From waveflux at gmail.com Wed May 3 15:38:25 2017 From: waveflux at gmail.com (Tom Beaudry) Date: Wed, 3 May 2017 15:38:25 -0400 Subject: [Loris-dev] DON'T OPEN MY OTHER GOOGLE DOC EMAIL Message-ID: Hi Everyone, Don't open my google doc email - it's a phishing scam https://www.reddit.com/r/google/comments/692cr4/new_ google_docs_phishing_scam_almost_undetectable/ Sorry, Tom -------------- next part -------------- An HTML attachment was scrubbed... URL: From carolina.mak3 at gmail.com Wed May 3 17:49:41 2017 From: carolina.mak3 at gmail.com (Carolina Makowski) Date: Wed, 3 May 2017 14:49:41 -0700 Subject: [Loris-dev] populating Visit_Windows based on administration of baseline test battery, not age Message-ID: Hi, I was wondering what the correct syntax would be when populating the Visit_Windows table for a longitudinal study that bases optimal visit windows against the baseline timepoint, and not necessarily based on age. For example, if I have two visits (baseline [V1] and 6-month follow up [V2]) and the optimal time window for the 6-month follow-up is within 60 days, would it be correct to populate Visit_Windows with the following for the 6-month follow up? INSERT INTO Visit_Windows (Visit_label, WindowMinDays, WindowMaxDays, OptimumMinDays, OptimumMaxDays, WindowMidpointDays) VALUES (?V2?, ?120?, ?240?, ?120?, ?240?, ?180?); I suspect something is missing here in terms of specifying the calculation based on the baseline assessment date. Also, is it possible to list the window for the baseline visit as NULL, or would you recommend going with what is outlined on the wiki page (i.e. 0 and 39999) Thanks in advance for your help! Carolina -------------- next part -------------- An HTML attachment was scrubbed... URL: From rida.loris at gmail.com Sat May 6 11:27:22 2017 From: rida.loris at gmail.com (Rida Abou-Haidar) Date: Sat, 6 May 2017 11:27:22 -0400 Subject: [Loris-dev] populating Visit_Windows based on administration of baseline test battery, not age In-Reply-To: References: Message-ID: Hi Carolina, The short answer with the current achitecture would be *NO*. However, that does not mean that it could not be added to our roadmap. I will add this item to our weekly discussion and see the response from the team. We actually have a similar case on the CCNA study that I am involved with and at this point in time I have the Visit_Windows table populated as suggested in the WIKI (i.e. 0 and 39999). On your end however, nothing says you can't have a prototype implementation of this. If you follow the link below, I am pointing to the code dealing with this functionality. The current code is calculating an age and comparing it to the otimum and max/min values; a few simple changes could change the age calculation to subtract the date of visit with the date of the first visit instead of the date of birth. Doing so, I would assume you could populate the Visit_Windows table as you wanted to and have it work. On our end, if the decision is made to implement this behaviour we need a much more generalised configurable approach to accommodate the needs of all different projects that would want this feature. Some things to keep in mind: - When comparing dates, you might want to compare the date of visit, date of creation of visit on loris, date a visit was actually started on loris, date of completion of the initial data-entry, date of completion of the entire visit, ... Depending on what you are trying to measure. Just make sure you choose the date that is most relevant to use for you. - If you have a third visit, do you want to compare it with V1 or V2 ? if you have a V4 ?? It gains complexity rather quickly so make sure those decisions are made early on. Finally regarding the NULL values in Visit_Windows, I have personally not made the attempt, however we used to use values (0,0) and this would cause the "Within permitted" field to constantly be red so we switched back to the recommended values (0 and 39999) Thank you for your patience and sorry for the delay in the reply, Rida Abou-Haidar CCNA Software Developer Montreal Neurological Institute McGill University rida.loris at gmail.com On May 3, 2017, at 5:49 PM, Carolina Makowski wrote: Hi, I was wondering what the correct syntax would be when populating the Visit_Windows table for a longitudinal study that bases optimal visit windows against the baseline timepoint, and not necessarily based on age. For example, if I have two visits (baseline [V1] and 6-month follow up [V2]) and the optimal time window for the 6-month follow-up is within 60 days, would it be correct to populate Visit_Windows with the following for the 6-month follow up? INSERT INTO Visit_Windows (Visit_label, WindowMinDays, WindowMaxDays, OptimumMinDays, OptimumMaxDays, WindowMidpointDays) VALUES (?V2?, ?120?, ?240?, ?120?, ?240?, ?180?); I suspect something is missing here in terms of specifying the calculation based on the baseline assessment date. Also, is it possible to list the window for the baseline visit as NULL, or would you recommend going with what is outlined on the wiki page (i.e. 0 and 39999) Thanks in advance for your help! Carolina _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: From carolina.mak3 at gmail.com Sat May 6 20:29:49 2017 From: carolina.mak3 at gmail.com (Carolina Makowski) Date: Sat, 6 May 2017 17:29:49 -0700 Subject: [Loris-dev] populating Visit_Windows based on administration of baseline test battery, not age In-Reply-To: References: Message-ID: Hi Rida, Thanks for your detailed and informative reply. If you could discuss this with the LORIS team that would be excellent - I definitely see the value in being able to configure more easily visit windows based on a particular date rather than age. In particular, I think LORIS will likely be getting this question more and more as more clinically and pharmacologically-oriented studies house their data in LORIS, where many of these studies have a time-critical component to assess treatment efficacy for instance. Just my two cents :) For our purposes, indeed we will have multiple visits (12 or more in some cases!) but the visit window will always be based on the same date at baseline, and these visit windows have already been clearly defined, so given the link you have shared with me, I do believe it shouldn't be too tricky for us to test this out. Thanks again and have a great weekend! Carolina On Sat, May 6, 2017 at 8:27 AM, Rida Abou-Haidar wrote: > Hi Carolina, > > The short answer with the current achitecture would be *NO*. > > However, that does not mean that it could not be added to our roadmap. I > will add this item to our weekly discussion and see the response from the > team. We actually have a similar case on the CCNA study that I am involved > with and at this point in time I have the Visit_Windows table populated as > suggested in the WIKI (i.e. 0 and 39999). > > On your end however, nothing says you can't have a prototype > implementation of this. If you follow the link below, I am pointing to the > code dealing with this functionality. The current code is calculating an > age and comparing it to the otimum and max/min values; a few simple changes > could change the age calculation to subtract the date of visit with the > date of the first visit instead of the date of birth. Doing so, I would > assume you could populate the Visit_Windows table as you wanted to and have > it work. > > On our end, if the decision is made to implement this behaviour we need a > much more generalised configurable approach to accommodate the needs of all > different projects that would want this feature. Some things to keep in > mind: > > - When comparing dates, you might want to compare the date of visit, > date of creation of visit on loris, date a visit was actually started on > loris, date of completion of the initial data-entry, date of completion of > the entire visit, ... Depending on what you are trying to measure. Just > make sure you choose the date that is most relevant to use for you. > - If you have a third visit, do you want to compare it with V1 or V2 ? > if you have a V4 ?? It gains complexity rather quickly so make sure those > decisions are made early on. > > Finally regarding the NULL values in Visit_Windows, I have personally not > made the attempt, however we used to use values (0,0) and this would cause > the "Within permitted" field to constantly be red so we switched back to > the recommended values (0 and 39999) > > Thank you for your patience and sorry for the delay in the reply, > Rida Abou-Haidar > CCNA Software Developer > Montreal Neurological Institute > McGill University > rida.loris at gmail.com > > On May 3, 2017, at 5:49 PM, Carolina Makowski > wrote: > > Hi, > I was wondering what the correct syntax would be when populating the > Visit_Windows table for a longitudinal study that bases optimal visit > windows against the baseline timepoint, and not necessarily based on age. > For example, if I have two visits (baseline [V1] and 6-month follow up > [V2]) and the optimal time window for the 6-month follow-up is within 60 > days, would it be correct to populate Visit_Windows with the following for > the 6-month follow up? > > INSERT INTO Visit_Windows (Visit_label, WindowMinDays, WindowMaxDays, > OptimumMinDays, OptimumMaxDays, WindowMidpointDays) VALUES (?V2?, ?120?, > ?240?, ?120?, ?240?, ?180?); > > I suspect something is missing here in terms of specifying the calculation > based on the baseline assessment date. > Also, is it possible to list the window for the baseline visit as NULL, or > would you recommend going with what is outlined on the wiki page (i.e. 0 > and 39999) > > Thanks in advance for your help! > > Carolina > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From rida.loris at gmail.com Sun May 7 21:47:28 2017 From: rida.loris at gmail.com (Rida Abou-Haidar) Date: Sun, 7 May 2017 21:47:28 -0400 Subject: [Loris-dev] populating Visit_Windows based on administration of baseline test battery, not age In-Reply-To: References: Message-ID: Hey Carolina, I will keep you up to date with the result of the discussion with the Loris team in that case. Best, Rida Abou-Haidar CCNA Software Developer Montreal Neurological Institute McGill University rida.loris at gmail.com On Sat, May 6, 2017 at 8:29 PM, Carolina Makowski wrote: > Hi Rida, > Thanks for your detailed and informative reply. If you could discuss this > with the LORIS team that would be excellent - I definitely see the value in > being able to configure more easily visit windows based on a particular > date rather than age. In particular, I think LORIS will likely be getting > this question more and more as more clinically and > pharmacologically-oriented studies house their data in LORIS, where many of > these studies have a time-critical component to assess treatment efficacy > for instance. Just my two cents :) > > For our purposes, indeed we will have multiple visits (12 or more in some > cases!) but the visit window will always be based on the same date at > baseline, and these visit windows have already been clearly defined, so > given the link you have shared with me, I do believe it shouldn't be too > tricky for us to test this out. > > Thanks again and have a great weekend! > > Carolina > > On Sat, May 6, 2017 at 8:27 AM, Rida Abou-Haidar > wrote: > >> Hi Carolina, >> >> The short answer with the current achitecture would be *NO*. >> >> However, that does not mean that it could not be added to our roadmap. I >> will add this item to our weekly discussion and see the response from the >> team. We actually have a similar case on the CCNA study that I am involved >> with and at this point in time I have the Visit_Windows table populated as >> suggested in the WIKI (i.e. 0 and 39999). >> >> On your end however, nothing says you can't have a prototype >> implementation of this. If you follow the link below, I am pointing to the >> code dealing with this functionality. The current code is calculating an >> age and comparing it to the otimum and max/min values; a few simple changes >> could change the age calculation to subtract the date of visit with the >> date of the first visit instead of the date of birth. Doing so, I would >> assume you could populate the Visit_Windows table as you wanted to and have >> it work. >> >> On our end, if the decision is made to implement this behaviour we need a >> much more generalised configurable approach to accommodate the needs of all >> different projects that would want this feature. Some things to keep in >> mind: >> >> - When comparing dates, you might want to compare the date of visit, >> date of creation of visit on loris, date a visit was actually started on >> loris, date of completion of the initial data-entry, date of completion of >> the entire visit, ... Depending on what you are trying to measure. Just >> make sure you choose the date that is most relevant to use for you. >> - If you have a third visit, do you want to compare it with V1 or V2 >> ? if you have a V4 ?? It gains complexity rather quickly so make sure those >> decisions are made early on. >> >> Finally regarding the NULL values in Visit_Windows, I have personally not >> made the attempt, however we used to use values (0,0) and this would cause >> the "Within permitted" field to constantly be red so we switched back to >> the recommended values (0 and 39999) >> >> Thank you for your patience and sorry for the delay in the reply, >> Rida Abou-Haidar >> CCNA Software Developer >> Montreal Neurological Institute >> McGill University >> rida.loris at gmail.com >> >> On May 3, 2017, at 5:49 PM, Carolina Makowski >> wrote: >> >> Hi, >> I was wondering what the correct syntax would be when populating the >> Visit_Windows table for a longitudinal study that bases optimal visit >> windows against the baseline timepoint, and not necessarily based on age. >> For example, if I have two visits (baseline [V1] and 6-month follow up >> [V2]) and the optimal time window for the 6-month follow-up is within 60 >> days, would it be correct to populate Visit_Windows with the following for >> the 6-month follow up? >> >> INSERT INTO Visit_Windows (Visit_label, WindowMinDays, WindowMaxDays, >> OptimumMinDays, OptimumMaxDays, WindowMidpointDays) VALUES (?V2?, ?120?, >> ?240?, ?120?, ?240?, ?180?); >> >> I suspect something is missing here in terms of specifying the >> calculation based on the baseline assessment date. >> Also, is it possible to list the window for the baseline visit as NULL, >> or would you recommend going with what is outlined on the wiki page (i.e. 0 >> and 39999) >> >> Thanks in advance for your help! >> >> Carolina >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mouna.safi-harb at mail.mcgill.ca Tue May 9 14:02:35 2017 From: mouna.safi-harb at mail.mcgill.ca (Mouna Safi-Harab) Date: Tue, 9 May 2017 18:02:35 +0000 Subject: [Loris-dev] Create DCCID and Organizing CIVET outputs In-Reply-To: References: , , Message-ID: Hi Michael, Sorry for the delays in getting back to you on this. The LORIS-MRI codebase does the generation of the CandID for you (check the function CreateMRICandidates in tarchive_validation which calls createNewCandID in MRI.pm). The PSCID, however, is not created (LORIS supports multiple ways in which you can create the PSCID, this is usually read from the config.xml file in the LORIS project directory, so it is a bit trickier than creating the CandID). But since your project would have the PSCID_VisitLabel already known and in the DICOM header, and the prod file is made to parse this, I have a workaround for your project needs. In the determineSubjectID() routine in MRIProcessingUtility.pm, after line 241 (on version 17.0.0), you can add a few lines that selects the CandID the pipeline created a step earlier to be used for the execution of the rest of the steps, while relying on your parsed PSCID from the prod file; as follows: # if the candidate was created from the backend, it won't be in the tarchiveInfo, so add it here my $dbh = &NeuroDB::DBI::connect_to_db(@Settings::db); if (!defined($subjectIDsref->{'CandID'}) && $Settings::createCandidates) { my $query = "SELECT CandID FROM candidate WHERE PSCID=?"; my $sth = ${$this->{'dbhr'}}->prepare($query); $sth->execute($subjectIDsref->{'PSCID'}); if ( $sth->rows > 0 ) { $subjectIDsref->{'CandID'} = $sth->fetchrow_array; } } This should allow you to proceed with candidate creation from the backend based on your project assumptions. Please note this is very specific to your project (in particular, due to the fact that you know the PSCID, but not the CandID, while there is a one-to-one correspondence between these two in LORIS). But I believe it addresses your request. Let me know if you have any further questions. - Mouna ________________________________ From: Michael Joseph Sent: Friday, April 28, 2017 12:49:50 PM To: Mouna Safi-Harab; loris-dev at bic.mni.mcgill.ca Subject: Re: Create DCCID and Organizing CIVET outputs Hi Mouna, Thank you for your reply. Your answers certainly help. For our images, the PatientName header is labeled as PSCID-VisitLabel. I've modified the regex in the prod file to parse this out. I didn't want to modify the header to also include a DCCID because there are other groups sharing the images. I was wondering if there's another way to create a DCCID when images are uploaded (similar to how the scanner is registered). The Imaging Uploader GUI isn't as important to us as we'll be relying on the Perl scripts to upload all our images. Thank you for directing me to the DTIPrep directory. It definitely helps as an example for registering processed data. Michael ________________________________ From: Mouna Safi-Harab Sent: April 27, 2017 2:06:58 PM To: Michael Joseph; loris-dev at bic.mni.mcgill.ca Subject: Re: Create DCCID and Organizing CIVET outputs Hi Michael, Here are my answers to your questions: 1) Setting createCandidates to 1 in the prod file does indeed allow for creation of the candidate from the MRI pipeline. You will need to make sure that 1) the PatientName header is anonymized properly in the DICOM files, and 2) getSubjectIDs() function in this prod file is a) splitting the PatientName header information in a way that is consistent with the anonymization and your project DCCID/PSCID/VisitLabel convention, and b) has the $subjectID{'createVisitLabel'} option set to 1 as you will also likely need the MRI pipeline to create the visit for that candidate as well. However, projects using the Imaging Uploader GUI unfortunately does not allow for this option. If you want a way to make it work for now, you can disable the check on Lines 378-395 in NDB_Menu_Filter_imaging_uploader.class.inc (which sole purpose is to check if the CandID is registered in the database). We can look at this from our end, and make sure the option createCandidate is propagated to the Imaging Uploader GUI as well in a seamless manner to the user (will discuss this at our internal meeting). 2) Loris-MRI codebase provides an example of how to insert files from another processing pipeline into the database. Check the DTIPrep/ directory for an example you can follow. Essentially, inserting processed files into LORIS is a two-step process: you will need a 1) wrapper script that "understands" or "knows" how/where the processed files are stored (this step is processing pipeline dependent), and then 2) have that wrapper script call a generic file called uploadNeuroDB/register_processed_data.pl. The register_processed_data.pl file would take in many required arguments, some of which are the full path of the file you are going to register. Other parameters are the acquisition protocol ID. So yes, the"white_matter", "pve", "tal_mask" were initially created to allow for CIVET outputs to be registered with the correct acquisition protocol. Other required parameters are the sourceFileID which would be the ID of the initial file you sent to CIVET for processing. The second step should be processing pipeline independent. I hope the above answers your questions, or at least, gives you a starting point. - Mouna ________________________________ From: loris-dev-bounces at bic.mni.mcgill.ca on behalf of Michael Joseph Sent: Wednesday, April 19, 2017 4:03 PM To: loris-dev at bic.mni.mcgill.ca Subject: [Loris-dev] Create DCCID and Organizing CIVET outputs Hi Loris dev community, I have 2 questions: 1) Is there a way to register new candidates into Loris from the back-end without a DCCID? Essentially, I'd like to add candidates and sessions while running the tarchiveLoader script. I noticed that the prod file has a createCandidates variable. Is there anything else that needs to be modified? 2) How are CIVET outputs typically organized in Loris? I noticed that in the mri_scan_type table, there are labels like "white_matter", "pve", "tal_msk". I'm assuming the most of the files from CIVET would get registered using these labels. Also, is there a good way of linking to the htmls from the CIVET QC pipeline? Thanks, Michael ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. -------------- next part -------------- An HTML attachment was scrubbed... URL: From christine.rogers at mcgill.ca Wed May 10 17:00:15 2017 From: christine.rogers at mcgill.ca (Christine Rogers) Date: Wed, 10 May 2017 17:00:15 -0400 Subject: [Loris-dev] LORIS Release 17.0.3 Message-ID: Hi Everyone, The new minor release 17.0.3 is now available on Github . All users of the LORIS 17.0 branch are strongly urged to upgrade immediately This release fixes two security holes introduced in features added in the LORIS v17.0.0 including a remote code execution exploit in one of the BrainBrowser ajax scripts. For existing projects using the MRI violations module, the link to launch BrainBrowser is now disabled. Some minor bug fixes found since v17.0.2 are also incorporated. (All pull requests in Loris 17.* ) Thanks, Christine -- 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 carolina.mak3 at gmail.com Fri May 12 21:23:32 2017 From: carolina.mak3 at gmail.com (Carolina Makowski) Date: Fri, 12 May 2017 18:23:32 -0700 Subject: [Loris-dev] troubleshooting MRI upload via image uploader and registering instrument in backend Message-ID: Hi there, I have two queries that are related to the imaging and behavioral domains of the database - please let me know if you would prefer that I separate the issues since they pertain to different aspects of the database, but for now I will put both issues here: *1) Failure uploading .tgz file through Image Uploader* Before getting to this point, we had completed everything outlined in the documentation online for the Imaging Database. The tgz file I tried to upload was anonymized and the header/Patient Name was parsed accordingly, and the file did upload, but its status is marked as "Failure". Next, we looked for the tgz file in the backend, and it does indeed appear in /data/incoming. We also followed all documentation in the Imaging Uploader documentation, changing the paths appropriately in the configuration module and updating the apache configuration file. After running the imaging_upload_file.pl script, we received the following error: lorisadmin at abcd-dataweb:/data/abcd/bin/mri$ uploadNeuroDB/imaging_upload_ file.pl -profile prod -verbose -upload_id 5 /data/incoming/ NDARINV1ET4JE3B_174450_baselineyear1arm1_T1.tgz ERROR: You don't have a configuration file named 'prod' in: /data/abcd/bin/mri/dicom-archive/.loris_mri/ The prod file does indeed exist in that directory, and we have tried running this as root and lorisadmin, with appropriate permissions, and can access prod independently of this script. Has this error come up before in your experience? *2) Registering an instrument that was created using the Instrument Builder GUI.* I am having a bit of trouble following the documentation online for this. In particular, we are getting stuck in populating the test_subgroups table. According to the documentation online, this statement should apply to us (from section 3: populate test_names and test_subgroups tables): "For all *.linst instruments created via the Instrument Builder, sourcing the *.sql file takes care of this step". However, test_subgroups was not automatically populated (test_names was populated properly). We started delving into the "Instrument Coding Guide" documentation but I am under the impression that creation of an instrument through the instrument builder and using a linst file should bypass some of the steps that are required in this Instrument Coding Guide. Perhaps some clarification on the steps after building a linst file and after creating and adding the instrument table to the database would be helpful here. Thanks in advance! I know I've been bombarding you guys with a lot of questions lately but I really appreciate the help :) Have a nice weekend, Carolina -------------- next part -------------- An HTML attachment was scrubbed... URL: From mouna.safi-harb at mail.mcgill.ca Sun May 14 08:00:39 2017 From: mouna.safi-harb at mail.mcgill.ca (Mouna Safi-Harab) Date: Sun, 14 May 2017 12:00:39 +0000 Subject: [Loris-dev] troubleshooting MRI upload via image uploader and registering instrument in backend In-Reply-To: References: Message-ID: Hi Carolina, I will try to address the first point, and let someone else in the Loris team address the second. For the prod file error, I have seen this and it can be caused by multiple issues, so I will attempt to list a few possible causes, and hopefully one of them would resolve your problem (I am suspecting 1)b) could solve your issue): 1) environment file: a) please confirm that the environment file (which is at /data/abcd/bin/mri/) includes the path to your dicom_archive directory: export LORIS_CONFIG=/data/abcd/bin/mri/dicom-archive b) source the environment file before running the pipeline: (just type: source environment at the command line), then type: echo $PATH to see if you get all the PATHS in the environment file sourced 2) permissions: just make sure we have 770 permissions on the directories (recusrively) leading up to .loris_mri; and that they are owned by lorisadmin and groupowned by the front0end user (www-data). Then ensure a 640 permission on the prod file itself (with the same ownership and group ownership). 3) prod file customised routines: If you edited the prod file, sometimes a syntax error in some of its project customizable routines could issue the error you are getting. Sp if for example you modified the getSubject() routine in the prod file, and opened a { and forgot to close it, you would get the error that the prod file is not readable... You can send me your file separately (WITHOUT the database credentials) if you wish and I can check if this is the cause. Let me know! - Mouna ________________________________ From: loris-dev-bounces at bic.mni.mcgill.ca on behalf of Carolina Makowski Sent: Friday, May 12, 2017 9:23:32 PM To: loris-dev at bic.mni.mcgill.ca Subject: [Loris-dev] troubleshooting MRI upload via image uploader and registering instrument in backend Hi there, I have two queries that are related to the imaging and behavioral domains of the database - please let me know if you would prefer that I separate the issues since they pertain to different aspects of the database, but for now I will put both issues here: 1) Failure uploading .tgz file through Image Uploader Before getting to this point, we had completed everything outlined in the documentation online for the Imaging Database. The tgz file I tried to upload was anonymized and the header/Patient Name was parsed accordingly, and the file did upload, but its status is marked as "Failure". Next, we looked for the tgz file in the backend, and it does indeed appear in /data/incoming. We also followed all documentation in the Imaging Uploader documentation, changing the paths appropriately in the configuration module and updating the apache configuration file. After running the imaging_upload_file.pl script, we received the following error: lorisadmin at abcd-dataweb:/data/abcd/bin/mri$ uploadNeuroDB/imaging_upload_file.pl -profile prod -verbose -upload_id 5 /data/incoming/NDARINV1ET4JE3B_174450_baselineyear1arm1_T1.tgz ERROR: You don't have a configuration file named 'prod' in: /data/abcd/bin/mri/dicom-archive/.loris_mri/ The prod file does indeed exist in that directory, and we have tried running this as root and lorisadmin, with appropriate permissions, and can access prod independently of this script. Has this error come up before in your experience? 2) Registering an instrument that was created using the Instrument Builder GUI. I am having a bit of trouble following the documentation online for this. In particular, we are getting stuck in populating the test_subgroups table. According to the documentation online, this statement should apply to us (from section 3: populate test_names and test_subgroups tables): "For all *.linst instruments created via the Instrument Builder, sourcing the *.sql file takes care of this step". However, test_subgroups was not automatically populated (test_names was populated properly). We started delving into the "Instrument Coding Guide" documentation but I am under the impression that creation of an instrument through the instrument builder and using a linst file should bypass some of the steps that are required in this Instrument Coding Guide. Perhaps some clarification on the steps after building a linst file and after creating and adding the instrument table to the database would be helpful here. Thanks in advance! I know I've been bombarding you guys with a lot of questions lately but I really appreciate the help :) Have a nice weekend, Carolina -------------- next part -------------- An HTML attachment was scrubbed... URL: From christine.rogers at mcgill.ca Mon May 15 18:14:37 2017 From: christine.rogers at mcgill.ca (Christine Rogers) Date: Mon, 15 May 2017 18:14:37 -0400 Subject: [Loris-dev] troubleshooting MRI upload via image uploader and registering instrument in backend In-Reply-To: References: Message-ID: Hi Carolina, Happy to address your second question -- thanks for catching that omission in the wiki, not sure why we haven't found this gap before in the LINST documentation - I've added notes to update this. note: Test subgroups do apply to LINST instruments exactly as they apply to PHP-coded instruments. Test subgroups are simply used to organize the list of instruments displayed in any given timepoint into blocks of related instruments. Typically, it's useful to visually break down a long list of instruments in a visit into categories such as (e.g.) "Developmental" measures, then "Communication" tests, followed by "Medical/Family History" questionnaires, etc. To define these test_subgroups, use a MySQL insert statement to add each to the *test_subgroups* table, e.g.: To display 'Developmental' instruments first in order within each timepoint page: > INSERT INTO *test_subgroups* (Subgroup_name, group_order) VALUES > ('Developmental', '1'); Next, associate each instruments to a subgroup, by updating the *test_names* table to populate the Sub_group field. (I'm assuming your instruments already exist in *test_names*; note only one subgroup per instrument is best.) e.g. To add the Vineland II (testname: 'vabs2') to the 'Developmental' measures subgroup : UPDATE *test_names* SET Sub_group = > (SELECT ID FROM *test_subgroups* > WHERE Subgroup_name = 'Developmental') > WHERE Test_name = 'vabs2' ; Hope this helps -- cheers, Christine On Fri, May 12, 2017 at 9:23 PM, Carolina Makowski wrote: > Hi there, > > I have two queries that are related to the imaging and behavioral domains > of the database - please let me know if you would prefer that I separate > the issues since they pertain to different aspects of the database, but for > now I will put both issues here: > > *1) Failure uploading .tgz file through Image Uploader* > Before getting to this point, we had completed everything outlined in the > documentation online for the Imaging Database. > The tgz file I tried to upload was anonymized and the header/Patient Name > was parsed accordingly, and the file did upload, but its status is marked > as "Failure". > Next, we looked for the tgz file in the backend, and it does indeed appear > in /data/incoming. We also followed all documentation in the Imaging > Uploader documentation, changing the paths appropriately in the > configuration module and updating the apache configuration file. > After running the imaging_upload_file.pl script, we received the > following error: > > lorisadmin at abcd-dataweb:/data/abcd/bin/mri$ uploadNeuroDB/imaging_upload_f > ile.pl -profile prod -verbose -upload_id 5 /data/incoming/NDARINV1ET4JE3B > _174450_baselineyear1arm1_T1.tgz > > ERROR: You don't have a > configuration file named 'prod' in: > /data/abcd/bin/mri/dicom-archive/.loris_mri/ > > The prod file does indeed exist in that directory, and we have tried > running this as root and lorisadmin, with appropriate permissions, and can > access prod independently of this script. Has this error come up before in > your experience? > > *2) Registering an instrument that was created using the Instrument > Builder GUI.* > I am having a bit of trouble following the documentation online for this. > In particular, we are getting stuck in populating the test_subgroups table. > According to the documentation online, this statement should apply to us > (from section 3: populate test_names and test_subgroups tables): "For all > *.linst instruments created via the Instrument Builder, sourcing the *.sql file > takes care of this step". However, test_subgroups was not automatically > populated (test_names was populated properly). We started delving into the > "Instrument Coding Guide" documentation but I am under the impression that > creation of an instrument through the instrument builder and using a linst > file should bypass some of the steps that are required in this Instrument > Coding Guide. Perhaps some clarification on the steps after building a > linst file and after creating and adding the instrument table to the > database would be helpful here. > > Thanks in advance! I know I've been bombarding you guys with a lot of > questions lately but I really appreciate the help :) > > Have a nice weekend, > Carolina > > _______________________________________________ > 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 McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: From mukhan at ualberta.ca Mon May 15 19:54:49 2017 From: mukhan at ualberta.ca (Muhammad Khan) Date: Mon, 15 May 2017 17:54:49 -0600 Subject: [Loris-dev] LORIS Instruments Message-ID: Hi guys, For our instruments, we have many dependent fields. For example: If a certain procedure was done (set to "Yes"), then a date must be provided. However, because the forms are not dynamic, a user is able to set a field to "No" and still be able to fill out the date. What would be the best way to deal with this issue? Would I be able to do a check using the addFormRule() function? Thanks, Muhammad -------------- next part -------------- An HTML attachment was scrubbed... URL: From christine.rogers at mcgill.ca Mon May 15 22:22:59 2017 From: christine.rogers at mcgill.ca (Christine Rogers) Date: Mon, 15 May 2017 22:22:59 -0400 Subject: [Loris-dev] LORIS Instruments In-Reply-To: References: Message-ID: Hi Muhammad, Thanks for your question -- for instruments coded in PHP, XIN Rules (see Wiki documentation) enforce exactly this kind of inter-field dependency logic, akin to addFormRule(). You may also find more helpful context on the How to Code an Instrument Wiki page in our Wiki, and via the sample instruments in the docs/instruments/ directory on our GitHub. Best, Christine On Mon, May 15, 2017 at 7:54 PM, Muhammad Khan wrote: > Hi guys, > > For our instruments, we have many dependent fields. For example: If a > certain procedure was done (set to "Yes"), then a date must be provided. > However, because the forms are not dynamic, a user is able to set a field > to "No" and still be able to fill out the date. > > What would be the best way to deal with this issue? Would I be able to do > a check using the addFormRule() function? > > Thanks, > > Muhammad > > > _______________________________________________ > 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 McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: From sylvain at bic.mni.mcgill.ca Tue May 16 09:21:56 2017 From: sylvain at bic.mni.mcgill.ca (Sylvain MILOT) Date: Tue, 16 May 2017 09:21:56 -0400 (EDT) Subject: [Loris-dev] Fwd: statistics module giving values as zero ("0") (fwd) Message-ID: please post your questions on the loris-dev mailing list. Sylvain --- Sylvain Milot (sylvain at bic.mni.mcgill.ca) (sylvain.milot at mcgill.ca) Brain Imaging Centre Montreal Neurological Institute 3801 University Street Webster 2B, Room 206 Montreal, Qc., Canada, H3A 2B4 Phone : (514) 398-4965, Fax: 398-8948 Mobile : (514) 712-1768 Office : 527 Av Des Pins O., Room 104 Montreal, Qc., H2W 1S4 ---------- Forwarded message ---------- Date: Tue, 16 May 2017 17:40:57 +0530 (IST) From: "Ganesh Chauhan (CBR)" To: mailman-owner at bic.mni.mcgill.ca Subject: Fwd: statistics module giving values as zero ("0") _______________________________________________________________________________________________________________________________________________________________________________________________________________ From: "Ganesh Chauhan (CBR)" To: "mailman" Sent: Tuesday, May 16, 2017 5:35:50 PM Subject: statistics module giving values as zero ("0") Hi, I am trying to get the statistics module working based on instructions on the following page?https://github.com/aces/Loris/wiki/LORIS-Modules. All values appear as zero ("0"). I have created two instruments called "family_info" and "anthropometry". I am able to start the visit of the person and enter the data for the various instruments. Many thanks for your help. -- Ganesh Chauhan (PhD) Scientist Centre for Brain Research (CBR) Indian Institute of Science (IISc) Bengaluru, INDIA +91 80 2293 3009 https://www.cbr.iisc.ac.in -- Ganesh Chauhan (PhD) Scientist Centre for Brain Research (CBR) Indian Institute of Science (IISc) Bengaluru, INDIA +91 80 2293 3009 https://www.cbr.iisc.ac.in From ganesh.chauhan at cbr.iisc.ac.in Wed May 17 00:48:29 2017 From: ganesh.chauhan at cbr.iisc.ac.in (Ganesh Chauhan (CBR)) Date: Wed, 17 May 2017 10:18:29 +0530 (IST) Subject: [Loris-dev] Activating the statistics module Message-ID: <594326182.9264.1494996509157.JavaMail.zimbra@cbr.iisc.ac.in> Hi, I am trying to get the statistics module working based on instructions on the following page [ https://github.com/aces/Loris/wiki/LORIS-Modules | https://github.com/aces/Loris/wiki/LORIS-Modules ] . "For example, to configure list of instruments for Behavioural statistics, copy NDB_Menu_statistics_site.class.inc from modules/statistics/php/libraries to project/libraries, and populate "var $instruments = array(...)" with instrument names." Hence I copied the file and made the following changes: var $instruments = array( 'family_info', 'anthropometry', ); After doing all this, all values appear as zero ("0") on the front-end webpage. I have created two instruments called "family_info" and "anthropometry". I am able to start the visit of the person and enter the data for the various instruments. Many thanks for your help. With best regards, Ganesh -- Ganesh Chauhan (PhD) Scientist Centre for Brain Research (CBR) Indian Institute of Science (IISc) Bengaluru, INDIA +91 80 2293 3009 https://www.cbr.iisc.ac.in -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: From rida.loris at gmail.com Wed May 17 00:52:48 2017 From: rida.loris at gmail.com (Rida Abou-Haidar) Date: Wed, 17 May 2017 00:52:48 -0400 Subject: [Loris-dev] Activating the statistics module In-Reply-To: <594326182.9264.1494996509157.JavaMail.zimbra@cbr.iisc.ac.in> References: <594326182.9264.1494996509157.JavaMail.zimbra@cbr.iisc.ac.in> Message-ID: Hi Ganesh, We will investigate this and get back to you as soon as possible. Cheers, Rida Abou-Haidar On May 17, 2017 12:49 AM, "Ganesh Chauhan (CBR)" < ganesh.chauhan at cbr.iisc.ac.in> wrote: > Hi, > > I am trying to get the statistics module working based on instructions on > the following page https://github.com/aces/Loris/wiki/LORIS-Modules. > "For example, to configure list of instruments for Behavioural statistics, > copy NDB_Menu_statistics_site.class.inc from modules/statistics/php/libraries > to project/libraries, and populate "var $instruments = array(...)" with > instrument names." > > Hence I copied the file and made the following changes: > > var $instruments = array( > 'family_info', > 'anthropometry', > ); > > > After doing all this, all values appear as zero ("0") on the front-end > webpage. I have created two instruments called "family_info" and > "anthropometry". I am able to start the visit of the person and enter the > data for the various instruments. > > Many thanks for your help. > > With best regards, > Ganesh > > -- > Ganesh Chauhan (PhD) > Scientist > Centre for Brain Research (CBR) > Indian Institute of Science (IISc) > Bengaluru, INDIA > +91 80 2293 3009 <+91%2080%202293%203009> > https://www.cbr.iisc.ac.in > > > -- > This message has been scanned for viruses and > dangerous content by *MailScanner* , and is > believed to be clean. > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From zvirani.mcin at gmail.com Wed May 17 17:09:06 2017 From: zvirani.mcin at gmail.com (Zain Virani) Date: Wed, 17 May 2017 17:09:06 -0400 Subject: [Loris-dev] Activating the statistics module In-Reply-To: <594326182.9264.1494996509157.JavaMail.zimbra@cbr.iisc.ac.in> References: <594326182.9264.1494996509157.JavaMail.zimbra@cbr.iisc.ac.in> Message-ID: Hello Ganesh, I need a few more details regarding your issue with the statistics module in order to determine what's going wrong. I am assuming you are running the 17.0 release? If not, please let me know. Additionally, are 0s being reported in all parts of the module (Demographic, Behavioural, and Imaging)? Thank you for your patience, Zain Virani On Wed, May 17, 2017 at 12:48 AM, Ganesh Chauhan (CBR) < ganesh.chauhan at cbr.iisc.ac.in> wrote: > Hi, > > I am trying to get the statistics module working based on instructions on > the following page https://github.com/aces/Loris/wiki/LORIS-Modules. > "For example, to configure list of instruments for Behavioural statistics, > copy NDB_Menu_statistics_site.class.inc from modules/statistics/php/libraries > to project/libraries, and populate "var $instruments = array(...)" with > instrument names." > > Hence I copied the file and made the following changes: > > var $instruments = array( > 'family_info', > 'anthropometry', > ); > > > After doing all this, all values appear as zero ("0") on the front-end > webpage. I have created two instruments called "family_info" and > "anthropometry". I am able to start the visit of the person and enter the > data for the various instruments. > > Many thanks for your help. > > With best regards, > Ganesh > > -- > Ganesh Chauhan (PhD) > Scientist > Centre for Brain Research (CBR) > Indian Institute of Science (IISc) > Bengaluru, INDIA > +91 80 2293 3009 <+91%2080%202293%203009> > https://www.cbr.iisc.ac.in > > > -- > This message has been scanned for viruses and > dangerous content by *MailScanner* , and is > believed to be clean. > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ganesh.chauhan at cbr.iisc.ac.in Mon May 22 00:38:04 2017 From: ganesh.chauhan at cbr.iisc.ac.in (Ganesh Chauhan (CBR)) Date: Mon, 22 May 2017 10:08:04 +0530 (IST) Subject: [Loris-dev] Activating the statistics module In-Reply-To: References: <594326182.9264.1494996509157.JavaMail.zimbra@cbr.iisc.ac.in> Message-ID: <1265014413.11114.1495427884489.JavaMail.zimbra@cbr.iisc.ac.in> Dear Zain, Yes, I am running LORIS version 17.0.2 Yes, I am getting 0s in all parts of the module (Demographic, Behavioural, Reliability and Imaging). Many thanks for your help. With best regards, Ganesh From: "Zain Virani" To: "Ganesh Chauhan (CBR)" Cc: "loris-dev" Sent: Thursday, May 18, 2017 2:39:06 AM Subject: Re: [Loris-dev] Activating the statistics module Hello Ganesh, I need a few more details regarding your issue with the statistics module in order to determine what's going wrong. I am assuming you are running the 17.0 release? If not, please let me know. Additionally, are 0s being reported in all parts of the module (Demographic, Behavioural, and Imaging)? Thank you for your patience, Zain Virani On Wed, May 17, 2017 at 12:48 AM, Ganesh Chauhan (CBR) < [ mailto:ganesh.chauhan at cbr.iisc.ac.in | ganesh.chauhan at cbr.iisc.ac.in ] > wrote: Hi, I am trying to get the statistics module working based on instructions on the following page [ https://github.com/aces/Loris/wiki/LORIS-Modules | https://github.com/aces/Loris/wiki/LORIS-Modules ] . "For example, to configure list of instruments for Behavioural statistics, copy NDB_Menu_statistics_site.class.inc from modules/statistics/php/libraries to project/libraries, and populate "var $instruments = array(...)" with instrument names." Hence I copied the file and made the following changes: var $instruments = array( 'family_info', 'anthropometry', ); After doing all this, all values appear as zero ("0") on the front-end webpage. I have created two instruments called "family_info" and "anthropometry". I am able to start the visit of the person and enter the data for the various instruments. Many thanks for your help. With best regards, Ganesh -- Ganesh Chauhan (PhD) Scientist Centre for Brain Research (CBR) Indian Institute of Science (IISc) Bengaluru, INDIA [ tel:+91%2080%202293%203009 | +91 80 2293 3009 ] [ https://www.cbr.iisc.ac.in/ | https://www.cbr.iisc.ac.in ] -- This message has been scanned for viruses and dangerous content by [ http://www.mailscanner.info/ | MailScanner ] , and is believed to be clean. _______________________________________________ Loris-dev mailing list [ mailto:Loris-dev at bic.mni.mcgill.ca | Loris-dev at bic.mni.mcgill.ca ] [ http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev | http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev ] -- Ganesh Chauhan (PhD) Scientist Centre for Brain Research (CBR) Indian Institute of Science (IISc) Bengaluru, INDIA +91 80 2293 3009 https://www.cbr.iisc.ac.in -------------- next part -------------- An HTML attachment was scrubbed... URL: From ganesh.chauhan at cbr.iisc.ac.in Mon May 22 05:51:19 2017 From: ganesh.chauhan at cbr.iisc.ac.in (Ganesh Chauhan (CBR)) Date: Mon, 22 May 2017 15:21:19 +0530 (IST) Subject: [Loris-dev] ACE-III instrument for LORIS Message-ID: <1153970956.11485.1495446679121.JavaMail.zimbra@cbr.iisc.ac.in> Hi, I just wanted to know if I can get a copy of the ACE-III and other cognitive test instruments/modules from the LORIS community. Many thanks for your help. With best regards, Ganesh -- Ganesh Chauhan (PhD) Scientist Centre for Brain Research (CBR) Indian Institute of Science (IISc) Bengaluru, INDIA +91 80 2293 3009 https://www.cbr.iisc.ac.in -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: From zvirani.mcin at gmail.com Tue May 23 17:10:40 2017 From: zvirani.mcin at gmail.com (Zain Virani) Date: Tue, 23 May 2017 17:10:40 -0400 Subject: [Loris-dev] Activating the statistics module In-Reply-To: <1265014413.11114.1495427884489.JavaMail.zimbra@cbr.iisc.ac.in> References: <594326182.9264.1494996509157.JavaMail.zimbra@cbr.iisc.ac.in> <1265014413.11114.1495427884489.JavaMail.zimbra@cbr.iisc.ac.in> Message-ID: Hello Ganesh, There are a few steps we can take to make sure everything is running smoothly (I will use the instrument name family_info as an example in order to be as clear as possible): 1. We need to make sure that the instruments were inserted correctly. Under Reports->Statistics->Demographic Statistics, scroll down to the 2nd table and open the drop down menu. If you do not see the names of all of your instruments there, then that is the issue and you will need to insert your instrument in the correct format. Before following the instructions, ensure your instrument class name is NDB_BVL_Instrument_family_info.class.inc. Then, follow the instructions here: https://github.com/aces/Loris/wiki/Instrument-Insertion. For the last step be sure to run the assign_missing_instrument.php script as opposed to fix_timepoint_date.php. While following these instructions, be sure that consistent naming conventions are followed. For example, test_names will have an entry where Test_name = family_info. Please ensure that this has the exact same name (case and underscore sensitive) as the family_info table. The Full Name field can be set to anything. Double check this in test_battery and instrument_subtests as well. 2. If the reports still only show 0s at this point, you should run the queries from the script modules/statistics/php/NDB_Form_statistics.class.inc manually in your database. If the queries return a value different from what is being reported, please email me and let me know. If not, then we are done! Regardless of whether or not these steps work, it will be very helpful to take a look at the error log. When you get a chance, attempt to access all 4 tabs of the statistics module, and then send me the error log, which is located at /var/log/apache2/loris-error.log Feel free to email me with any questions, or if any of these steps don't work. Good luck! Zain On Mon, May 22, 2017 at 12:38 AM, Ganesh Chauhan (CBR) < ganesh.chauhan at cbr.iisc.ac.in> wrote: > Dear Zain, > > Yes, I am running LORIS version 17.0.2 > Yes, I am getting 0s in all parts of the module (Demographic, Behavioural, > Reliability and Imaging). > > Many thanks for your help. > > With best regards, > Ganesh > > ------------------------------ > *From: *"Zain Virani" > *To: *"Ganesh Chauhan (CBR)" > *Cc: *"loris-dev" > *Sent: *Thursday, May 18, 2017 2:39:06 AM > *Subject: *Re: [Loris-dev] Activating the statistics module > > Hello Ganesh, > I need a few more details regarding your issue with the statistics module > in order to determine what's going wrong. I am assuming you are running the > 17.0 release? If not, please let me know. Additionally, are 0s being > reported in all parts of the module (Demographic, Behavioural, and Imaging)? > Thank you for your patience, > > Zain Virani > > On Wed, May 17, 2017 at 12:48 AM, Ganesh Chauhan (CBR) < > ganesh.chauhan at cbr.iisc.ac.in> wrote: > >> Hi, >> >> I am trying to get the statistics module working based on instructions on >> the following page https://github.com/aces/Loris/wiki/LORIS-Modules. >> "For example, to configure list of instruments for Behavioural >> statistics, copy NDB_Menu_statistics_site.class.inc from >> modules/statistics/php/libraries to project/libraries, and populate "var >> $instruments = array(...)" with instrument names." >> >> Hence I copied the file and made the following changes: >> >> var $instruments = array( >> 'family_info', >> 'anthropometry', >> ); >> >> >> After doing all this, all values appear as zero ("0") on the front-end >> webpage. I have created two instruments called "family_info" and >> "anthropometry". I am able to start the visit of the person and enter the >> data for the various instruments. >> >> Many thanks for your help. >> >> With best regards, >> Ganesh >> >> -- >> Ganesh Chauhan (PhD) >> Scientist >> Centre for Brain Research (CBR) >> Indian Institute of Science (IISc) >> Bengaluru, INDIA >> +91 80 2293 3009 <+91%2080%202293%203009> >> https://www.cbr.iisc.ac.in >> >> >> -- >> This message has been scanned for viruses and >> dangerous content by *MailScanner* , and >> is >> believed to be clean. >> >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> >> > > -- > Ganesh Chauhan (PhD) > Scientist > Centre for Brain Research (CBR) > Indian Institute of Science (IISc) > Bengaluru, INDIA > +91 80 2293 3009 <+91%2080%202293%203009> > https://www.cbr.iisc.ac.in > -------------- next part -------------- An HTML attachment was scrubbed... URL: From christine.rogers at mcgill.ca Fri May 26 18:45:10 2017 From: christine.rogers at mcgill.ca (Christine Rogers) Date: Fri, 26 May 2017 18:45:10 -0400 Subject: [Loris-dev] ACE-III instrument for LORIS In-Reply-To: <1153970956.11485.1495446679121.JavaMail.zimbra@cbr.iisc.ac.in> References: <1153970956.11485.1495446679121.JavaMail.zimbra@cbr.iisc.ac.in> Message-ID: Hi Ganesh, Thanks for your inquiry. We don't have ACE-III coded on any project (that we know of) available to share, and will probably be looking into making an open-license instrument library later this year. Our sample instruments (available on GitHub ) don't presently include any cognitive tests. Best regards, Christine On Mon, May 22, 2017 at 5:51 AM, Ganesh Chauhan (CBR) < ganesh.chauhan at cbr.iisc.ac.in> wrote: > Hi, > > I just wanted to know if I can get a copy of the ACE-III and other > cognitive test instruments/modules from the LORIS community. > > Many thanks for your help. > > With best regards, > Ganesh > > -- > Ganesh Chauhan (PhD) > Scientist > Centre for Brain Research (CBR) > Indian Institute of Science (IISc) > Bengaluru, INDIA > +91 80 2293 3009 <+91%2080%202293%203009> > https://www.cbr.iisc.ac.in > > > -- > This message has been scanned for viruses and > dangerous content by *MailScanner* , and is > believed to be clean. > > _______________________________________________ > 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 McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: From ganesh.chauhan at cbr.iisc.ac.in Mon May 29 00:09:06 2017 From: ganesh.chauhan at cbr.iisc.ac.in (Ganesh Chauhan (CBR)) Date: Mon, 29 May 2017 09:39:06 +0530 (IST) Subject: [Loris-dev] ACE-III instrument for LORIS In-Reply-To: References: <1153970956.11485.1495446679121.JavaMail.zimbra@cbr.iisc.ac.in> Message-ID: <682252090.12952.1496030946475.JavaMail.zimbra@cbr.iisc.ac.in> Dear Christine, Thanks for the information and looking forward to the open-license instrument library. With best regards, Ganesh From: "Christine Rogers" To: "Ganesh Chauhan (CBR)" Cc: "loris-dev" Sent: Saturday, May 27, 2017 4:15:10 AM Subject: Re: [Loris-dev] ACE-III instrument for LORIS Hi Ganesh, Thanks for your inquiry. We don't have ACE-III coded on any project (that we know of) available to share, and will probably be looking into making an open-license instrument library later this year. Our sample instruments ( [ https://github.com/aces/Loris/tree/master/docs/instruments | available on GitHub ] ) don't presently include any cognitive tests. Best regards, Christine On Mon, May 22, 2017 at 5:51 AM, Ganesh Chauhan (CBR) < [ mailto:ganesh.chauhan at cbr.iisc.ac.in | ganesh.chauhan at cbr.iisc.ac.in ] > wrote: Hi, I just wanted to know if I can get a copy of the ACE-III and other cognitive test instruments/modules from the LORIS community. Many thanks for your help. With best regards, Ganesh -- Ganesh Chauhan (PhD) Scientist Centre for Brain Research (CBR) Indian Institute of Science (IISc) Bengaluru, INDIA [ tel:+91%2080%202293%203009 | +91 80 2293 3009 ] [ https://www.cbr.iisc.ac.in/ | https://www.cbr.iisc.ac.in ] -- This message has been scanned for viruses and dangerous content by [ http://www.mailscanner.info/ | MailScanner ] , and is believed to be clean. _______________________________________________ Loris-dev mailing list [ mailto:Loris-dev at bic.mni.mcgill.ca | Loris-dev at bic.mni.mcgill.ca ] [ http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev | http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev ] -- [ mailto:christine.rogers at mcgill.ca | christine.rogers at mcgill.ca ] McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -- Ganesh Chauhan (PhD) Scientist Centre for Brain Research (CBR) Indian Institute of Science (IISc) Bengaluru, INDIA +91 80 2293 3009 https://www.cbr.iisc.ac.in -------------- next part -------------- An HTML attachment was scrubbed... URL: From carolina.mak3 at gmail.com Wed May 31 17:15:28 2017 From: carolina.mak3 at gmail.com (Carolina Makowski) Date: Wed, 31 May 2017 14:15:28 -0700 Subject: [Loris-dev] using media module through front end Message-ID: Hi there, I have a question about properly setting up the Media Module in LORIS. I am having trouble uploading a file through the front end of the database. I have gone through the readme in the /modules directory, and have ensured my path in the front end Configuration module matches where the data is expected to come in (i.e. /data/uploads/) and I have ensured /data/uploads has 775 permission and www-data permissions. On the front end, the file is uploading and the progress bar reaches 100%, but at this point nothing happens and progress simply stalls there (not sure if a "successfully uploaded" message or something of the like is supposed to appear here). Moving to the Browse tab shows that nothing was uploaded. It is only a 200K file and is well within the upload limits we set for our database. I know this is a relatively new module - let me know if something jumps out at you here. Thanks! Carolina -------------- next part -------------- An HTML attachment was scrubbed... URL: From christine.rogers at mcgill.ca Wed May 31 18:06:33 2017 From: christine.rogers at mcgill.ca (Christine Rogers) Date: Wed, 31 May 2017 18:06:33 -0400 Subject: [Loris-dev] using media module through front end In-Reply-To: References: Message-ID: Hi Carolina, Do you see the file on the server? Also does the database have an entry written to it recording the upload of this file? These two things could help with troubleshooting... C > On May 31, 2017, at 5:15 PM, Carolina Makowski wrote: > > Hi there, > I have a question about properly setting up the Media Module in LORIS. I am having trouble uploading a file through the front end of the database. > I have gone through the readme in the /modules directory, and have ensured my path in the front end Configuration module matches where the data is expected to come in (i.e. /data/uploads/) and I have ensured /data/uploads has 775 permission and www-data permissions. > > On the front end, the file is uploading and the progress bar reaches 100%, but at this point nothing happens and progress simply stalls there (not sure if a "successfully uploaded" message or something of the like is supposed to appear here). Moving to the Browse tab shows that nothing was uploaded. It is only a 200K file and is well within the upload limits we set for our database. > > I know this is a relatively new module - let me know if something jumps out at you here. Thanks! > > Carolina > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev From christine.rogers at mcgill.ca Wed May 31 18:06:33 2017 From: christine.rogers at mcgill.ca (Christine Rogers) Date: Wed, 31 May 2017 18:06:33 -0400 Subject: [Loris-dev] using media module through front end In-Reply-To: References: Message-ID: Hi Carolina, Do you see the file on the server? Also does the database have an entry written to it recording the upload of this file? These two things could help with troubleshooting... C > On May 31, 2017, at 5:15 PM, Carolina Makowski wrote: > > Hi there, > I have a question about properly setting up the Media Module in LORIS. I am having trouble uploading a file through the front end of the database. > I have gone through the readme in the /modules directory, and have ensured my path in the front end Configuration module matches where the data is expected to come in (i.e. /data/uploads/) and I have ensured /data/uploads has 775 permission and www-data permissions. > > On the front end, the file is uploading and the progress bar reaches 100%, but at this point nothing happens and progress simply stalls there (not sure if a "successfully uploaded" message or something of the like is supposed to appear here). Moving to the Browse tab shows that nothing was uploaded. It is only a 200K file and is well within the upload limits we set for our database. > > I know this is a relatively new module - let me know if something jumps out at you here. Thanks! > > Carolina > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev From carolina.mak3 at gmail.com Wed May 31 18:13:41 2017 From: carolina.mak3 at gmail.com (Carolina Makowski) Date: Wed, 31 May 2017 15:13:41 -0700 Subject: [Loris-dev] using media module through front end In-Reply-To: References: Message-ID: Hi Christine, No, there was no file uploaded onto the server and nothing on the database regarding status of the upload - after about 10 minutes I just navigated away from the page, so there doesn't seem to be a trace of the attempt. Carolina On Wed, May 31, 2017 at 3:06 PM, Christine Rogers < christine.rogers at mcgill.ca> wrote: > Hi Carolina, > > Do you see the file on the server? > Also does the database have an entry written to it recording the upload of > this file? > These two things could help with troubleshooting... > C > > > > > On May 31, 2017, at 5:15 PM, Carolina Makowski > wrote: > > > > Hi there, > > I have a question about properly setting up the Media Module in LORIS. I > am having trouble uploading a file through the front end of the database. > > I have gone through the readme in the /modules directory, and have > ensured my path in the front end Configuration module matches where the > data is expected to come in (i.e. /data/uploads/) and I have ensured > /data/uploads has 775 permission and www-data permissions. > > > > On the front end, the file is uploading and the progress bar reaches > 100%, but at this point nothing happens and progress simply stalls there > (not sure if a "successfully uploaded" message or something of the like is > supposed to appear here). Moving to the Browse tab shows that nothing was > uploaded. It is only a 200K file and is well within the upload limits we > set for our database. > > > > I know this is a relatively new module - let me know if something jumps > out at you here. Thanks! > > > > Carolina > > _______________________________________________ > > Loris-dev mailing list > > Loris-dev at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From christine.rogers at mcgill.ca Wed May 31 18:33:43 2017 From: christine.rogers at mcgill.ca (Christine Rogers) Date: Wed, 31 May 2017 18:33:43 -0400 Subject: [Loris-dev] using media module through front end In-Reply-To: <49687b198ff64b4dad2ddaee934d01f5@BY2PR0301MB0662.namprd03.prod.outlook.com> References: <49687b198ff64b4dad2ddaee934d01f5@BY2PR0301MB0662.namprd03.prod.outlook.com> Message-ID: Hi Carolina, Thanks, great to know. What does the Apache error log say? That would be the next thing for the team to know. Cheers, Christine > On May 31, 2017, at 6:13 PM, Carolina Makowski wrote: > > Hi Christine, > No, there was no file uploaded onto the server and nothing on the database regarding status of the upload - after about 10 minutes I just navigated away from the page, so there doesn't seem to be a trace of the attempt. > > Carolina > >> On Wed, May 31, 2017 at 3:06 PM, Christine Rogers wrote: >> Hi Carolina, >> >> Do you see the file on the server? >> Also does the database have an entry written to it recording the upload of this file? >> These two things could help with troubleshooting... >> C >> >> >> >> > On May 31, 2017, at 5:15 PM, Carolina Makowski wrote: >> > >> > Hi there, >> > I have a question about properly setting up the Media Module in LORIS. I am having trouble uploading a file through the front end of the database. >> > I have gone through the readme in the /modules directory, and have ensured my path in the front end Configuration module matches where the data is expected to come in (i.e. /data/uploads/) and I have ensured /data/uploads has 775 permission and www-data permissions. >> > >> > On the front end, the file is uploading and the progress bar reaches 100%, but at this point nothing happens and progress simply stalls there (not sure if a "successfully uploaded" message or something of the like is supposed to appear here). Moving to the Browse tab shows that nothing was uploaded. It is only a 200K file and is well within the upload limits we set for our database. >> > >> > I know this is a relatively new module - let me know if something jumps out at you here. Thanks! >> > >> > Carolina >> > _______________________________________________ >> > Loris-dev mailing list >> > Loris-dev at bic.mni.mcgill.ca >> > http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: