assigned to them. 1. Does anyone have a suggestion as to what I should do for these candidates, and 2. Is there anything else that I need to delete to have a fresh instance (aside from the mri data)? Thanks, Tom -------------- next part -------------- An HTML attachment was scrubbed... URL: From najmeh.khalilimahani at mcgill.ca Mon Oct 19 11:48:17 2015 From: najmeh.khalilimahani at mcgill.ca (Najmeh Khalili-Mahani, Dr) Date: Mon, 19 Oct 2015 11:48:17 -0400 Subject: [Loris-dev] UBUNTU LORIS/MAchine requirements Message-ID: Hi everyone, Can you please point me to where I can find information about the ubuntu14-installation of LORIS? Also, I am trying to set LORIS up on a new machine, for the simple purpose of transferring images from the scanner (GE) to this machine, and viewing/QCing them through the LORIS interface. Would you be able to advise me on what is the minimum requirement for such machine? I apologize if these information are on the wiki page and I have not been able to find them. Thanks for your help. Naj -- ================================== Najmeh Khalili-Mahani, PhD Research Associate McGill Centre for Integrative Neuroscience Montreal Neurological Institute McGill University NW-143, 3801 University St. Montreal, QC, H3A 2B4 Office: 514-398-1799 email: najma at bic.mni.mcgill.ca -------------- next part -------------- An HTML attachment was scrubbed... URL: From christine.rogers at mcgill.ca Mon Oct 19 16:00:56 2015 From: christine.rogers at mcgill.ca (Christine Rogers) Date: Mon, 19 Oct 2015 16:00:56 -0400 Subject: [Loris-dev] UBUNTU LORIS/MAchine requirements In-Reply-To: References: Message-ID: Hi Naj, In our webpage (www.loris.ca) under the section "Technical Framework and Requirements" -- we have listed the key technical specs for a server on which a typical Loris instance will be installed. For the latest release of LORIS (15.04, Spring 2015) and its package installation pre-requisites, please see the Readme tagged for that release : https://github.com/aces/Loris/tree/v15.4k To generate an initial space estimate for a new instance of Loris, we recommend tripling the estimated size of your raw imaging data, to accommodate backups and data stored in multiple formats (e.g. MINC and NIfTI, raw and processed). Be sure to anticipate needs for longitudinal data storage if imaging data is to be acquired at multiple time-points over the lifespan of a project or institution. For example: 200 study participants * 3 data collection time-points * 500MB data per MRI session * 3 (tripled) -> 1 TB (rounded up) Any plans to house genetic data (summary results or compressed datasets) would add a further consideration for size requirements. Best, Christine on behalf of the Loris Team On Mon, Oct 19, 2015 at 11:48 AM, Najmeh Khalili-Mahani, Dr < najmeh.khalilimahani at mcgill.ca> wrote: > > Hi everyone, > > Can you please point me to where I can find information about the > ubuntu14-installation of LORIS? > > Also, I am trying to set LORIS up on a new machine, for the simple purpose > of transferring images from the scanner (GE) to this machine, and > viewing/QCing them through the LORIS interface. Would you be able to advise > me on what is the minimum requirement for such machine? > > I apologize if these information are on the wiki page and I have not been > able to find them. > > Thanks for your help. > > Naj > > -- > ================================== > Najmeh Khalili-Mahani, PhD > Research Associate > McGill Centre for Integrative Neuroscience > Montreal Neurological Institute > McGill University > > NW-143, 3801 University St. > Montreal, QC, H3A 2B4 > Office: 514-398-1799 > email: najma at bic.mni.mcgill.ca > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > -- christine.rogers at mcgill.ca LORIS data systems | loris.ca McGill Centre for Integrative Neuroscience| MCIN.ca McConnell Brain Imaging Centre Montreal Neurological Institute McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: From najmeh.khalilimahani at mcgill.ca Wed Oct 28 15:37:14 2015 From: najmeh.khalilimahani at mcgill.ca (Najmeh Khalili-Mahani, Dr) Date: Wed, 28 Oct 2015 15:37:14 -0400 Subject: [Loris-dev] What MINC needs to be installed as a prereq. to imaging uploader? Message-ID: Hi, The LORIS git hub/WIKI do not instruct where to get the MINC installation from. Thanks Naj -- ================================== Najmeh Khalili-Mahani, PhD Research Associate McGill Centre for Integrative Neuroscience Montreal Neurological Institute McGill University NW-143, 3801 University St. Montreal, QC, H3A 2B4 Office: 514-398-1799 email: najma at bic.mni.mcgill.ca -------------- next part -------------- An HTML attachment was scrubbed... URL: From christine.rogers at mcgill.ca Wed Oct 28 20:27:53 2015 From: christine.rogers at mcgill.ca (Christine Rogers) Date: Wed, 28 Oct 2015 20:27:53 -0400 Subject: [Loris-dev] What MINC needs to be installed as a prereq. to imaging uploader? In-Reply-To: References: Message-ID: Hi Naj, If you're following the setup instructions for the Imaging side of Loris -- https://github.com/aces/Loris/wiki/Imaging-Database -- you'll note that Step 1 asks readers to follow the Readme in the LORIS-MRI git repository. (The Loris-MRI wiki also directs readers there.) This Readme (https://github.com/aces/Loris-MRI/) states in step 3 that the imaging_install.sh script will install the MINC toolkit (line 63 of the script: sudo -S apt-get install minc-tools). Is this the information you were looking for? cheers, Christine On Wed, Oct 28, 2015 at 3:37 PM, Najmeh Khalili-Mahani, Dr < najmeh.khalilimahani at mcgill.ca> wrote: > Hi, > > The LORIS git hub/WIKI do not instruct where to get the MINC installation > from. > > Thanks > Naj > > > -- > ================================== > Najmeh Khalili-Mahani, PhD > Research Associate > McGill Centre for Integrative Neuroscience > Montreal Neurological Institute > McGill University > > NW-143, 3801 University St. > Montreal, QC, H3A 2B4 > Office: 514-398-1799 > email: najma at bic.mni.mcgill.ca > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > -- christine.rogers at mcgill.ca LORIS data systems | loris.ca McGill Centre for Integrative Neuroscience| MCIN.ca McConnell Brain Imaging Centre Montreal Neurological Institute McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: From naj.mahani at gmail.com Wed Oct 28 21:29:14 2015 From: naj.mahani at gmail.com (Naj) Date: Wed, 28 Oct 2015 21:29:14 -0400 Subject: [Loris-dev] What MINC needs to be installed as a prereq. to imaging uploader? In-Reply-To: References: Message-ID: Thanks Christine. Actually here was the confusing part: In the first section of read me, the requirements are minc, perl and dcmtk. So logically, I first installed those before following the rest of instructions. (I installed minc for Ubuntu 14, from nitrc, which alerted 'bad package', which I reported to Vlad and Bert). I got dcmtk with apt get. For someone familiar with MINC, the LORIS wiki does not inform what the official minc release for LORIS is. For those who come to LORIS for the first time, they have no clue where to find MINC tools. When they google, it becomes more confusing: (On bic packages? On GIT? On NITRC? And which minc? 1, 2?) Samir told me to get whichever version that has the latest version of dcm2mnc. But Bert told me that the latest minc tools were not accessible via apt get. (Redmine ticket?) Cheers Naj Sent from my iPhone > On Oct 28, 2015, at 8:27 PM, "Christine Rogers, Ms." wrote: > > Hi Naj, > > If you're following the setup instructions for the Imaging side of Loris -- https://github.com/aces/Loris/wiki/Imaging-Database -- you'll note that Step 1 asks readers to follow the Readme in the LORIS-MRI git repository. (The Loris-MRI wiki also directs readers there.) > > This Readme (https://github.com/aces/Loris-MRI/) states in step 3 that the imaging_install.sh script will install the MINC toolkit (line 63 of the script: sudo -S apt-get install minc-tools). > > Is this the information you were looking for? > cheers, > Christine > > >> On Wed, Oct 28, 2015 at 3:37 PM, Najmeh Khalili-Mahani, Dr wrote: >> Hi, >> >> The LORIS git hub/WIKI do not instruct where to get the MINC installation from. >> >> Thanks >> Naj >> >> >> -- >> ================================== >> Najmeh Khalili-Mahani, PhD >> Research Associate >> McGill Centre for Integrative Neuroscience >> Montreal Neurological Institute >> McGill University >> >> NW-143, 3801 University St. >> Montreal, QC, H3A 2B4 >> Office: 514-398-1799 >> email: najma at bic.mni.mcgill.ca >> >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > > > -- > > christine.rogers at mcgill.ca > LORIS data systems | loris.ca > McGill Centre for Integrative Neuroscience| MCIN.ca > McConnell Brain Imaging Centre > Montreal Neurological Institute > McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: