From matthew at biospective.com  Mon Jul  4 16:46:31 2016
From: matthew at biospective.com (Matthew Lee)
Date: Mon, 4 Jul 2016 16:46:31 -0400
Subject: [Loris-dev] Scan upload data path
Message-ID: <CADxcC9dgb+yPiCh+gfGMrfs1OELS-4qOk2ynBsszviXsxn_N0Q@mail.gmail.com>

Hi,

I am trying to upload some scan data, using a wrapper around dcm2mnc
instead of calling it directly.  I am running into problems though, and the
upload process is failing after the call to tarchiveLoader with the message
"The insertion scripts have failed".  When I tweak something, and try to
run imaging_upload_file.pl again, I can't unless I get a new UploadID.

Is there a quick way to rerun this without having to start from the imaging
uploader module or an equivalent script?
Is there documentation anywhere about the program execution flow of the
upload process?  A diagram would be ideal, but something showing the order
scripts that get called, and what they each do/check would be really
helpful.
What are some places I should check first to debug this process?

I am running a modified version of LORIS v15.10.2 and LORIS_MRI v15.10 on
Ubuntu 14.04.

Thanks,

Matthew
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From christine.rogers at mcgill.ca  Tue Jul  5 16:27:40 2016
From: christine.rogers at mcgill.ca (Christine Rogers)
Date: Tue, 5 Jul 2016 16:27:40 -0400
Subject: [Loris-dev] Scan upload data path
In-Reply-To: <CADxcC9dgb+yPiCh+gfGMrfs1OELS-4qOk2ynBsszviXsxn_N0Q@mail.gmail.com>
References: <CADxcC9dgb+yPiCh+gfGMrfs1OELS-4qOk2ynBsszviXsxn_N0Q@mail.gmail.com>
Message-ID: <CALbt7NDm969FCe9vh=MxVe5C4bZHJ4epTTQ4uFXb65T1FkdTQA@mail.gmail.com>

For the Loris-dev community:

Detailed information on the Imaging Insertion (pipeline) scripts and the
Imaging Uploader can be found in our main GitHub Wiki, within the Loris
Setup Guide - Imaging Database page:
https://github.com/aces/Loris/wiki/Imaging-Database
This documentation includes diagrams, setup instructions, and
troubleshooting notes - some links are enclosed in the text below.

Yes, there's no need to re-upload data in order to re-run and troubleshoot
<https://github.com/aces/Loris/wiki/Imaging-Database#troubleshooting-insertion-of-uploaded-datasets>
the imaging insertion scripts, for projects using the Imaging Uploader
module.  The GitHub Wiki contains details on how to execute, troubleshoot
<https://github.com/aces/Loris/wiki/Imaging-Database#3-executing-and-troubleshooting-the-imaging-insertion-scripts>
and re-run
<https://github.com/aces/Loris/wiki/Imaging-Database#re-running-the-imaging-pipeline>
individual scripts.
In Matthew's case, the last step which is run by the tarchiveLoader
<https://github.com/aces/Loris/wiki/Imaging-Database#3-executing-and-troubleshooting-the-imaging-insertion-scripts>
script may be all you need to re-run.

Log files <https://github.com/aces/Loris/wiki/Imaging-Database#log-files>
containing error and output messages from the imaging insertion scripts are
created under the /data/$PROJ/data/logs/ directory. To view messages from
the last script run, consult the most recent log file modified in this
directory. These log files reference an upload ID used to identify each
imaging dataset -- consult the mri_upload database table to look up which
upload ID has been assigned to your scans.

Loris 16.0 was recently released with improvements to message logging and
notifications (main <https://github.com/aces/Loris/releases> and Imaging
<https://github.com/aces/Loris-MRI/releases> repos).

Best,
Christine
-- 
LORIS data systems | loris.ca
McGill Centre for Integrative Neuroscience| MCIN.ca
McConnell Brain Imaging Centre
Montreal Neurological Institute
McGill University | Montreal | Canada


On Mon, Jul 4, 2016 at 4:46 PM, Matthew Lee <matthew at biospective.com> wrote:

> Hi,
>
> I am trying to upload some scan data, using a wrapper around dcm2mnc
> instead of calling it directly.  I am running into problems though, and the
> upload process is failing after the call to tarchiveLoader with the message
> "The insertion scripts have failed".  When I tweak something, and try to
> run imaging_upload_file.pl again, I can't unless I get a new UploadID.
>
> Is there a quick way to rerun this without having to start from the
> imaging uploader module or an equivalent script?
> Is there documentation anywhere about the program execution flow of the
> upload process?  A diagram would be ideal, but something showing the order
> scripts that get called, and what they each do/check would be really
> helpful.
> What are some places I should check first to debug this process?
>
> I am running a modified version of LORIS v15.10.2 and LORIS_MRI v15.10 on
> Ubuntu 14.04.
>
> Thanks,
>
> Matthew
>
> _______________________________________________
> 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 sromanzetti at ukaachen.de  Mon Jul 25 11:40:20 2016
From: sromanzetti at ukaachen.de (Romanzetti, Sandro)
Date: Mon, 25 Jul 2016 15:40:20 +0000
Subject: [Loris-dev] upload of nifti images?
Message-ID: <5396CC4C-FDB1-424A-A987-0A67ADBEA7DF@ukaachen.de>

Dear Loris Users and Gurus, 

is it possible to upload nifti images in a LORIS DB instead of anonymised DICOMS?

Thanks ,

Sandro

From matthew at biospective.com  Mon Jul 25 16:27:28 2016
From: matthew at biospective.com (Matthew Lee)
Date: Mon, 25 Jul 2016 16:27:28 -0400
Subject: [Loris-dev] LORIS Demo modules broken with old browser
Message-ID: <CADxcC9fJLTWVJNJkg0zT0FXjkvi3GWBYRGfXxNBiN8Y449hqZA@mail.gmail.com>

Hi,

I was looking at the LORIS demo, and some modules did not work on an old
version of Chromium (v 37, the latest version available on Ubuntu 12.04
LTS).  The Candidate List, Dicom Archive, and Imaging Browser modules would
load the selection filters and the loading icon, but would not actually
load the table of subjects.  The Document Repository, Imaging Uploader, and
Mri Violations modules loaded without issue.

Do you know what might cause this?  I don't have this issue on version
15.10.2.

Thanks,

Matthew
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From christine.rogers at mcgill.ca  Tue Jul 26 10:53:55 2016
From: christine.rogers at mcgill.ca (Christine Rogers)
Date: Tue, 26 Jul 2016 10:53:55 -0400
Subject: [Loris-dev] upload of nifti images?
In-Reply-To: <5396CC4C-FDB1-424A-A987-0A67ADBEA7DF@ukaachen.de>
References: <5396CC4C-FDB1-424A-A987-0A67ADBEA7DF@ukaachen.de>
Message-ID: <CALbt7NBGuD4jsnnLs7=KvBgxBW75w5HX9+Rutk7xPTbG6MKDzg@mail.gmail.com>

Hi Sandro,
Currently LORIS' imaging uploader and insertion scripts take anonymized
DICOM datasets as input.  Scripts provided within the Loris-MRI repo
<https://github.com/aces/Loris-MRI> such as minc_insertion.pl can be
modified to insert NIfTI files, while checking or creating
candidate/session.  Adding this functionality to the Loris-MRI insertion
scripts is in our tentative roadmap for the next major release.
Best,
Christine

On Mon, Jul 25, 2016 at 11:40 AM, Romanzetti, Sandro <
sromanzetti at ukaachen.de> wrote:

> Dear Loris Users and Gurus,
>
> is it possible to upload nifti images in a LORIS DB instead of anonymised
> DICOMS?
>
> Thanks ,
>
> Sandro
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>



-- 

christine.rogers at mcgill.ca
LORIS data systems | loris.ca
McGill Centre for Integrative Neuroscience| MCIN.ca
McConnell Brain Imaging Centre
Montreal Neurological Institute
McGill University | Montreal | Canada
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From christine.rogers at mcgill.ca  Wed Jul 27 12:05:12 2016
From: christine.rogers at mcgill.ca (Christine Rogers)
Date: Wed, 27 Jul 2016 12:05:12 -0400
Subject: [Loris-dev] LORIS Demo modules broken with old browser
In-Reply-To: <CADxcC9fJLTWVJNJkg0zT0FXjkvi3GWBYRGfXxNBiN8Y449hqZA@mail.gmail.com>
References: <CADxcC9fJLTWVJNJkg0zT0FXjkvi3GWBYRGfXxNBiN8Y449hqZA@mail.gmail.com>
Message-ID: <CALbt7NBQJoY2U63e9tR-Xt7xg3+jo6SaiCy9-R=A5t+ycsyO7w@mail.gmail.com>

Hi Matthew and Community,
We've added React in Loris 16.* to improve rendering of many modules - this
may not be supported by some older browsers.  In general that we support
Browser versions that are currently supported, for Chrome and Firefox.
(e.g. Chromium 37
<https://en.wikipedia.org/wiki/Google_Chrome_release_history> is no longer
supported).  Thanks for writing and please do feel free to continue
reporting such issues,
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



On Mon, Jul 25, 2016 at 4:27 PM, Matthew Lee <matthew at biospective.com>
wrote:

> Hi,
>
> I was looking at the LORIS demo, and some modules did not work on an old
> version of Chromium (v 37, the latest version available on Ubuntu 12.04
> LTS).  The Candidate List, Dicom Archive, and Imaging Browser modules would
> load the selection filters and the loading icon, but would not actually
> load the table of subjects.  The Document Repository, Imaging Uploader, and
> Mri Violations modules loaded without issue.
>
> Do you know what might cause this?  I don't have this issue on version
> 15.10.2.
>
> Thanks,
>
> Matthew
>
> _______________________________________________
> 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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