From tikal004 at umn.edu  Thu Dec  1 12:06:37 2022
From: tikal004 at umn.edu (Barry Tikalsky)
Date: Thu, 1 Dec 2022 11:06:37 -0600
Subject: [Loris-dev] Flag Table Status Options
Message-ID: <CAJoAM3=HCxqpM9VP4cZfx0ativFcJtS-6cJ8G1vbDScG7_BwXQ@mail.gmail.com>

Hello LORIS devs,

We're looking to have a more robust way to track the status of an
individual instrument for a specific candidate.
This would address two workflow issues we are experiencing:

   1. Turning off one specific instrument for one candidate in the front
   end. Similar to how the session and candidate tables have an Active column
   that can be set to 'Y' or 'N' where 'N' keeps the data in the database but
   hides it from the session/candidate list on the front end.
   2. Marking an entire visit as complete even if there is a missing or
   incomplete instrument in that visit. Right now it seems there is not a way
   to track exceptions in a way that allows the visit to be passed even with
   partial data, and note the exception visibly.

We were expecting the Flag_status column to help with these, but we can't
figure out what it does. The enum options are 'P', 'Y', 'N' and 'F', what
do they stand for? Is this column used anywhere or was it never implemented?

We have considered adding an Active column to flag to solve our workflow
issue #1 above, is this reasonable or is there an existing method to manage
this? How could we work with the existing code and your group to implement
this?
Could we co-opt the Flag_status column to help us with #2? Should we make a
new column here as well?

Let us know your thoughts.
Thanks!


-- 

Barry Tikalsky
Research Professional | Developmental Cognition and Neuroimaging Labs |
Masonic Institute for the Developing Brain
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From AMORALESPINZON at BWH.HARVARD.EDU  Fri Dec  2 12:36:34 2022
From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo)
Date: Fri, 2 Dec 2022 17:36:34 +0000
Subject: [Loris-dev] LORIS - Change visit label
In-Reply-To: <CAMkiY3eAAO00WQxX90zOhOFpHzO6D89FuEcH2PU=45rB+B2tJQ@mail.gmail.com>
References: <260179D8-16F7-4CFA-B132-BD6A9AE04CE0@bwh.harvard.edu>
 <CAMkiY3eAAO00WQxX90zOhOFpHzO6D89FuEcH2PU=45rB+B2tJQ@mail.gmail.com>
Message-ID: <FABED7BB-5839-40E5-A796-F05C559F82F4@bwh.harvard.edu>

Hi C?cile,

We are in the first situation: DICOMs uploaded converted to MINC and nifti. We?ll then remove the imaging files, create the proper visit label and upload the images, with corresponding changes, to the visit.

Thank you.

Alfredo.

On Nov 28, 2022, at 4:52 PM, Cecile Madjar <cecile.madjar at mcin.ca> wrote:


        External Email - Use Caution

Hi Alfredo,

I guess that would depend on the imaging data that was uploaded into LORIS.

Are they DICOM images converted to MINC images etc... If so, then the visit label is going to be in all the headers. In that case, we usually remove the imaging files, change the visit label on the DB, rename PatientName in the DICOM images and reupload the data.

For files uploaded directly as BIDS datasets, I don't think the visit label ends up in the JSON file or any header, so in that case, I guess you could rename the files and then update the DB with the correct file paths and visit label.

Let me know which situation corresponds to yours or if you have questions on how to do those changes,

C?cile

On Mon, Nov 28, 2022 at 8:53 AM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Dear LorisDev Team,

By mistake we have mislabeled a visit label for some scans. For instance instead of using ?w24? we used ?et1?, and have uploaded some images to the ?et1? visit. What would you suggest to change the label of the visit? In the example that would be changing the visit label from ?et1? to ?w24?.

Thank you for your help.

Best regards,
Alfredo.
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From tikal004 at umn.edu  Wed Dec  7 12:36:37 2022
From: tikal004 at umn.edu (Barry Tikalsky)
Date: Wed, 7 Dec 2022 11:36:37 -0600
Subject: [Loris-dev] S3 bucket for Imaging Uploads
Message-ID: <CAJoAM3=wGb0QEMz8F-W4v1h+xMhYYxM7maCLfi+xDdVxUp8KDw@mail.gmail.com>

Hello LORIS devs,
Is it possible to send all data uploaded from the imaging uploader to an S3
bucket instead of the file system?
I have seen references to S3 in the code base but I'm failing to find
documentation on how to configure this.

-- 

Barry Tikalsky
Research Professional | Developmental Cognition and Neuroimaging Labs |
Masonic Institute for the Developing Brain
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From cecile.madjar at mcin.ca  Thu Dec  8 14:51:18 2022
From: cecile.madjar at mcin.ca (Cecile Madjar)
Date: Thu, 8 Dec 2022 14:51:18 -0500
Subject: [Loris-dev]  S3 bucket for Imaging Uploads
Message-ID: <CAMkiY3eyL776voOTD6BE2nNjF1JZXWXq6j49Pvp9aN032u-Oag@mail.gmail.com>

Hi Barry,

For the imaging side, we currently support sending NIfTI/MINC files
inserted into LORIS to an S3 bucket in the latest versions of LORIS. This
feature is still fairly new to LORIS.

There are configs available in the Config module to specify under the
section AWS Settings. Those will be read by the
run_push_imaging_files_to_s3_pipeline.py
<https://github.com/aces/Loris-MRI/blob/main/python/run_push_imaging_files_to_s3_pipeline.py>
LORIS-MRI
script.[image: Screen Shot 2022-12-08 at 2.14.53 PM.png]

For the frontend to be able to read the images, two apache environment
variables need to be set with the user's S3 access keys: AWS_ACCESS_KEY_ID
and AWS_SECRET_ACCESS_KEY

Currently, this has been mainly tested for images converted from DICOMs to
BIDS (via the python side of LORIS) but the script should work as well
after having run the DICOM to MINC pipeline via our usual perl pipeline.

Hope this helps answer your question,

C?cile

From: Barry Tikalsky <tikal004 at umn.edu>
Date: Wed, Dec 7, 2022 at 12:37 PM
Subject: [Loris-dev] S3 bucket for Imaging Uploads
To: <loris-dev at bic.mni.mcgill.ca>


Hello LORIS devs,
Is it possible to send all data uploaded from the imaging uploader to an S3
bucket instead of the file system?
I have seen references to S3 in the code base but I'm failing to find
documentation on how to configure this.

--

Barry Tikalsky
Research Professional | Developmental Cognition and Neuroimaging Labs |
Masonic Institute for the Developing Brain
_______________________________________________
Loris-dev mailing list
Loris-dev at bic.mni.mcgill.ca
https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev


--
Research Project Officer
christine.rogers at mcgill.ca
McGill Centre for Integrative Neuroscience | MCIN.ca
Montreal Neurological Institute-Hospital
McGill University | Montreal | Canada
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