From rida.loris at gmail.com  Sat Aug 11 08:53:22 2018
From: rida.loris at gmail.com (Rida Abou-Haidar)
Date: Sat, 11 Aug 2018 08:53:22 -0400
Subject: [Loris-dev] LORIS Release v19.1.2 and v20.0.0
Message-ID: <CAO0Avk6zEsCY_PFAiCutxHgu29FpR46WsSwo7sSUvUidMPqRhA@mail.gmail.com>

Hi LORIS developer community,

*LORIS 20.0* is now available on GitHub --

Both core LORIS 20.0.0 <https://github.com/aces/Loris/releases/tag/v20.0.0>
 and Loris-MRI 20.0.0
<https://github.com/aces/Loris-MRI/releases/tag/v20.0.0> have been released.
Major features and updates are described in the Release Notes in both repos.

Please note that a v19.1.2
<https://github.com/aces/Loris/releases/tag/v19.1.2> has also been released
to fix a bug in the 19.1 version Refer to the release notes for more
information.

Upgrade Process notes are included to walk existing projects through
scripts and special patches to apply for this release.

Best,
The LORIS Team
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From mouna.safi-harb at mail.mcgill.ca  Tue Aug 14 12:49:10 2018
From: mouna.safi-harb at mail.mcgill.ca (Mouna Safi-Harab)
Date: Tue, 14 Aug 2018 16:49:10 +0000
Subject: [Loris-dev] Fw:  Data insertion problem
In-Reply-To: <YQXPR0101MB2038E66DD0B844F62EDAA6858E380@YQXPR0101MB2038.CANPRD01.PROD.OUTLOOK.COM>
References: <CALeJdv=GcP6wG9geie_C+2h=rqZY2M6_m3B+=zZHo+QHOCSeQg@mail.gmail.com>
	<YQXPR0101MB2038B2F7EE49CC642B5BC6B28E560@YQXPR0101MB2038.CANPRD01.PROD.OUTLOOK.COM>,
	<CALeJdvnoZ4SAVThFex-5bFJuDyhKdo_zVwxzv9AriZSava5GAA@mail.gmail.com>,
	<YQXPR0101MB2038E66DD0B844F62EDAA6858E380@YQXPR0101MB2038.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <YQXPR0101MB20388098019A8A71EF425E9F8E380@YQXPR0101MB2038.CANPRD01.PROD.OUTLOOK.COM>

cc'ing the loris-dev mailing list on my reply to you, Ali


________________________________
From: Mouna Safi-Harab
Sent: Tuesday, August 14, 2018 12:47 PM
To: Ali Aarefi
Subject: Re: [Loris-dev] Data insertion problem


Hi Ali,


I am going to propose a few steps you can look into to try to debug further. Let me know what you get based on the recommendations below.


- Try running the command 'source environment' (without the single quotations), BEFORE running the uploadNeuroDB/imaging_upload_file.pl command. Then type 'echo $PATH' (without single quotations) and let me know what it gives you. In parallel, can you please send me what is inside your 'environment' file which is located in /data/%YOURProject/bin/mri/ directory?

- Make sure that the prod file is indeed present in the dicom-archive/.loris_mri/ directory, and is accessible by lorisadmin (or whichever user running the imaging_upload_file.pl). Then open it and make sure there is a line in there like that:

@db = ('database_name','database_user', 'database_password', 'database_host');

and make sure all these database information on the line above the way you have them in your prod file are correct (perhaps you can try to connect directly to the mysql host from the command line to make sure this works outside of the scripts).


Let me know!


- Mouna

________________________________
From: Ali Aarefi <aliaarefi1997 at gmail.com>
Sent: Wednesday, August 8, 2018 9:22:50 AM
To: Mouna Safi-Harab
Subject: Re: [Loris-dev] Data insertion problem

Dear Mouna,

Hello,

First of all thank you very much for your help,

Regarding your previous response, Yes, the scans are uploaded into /tmp directory and the MRI-Upload Directory in the Configuration module was set and the permissions of /data/incoming directory has been changed, so the scan .zip file successfully moved into /data/incoming directory.
So, in the browser of imaging uploader module, for our last try, the uploadLocation changed from /tmp directory to /data/incoming directory.[screenshot 1]

The missing dependencies installed and error of executing  uploadNeuroDB/imaging_upload_file.pl<http://imaging_upload_file.pl>  file has changed to:

[command]$ ./imaging_upload_file.pl<http://imaging_upload_file.pl> -profile prod -verbose -upload_id 6 /data/incoming/MTL0000_336898_V1.zip

STDERR:

Use of uninitialized value $ENV{"LORIS_CONFIG"} in concatenation (.) or string at ./imaging_upload_file.pl<http://imaging_upload_file.pl> line 108.
Use of uninitialized value $ENV{"LORIS_CONFIG"} in concatenation (.) or string at ./imaging_upload_file.pl<http://imaging_upload_file.pl> line 110.

ERROR: You don't have a @db setting in the file /.loris_mri/prod

Also, I have attached related screenshots. Thanks again for your time and consideration.


Best Regards,
Ali


On Mon, Jul 23, 2018 at 9:42 PM Mouna Safi-Harab <mouna.safi-harb at mail.mcgill.ca<mailto:mouna.safi-harb at mail.mcgill.ca>> wrote:

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<mailto:loris-dev-bounces at bic.mni.mcgill.ca> <loris-dev-bounces at bic.mni.mcgill.ca<mailto:loris-dev-bounces at bic.mni.mcgill.ca>> on behalf of Ali Aarefi <aliaarefi1997 at gmail.com<mailto:aliaarefi1997 at gmail.com>>
Sent: Sunday, July 22, 2018 11:54:34 AM
To: loris-dev at bic.mni.mcgill.ca<mailto: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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From aliaarefi1997 at gmail.com  Tue Aug 21 08:00:10 2018
From: aliaarefi1997 at gmail.com (Ali Aarefi)
Date: Tue, 21 Aug 2018 16:30:10 +0430
Subject: [Loris-dev] inquiry about BIDS as LORIS input
Message-ID: <CALeJdv=xnbwxQM9nSCHfSwmxB=k_4JbhegDXVeHhPD=2_f0QoA@mail.gmail.com>

Hello Loris-dev team,

We have some data that converted from dicom to BIDS by bidskit
<https://github.com/jmtyszka/bidskit> (containing .json, .bval, .bvec,
.nii.gz files)
I was wondering if it is possible to insert our data in BIDS format to
LORIS directly?
We could not find anything about that in the LORIS github wiki.

Thanks for your help

- NeuroImaging & Analysis Group (NIAG <http://niag.ir/>)
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From dave.macfarlane at mcin.ca  Tue Aug 21 09:14:50 2018
From: dave.macfarlane at mcin.ca (Dave MacFarlane)
Date: Tue, 21 Aug 2018 09:14:50 -0400
Subject: [Loris-dev] inquiry about BIDS as LORIS input
In-Reply-To: <CALeJdv=xnbwxQM9nSCHfSwmxB=k_4JbhegDXVeHhPD=2_f0QoA@mail.gmail.com>
References: <CALeJdv=xnbwxQM9nSCHfSwmxB=k_4JbhegDXVeHhPD=2_f0QoA@mail.gmail.com>
Message-ID: <CAN9cDwHAQVh5H01wew_6UozBOZPgqVKXUR5viwmHKZp=7h-F7A@mail.gmail.com>

Hi Ali,

Can you clarify what you mean by "insert in BIDS format to LORIS directly"?
What is it that you'd like to do with the data once it's in LORIS? Someone
else can probably give better advice than me on how to deal with BIDS data
and how/if it's possible, but I think what you're trying to do with it will
have an effect on the best way to proceed..

On Tue, Aug 21, 2018 at 8:00 AM, Ali Aarefi <aliaarefi1997 at gmail.com> wrote:

> Hello Loris-dev team,
>
> We have some data that converted from dicom to BIDS by bidskit
> <https://github.com/jmtyszka/bidskit> (containing .json, .bval, .bvec,
> .nii.gz files)
> I was wondering if it is possible to insert our data in BIDS format to
> LORIS directly?
> We could not find anything about that in the LORIS github wiki.
>
> Thanks for your help
>
> - NeuroImaging & Analysis Group (NIAG <http://niag.ir/>)
>
> _______________________________________________
> 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 iris.rodriguez at cneuro.edu.cu  Tue Aug 21 11:39:31 2018
From: iris.rodriguez at cneuro.edu.cu (=?iso-8859-1?Q?Iris_Rodr=EDguez_Gil?=)
Date: Tue, 21 Aug 2018 10:39:31 -0500
Subject: [Loris-dev] EEG-Data in Loris
Message-ID: <C3A14E086354C04B8DB16023948F98BAA1834BF48B@exchange.cneuro.edu.cu>

Hello Loris-dev team,

We have data in eeg format and we wanted to know when a version of Loris will be available that supports this type of data.

Thanks for your help

Cuban Neurosciences Center (CNEURO)

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From cecile.madjar at gmail.com  Tue Aug 21 12:13:25 2018
From: cecile.madjar at gmail.com (Cecile Madjar)
Date: Tue, 21 Aug 2018 12:13:25 -0400
Subject: [Loris-dev] EEG-Data in Loris
In-Reply-To: <C3A14E086354C04B8DB16023948F98BAA1834BF48B@exchange.cneuro.edu.cu>
References: <C3A14E086354C04B8DB16023948F98BAA1834BF48B@exchange.cneuro.edu.cu>
Message-ID: <CAMkiY3eOhxoJT9bFP5Bjxc5zApuv31oObNkdYuq-gonovFQ=Mg@mail.gmail.com>

Hello Iris,

this is good to hear from you! Hope everything is going well in Cuba!!

I have been working the past few months on integrating EEG data into LORIS
via the BIDS structure. The pipeline for the insertion of BIDSified raw EEG
data into LORIS is pretty much ready and needs to be tested on more
projects :). It is currently on my own fork of the LORIS-MRI repo and we
are aiming to get this released for the next major release of LORIS.
Usually, these happen every 6 months or so depending on the time the
release process and testing takes.

In the meantime, here is the link to my branch with the BIDSified EEG
insertion pipeline
<https://github.com/cmadjar/Loris-MRI/tree/EegBidsInsertionPython> so that
you could test it on your sandbox if you wish to do so. This part of the
pipeline should not change much unless we find major bugs when you or I
test on more sample datasets. All the code for this EEG insertion is
located in the python
<https://github.com/cmadjar/Loris-MRI/tree/EegBidsInsertionPython/python>
folder of my branch and it comes with documentation regarding that new
pipeline and database infrastructure in the docs
<https://github.com/cmadjar/Loris-MRI/tree/EegBidsInsertionPython/python/docs>
directory within the python
<https://github.com/cmadjar/Loris-MRI/tree/EegBidsInsertionPython/python>
folder (including the install process). In that python
<https://github.com/cmadjar/Loris-MRI/tree/EegBidsInsertionPython/python>
folder, there is also an SQL patch that you would need to run (
BIDS_EEG_tables.sql
<https://github.com/cmadjar/Loris-MRI/blob/EegBidsInsertionPython/python/BIDS_EEG_tables.sql>)
before running the main insertion script called bids_import.py
<https://github.com/cmadjar/Loris-MRI/blob/EegBidsInsertionPython/python/bids_import.py>
.

We are currently also working on the front-end module to display the
inserted EEG files and it might take another few months to complete the
interactive view of EEG files.

Feel free to look through the documentation on my branch for the EEG
insertion into LORIS, it should help you get it on your sandbox and test it
with your dataset. Note that for it to work, it has to be BIDS compliant
(feel free to refer to that document that is the final proposal for raw
BIDS EEG
<https://docs.google.com/document/d/1ArMZ9Y_quTKXC-jNXZksnedK2VHHoKP3HCeO5HPcgLE/edit>
).

Finally, if you have any question or problem with this pipeline, please let
me know so I can help you out.

Best,

C?cile

On Tue, Aug 21, 2018 at 10:38 AM Iris Rodr?guez Gil <
iris.rodriguez at cneuro.edu.cu> wrote:

> Hello Loris-dev team,
>
>
>
> We have data in eeg format and we wanted to know when a version of Loris
> will be available that supports this type of data.
>
>
>
> Thanks for your help
>
>
>
> Cuban Neurosciences Center (CNEURO)
>
>
> _______________________________________________
> 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 samuel.danso at ed.ac.uk  Thu Aug 30 12:16:12 2018
From: samuel.danso at ed.ac.uk (DANSO Sammy)
Date: Thu, 30 Aug 2018 16:16:12 +0000
Subject: [Loris-dev] Installing Data Query Tool on centOS 6.10
Message-ID: <DB6PR05MB3205448345385558699EDA2ABD080@DB6PR05MB3205.eurprd05.prod.outlook.com>

Hi All,

I am trying to install Data Query Tool on centOS 6.10 but having difficulties and would need some help.


 - I have Erlang/OTP 21 installed

-  Tested erl  with  crypto:start().  showing OK - suggesting crypto is also installed.

-  I have erica-0.3.0 successfully compiled and installed.



However testing erica gives the following error:


=> erica create-app

Uncaugt error in erica : {'EXIT',

                                                 {undef,

                                                      [{couchbeam, start,[ ] ,[ ]},

                                                        {erica_core, run,1,

                                                            [file,"src/erica_core.erl"} , {line, 41} ] },

                                                        {erica, main, 1,

                                                            [file,"src/erica.erl"} , {line, 12} ] },

                                                        {escript, run, 2,

                                                             [file,"escript.erl"} , {line, 758} ] },

                                                        {escript, start, 1,

                                                              [file,"escript.erl"} , {line, 277} ] },

                                                        {init, start_em, 1, [ ] }

                                                        {init, do_boot, 3 [ ] } ] } }



Any suggestions would be much appreciated !


Thanks


Sammy

__

Centre for Dementia Prevention & Centre for Clinical Brain Sciences.

The University of Edinburgh

Email: samuel.danso at ed.ac.uk
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