From christine.rogers at mcgill.ca  Wed Jul  4 10:29:16 2018
From: christine.rogers at mcgill.ca (Christine Rogers)
Date: Wed, 4 Jul 2018 16:29:16 +0200
Subject: [Loris-dev] dataquery
In-Reply-To: <e62df8886b3b4247987ff53fefe0b386@med.umich.edu>
References: <e62df8886b3b4247987ff53fefe0b386@med.umich.edu>
Message-ID: <57FF8055-EF68-481A-B300-DA64CE1F8A22@mcgill.ca>

Hi Garry,
At the time of LORIS 14.12 (released late 2014), I believe the Data Querying Tool was designed to be set up as a CouchApp adjacent to LORIS. Since 2016 (if I recall) the DQT has been integrated as a module within LORIS, hence the code you see. 
Cheers,
Christine 

> On Jun 15, 2018, at 9:28 PM, Cardillo, Garry <cardillo at med.umich.edu> wrote:
> 
> Does anyone know if there is something similar to this in version 14.12.1?  I'm trying to access the files controlling the data query tool.
> 
> 
> Loris/modules/dataquery/php/dataquery.class.inc
> 
> Garry Cardillo
> 
> Database Analyst/Programmer Intermediate
> Department of Radiology
> Functional Neuroimaging, Cognitive and Mobility Laboratory
> Domino?s Farms  Lobby B Suite 1000
> 24 Frank Lloyd Wright Dr  PO BOX 362
> Ann Arbor, MI 48106
> t: 734-936-0630
> f: 734-998-8403
> e: cardillo at umich.edu
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
> 
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
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From zvirani.mcin at gmail.com  Wed Jul 11 12:14:17 2018
From: zvirani.mcin at gmail.com (Zain Virani)
Date: Wed, 11 Jul 2018 12:14:17 -0400
Subject: [Loris-dev] using same instrument multiple times in the same
	timepoint
In-Reply-To: <461ccdc175f34f989b6c050104c3cd1e@med.umich.edu>
References: <461ccdc175f34f989b6c050104c3cd1e@med.umich.edu>
Message-ID: <CA+YkqC7=E-XY7O-CAihVRG3qrX7F0ZBJbQ8L=tG-a68VX8ausQ@mail.gmail.com>

Hi Garry,

In response to your question: "Does anyone use the same instrument multiple
times within the same timepoint [without creating multiple copies of tables
or instruments]?"

Currently this is not supported in LORIS. Additionally, we cannot guarantee
LORIS-wide success of duplicating instruments in the battery, as modules
are not expecting a one-to-many relationship between candidates and
individual instruments.

Please feel free to reach out again if you have any more questions,
Zain

On Fri, Jun 22, 2018 at 8:27 AM, Cardillo, Garry <cardillo at med.umich.edu>
wrote:

> Hello All,
>
>
> Does anyone use the same instrument multiple times within the same
> timepoint?  I'm trying to figure out the best way to do this without
> creating multiple copies of tables or instruments.  Thanks for any
> suggestions.
>
>
> Garry Cardillo
> [image: 1523292633747_image001.png]
>
> Database Analyst/Programmer Intermediate
>
> Department of Radiology
>
> Functional Neuroimaging, Cognitive and Mobility Laboratory
>
> Domino?s Farms  Lobby B Suite 1000
>
> 24 Frank Lloyd Wright Dr  PO BOX 362
>
> Ann Arbor, MI 48106
>
> t: 734-936-0630
>
> f: 734-998-8403
>
> e: cardillo at umich.edu
>
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should not
> be used for urgent or sensitive issues
>
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>
>
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From cardillo at med.umich.edu  Mon Jul 16 11:46:56 2018
From: cardillo at med.umich.edu (Cardillo, Garry)
Date: Mon, 16 Jul 2018 15:46:56 +0000
Subject: [Loris-dev] reporting and statistics
Message-ID: <339a13f6758c46e7bc71b10787b0c282@med.umich.edu>

Hello All,


I'm interested to find out how people are handling their reporting and statistical analysis.  Are you using Loris for reporting and statistical analysis, or other tools?  The reporting functionality seems to work pretty well, however the statistical analysis piece seems limited (I'm basing this on the way the demo site works - we are a few releases behind).  Has anyone done anything with customizing the statistics module?  Is it limited to basic breakdowns of demographic information, data entry completion status, etc., or has anyone developed something more robust?


Also, does the latest release have any functionality in the way of visualizations (https://demo.loris.ca/main.php) or are these more canned and basic?


Thanks for any input!

Garry Cardillo
[1523292633747_image001.png]
Database Analyst/Programmer Intermediate
Department of Radiology
Functional Neuroimaging, Cognitive and Mobility Laboratory
Domino?s Farms  Lobby B Suite 1000
24 Frank Lloyd Wright Dr  PO BOX 362
Ann Arbor, MI 48106
t: 734-936-0630
f: 734-998-8403
e: cardillo at umich.edu
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues 
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From zvirani.mcin at gmail.com  Tue Jul 17 16:02:04 2018
From: zvirani.mcin at gmail.com (Zain Virani)
Date: Tue, 17 Jul 2018 16:02:04 -0400
Subject: [Loris-dev] reporting and statistics
In-Reply-To: <339a13f6758c46e7bc71b10787b0c282@med.umich.edu>
References: <339a13f6758c46e7bc71b10787b0c282@med.umich.edu>
Message-ID: <CA+YkqC7traOBBWxy5DC+zs_R2fMo+YisW6SQipQnkBoZmA3U-w@mail.gmail.com>

Hey Garry,

The vanilla statistics module is not very robust, but its functionality can
be expanded by adding custom tabs. You can do this by adding an entry to
the `StatisticsTabs` table, and then writing the relevant PHP, JS, and
Template files (you can follow the naming convention for these files
established in the module). Unfortunately we don't have any in-house
customizations, just the tabs that ship with normal LORIS installations.

The visualization has not changed in the latest release, however there are
security updates and other general improvements, so we would suggest
upgrading anyway.

Thanks!
Zain

On Mon, Jul 16, 2018 at 11:46 AM, Cardillo, Garry <cardillo at med.umich.edu>
wrote:

> Hello All,
>
>
> I'm interested to find out how people are handling their reporting and
> statistical analysis.  Are you using Loris for reporting and statistical
> analysis, or other tools?  The reporting functionality seems to work pretty
> well, however the statistical analysis piece seems limited (I'm basing this
> on the way the demo site works - we are a few releases behind).  Has anyone
> done anything with customizing the statistics module?  Is it limited to
> basic breakdowns of demographic information, data entry completion status,
> etc., or has anyone developed something more robust?
>
>
> Also, does the latest release have any functionality in the way of
> visualizations (https://demo.loris.ca/main.php) or are these more canned
> and basic?
>
>
> Thanks for any input!
>
>
> Garry Cardillo
> [image: 1523292633747_image001.png]
>
> Database Analyst/Programmer Intermediate
>
> Department of Radiology
>
> Functional Neuroimaging, Cognitive and Mobility Laboratory
>
> Domino?s Farms  Lobby B Suite 1000
>
> 24 Frank Lloyd Wright Dr  PO BOX 362
>
> Ann Arbor, MI 48106
>
> t: 734-936-0630
>
> f: 734-998-8403
>
> e: cardillo at umich.edu
>
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should not
> be used for urgent or sensitive issues
>
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>
>
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From aliaarefi1997 at gmail.com  Sun Jul 22 11:54:34 2018
From: aliaarefi1997 at gmail.com (Ali Aarefi)
Date: Sun, 22 Jul 2018 20:24:34 +0430
Subject: [Loris-dev] Data insertion problem
Message-ID: <CALeJdv=GcP6wG9geie_C+2h=rqZY2M6_m3B+=zZHo+QHOCSeQg@mail.gmail.com>

Dear LORIS support team,
I'm a research assistant at NIAG (Neuro Imaging and Analysis Group) at
NeuroImaging Center, Imam Khomeini Hospital, Tehran, Iran as a part of TUMS
(Tehran University of Medical Science).

We've been trying to upload DICOM files using imaging uploader on our
already installed LORIS server but we faced some problems.

All of following sections were done successfully with respect to github
wiki page:
1. Installing loris
2. Project customization

Third section (Behavioural database) ignored (does it matter?)

And in the fourth section (imaging database) the subsections mentioned
below was done successfully:
1. Install the imaging pipeline codebase
2. Setup imaging insertion scripts
3. Loading a scan into loris

In this subsection, while executing post-upload script (pre-processing and
insertion into loris) an error has occurred in line 19 in
imaging_upload_file.pl with this following message:


command : uploadNeuroDB/imaging_upload_file.pl -profile prod -verbose
-upload_id 1 ~/Desktop/MTL0000_336898_V1.zip # we know that the .zip file
should be in /data/incoming , but after loading the scan into loris, this
directory kept empty !

```
Can't locate DBI.pm in @INC (you may need to install the DBI module) (@INC
contains: /data/project-name/bin/mri/uploadNeuroDB /etc/perl
/usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1
/usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5
/usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22
/usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at
/data/project-name/bin/mri/uploadNeuroDB/NeuroDB/DBI.pm line 19.
BEGIN failed--compilation aborted at
/data/project-name/bin/mri/uploadNeuroDB/NeuroDB/DBI.pm line 19.
Compilation failed in require at uploadNeuroDB/imaging_upload_file.pl line
19.
BEGIN failed--compilation aborted at uploadNeuroDB/imaging_upload_file.pl
line 19.
```

And also the /data/incoming directory is empty (the uploaded file that was
assigned an upload_id, doesn't exist in this directory)

Some other information that might be useful:
- The upload successful pop-up message was shown in imaging uploader module.
- upload_id was assigned to our upload tries.
- In the imaging uploader, there is no progress status.
- In the server processes manager module, some columns are meaningless like
error codes with respect to loris documents.

Some screenshots attacked to this email for more information.
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From mouna.safi-harb at mail.mcgill.ca  Mon Jul 23 13:12:38 2018
From: mouna.safi-harb at mail.mcgill.ca (Mouna Safi-Harab)
Date: Mon, 23 Jul 2018 17:12:38 +0000
Subject: [Loris-dev] Data insertion problem
In-Reply-To: <CALeJdv=GcP6wG9geie_C+2h=rqZY2M6_m3B+=zZHo+QHOCSeQg@mail.gmail.com>
References: <CALeJdv=GcP6wG9geie_C+2h=rqZY2M6_m3B+=zZHo+QHOCSeQg@mail.gmail.com>
Message-ID: <YQXPR0101MB2038B2F7EE49CC642B5BC6B28E560@YQXPR0101MB2038.CANPRD01.PROD.OUTLOOK.COM>

Hi Ali,


Based on your screenshots,


1) it looks like your scans are being uploaded into the `/tmp/` directory. So if you want them to go to `/data/incoming`/, can you please configure the MRI-Upload Directory in the Configuration module, under the Path submenu, to read /data/incoming/, and ensure this path is accessible and writable by the front end user


2) it looks like some dependencies are missing in your install; can you please refer to Installation Troubleshooting Notes in: https://github.com/aces/Loris/wiki/Imaging-Database (there is a section on missing dependencies, and the ones in the example on the Wiki seem to be the ones you are missing as well)



3) Setting/Not setting up the instruments should not impact your scan insertion workflow


Let me know if this answers your questions!


- Mouna



________________________________
From: loris-dev-bounces at bic.mni.mcgill.ca <loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Ali Aarefi <aliaarefi1997 at gmail.com>
Sent: Sunday, July 22, 2018 11:54:34 AM
To: loris-dev at bic.mni.mcgill.ca
Subject: [Loris-dev] Data insertion problem

Dear LORIS support team,
I'm a research assistant at NIAG (Neuro Imaging and Analysis Group) at NeuroImaging Center, Imam Khomeini Hospital, Tehran, Iran as a part of TUMS (Tehran University of Medical Science).

We've been trying to upload DICOM files using imaging uploader on our already installed LORIS server but we faced some problems.

All of following sections were done successfully with respect to github wiki page:
1. Installing loris
2. Project customization

Third section (Behavioural database) ignored (does it matter?)

And in the fourth section (imaging database) the subsections mentioned below was done successfully:
1. Install the imaging pipeline codebase
2. Setup imaging insertion scripts
3. Loading a scan into loris

In this subsection, while executing post-upload script (pre-processing and insertion into loris) an error has occurred in line 19 in imaging_upload_file.pl<http://imaging_upload_file.pl> with this following message:


command : uploadNeuroDB/imaging_upload_file.pl<http://imaging_upload_file.pl> -profile prod -verbose -upload_id 1 ~/Desktop/MTL0000_336898_V1.zip # we know that the .zip file should be in /data/incoming , but after loading the scan into loris, this directory kept empty !

```
Can't locate DBI.pm in @INC (you may need to install the DBI module) (@INC contains: /data/project-name/bin/mri/uploadNeuroDB /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at /data/project-name/bin/mri/uploadNeuroDB/NeuroDB/DBI.pm line 19.
BEGIN failed--compilation aborted at /data/project-name/bin/mri/uploadNeuroDB/NeuroDB/DBI.pm line 19.
Compilation failed in require at uploadNeuroDB/imaging_upload_file.pl<http://imaging_upload_file.pl> line 19.
BEGIN failed--compilation aborted at uploadNeuroDB/imaging_upload_file.pl<http://imaging_upload_file.pl> line 19.
```

And also the /data/incoming directory is empty (the uploaded file that was assigned an upload_id, doesn't exist in this directory)

Some other information that might be useful:
- The upload successful pop-up message was shown in imaging uploader module.
- upload_id was assigned to our upload tries.
- In the imaging uploader, there is no progress status.
- In the server processes manager module, some columns are meaningless like error codes with respect to loris documents.

Some screenshots attacked to this email for more information.

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