[Loris-dev] Questions regarding querying LORIS

Wed Sep 4 09:38:32 EDT 2019

Hi Remya,

Thanks for your comments and followup --

I have a setup where all my imaging data is already stored in an XNAT database and  if I now store my behavioral data and other subject metadata in LORIS and want to use the DQT (or some tool) for querying the LORIS DB and well as the xnat database, is this possible currently?

Yes, this is definitely possible, since the current LORIS API can be used to load imaging data for existing subjects/visits (and many other tasks).
LORIS' API (documentation here)<https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md> can be used to insert imaging data into the main LORIS database from XNAT, depending on the appropriate level of anonymization and labelling (e.g. with LORIS-recognizable IDs and visit labels).
If you have specific questions on what the API can do, please don't hesitate.

To do this, you'd want to create custom scripts to load images and their metadata either into LORIS via API, or just into the DQT via a custom PHP script.
The imaging data from XNAT may need to be scrubbed, relabelled and/or re-packaged for insertion, and the IDs would need to match those stored in LORIS for each subject. For example, LORIS uses 2 subject IDs with a visit label to identify incoming DICOM packages.

In additions to the scans, you'd also want to import any Quality Control information and metadata (like provenance and DICOM header fields). If you have detailed parameterized QC (e.g. to annotate the quality of scans), this can be loaded in LORIS as well.

In the bigger picture -- if your data collection is still growing, and still undergoing curation and/or QC -- you'd want to set up syncing between the two repositories, to refresh LORIS as soon as any data is updated in XNAT.  This should be done very regularly (and automated) if data collection or curation is ongoing, for example.
In our experience the challenge of working with two systems simultaneously to maintain this sync requires careful planning and skilled execution, particularly to maintain the integrity of the linked datasets in the long term.

Let me know if we can help further --
Best,
Christine

On Tue, Sep 3, 2019 at 3:13 PM Remya Nair <rnair at caltech.edu<mailto:rnair at caltech.edu>> wrote:
Hi Christine,

Thank you for your replies. They are very helpful and I will test out the DQT shortly. I have one more follow up question for you :

I have a setup where all my imaging data is already stored in an XNAT database and  if I now store my behavioral data and other subject metadata in LORIS and want to use the DQT (or some tool) for querying the LORIS DB and well as the xnat database, is this possible currently?

In short, is there any way to interface between XNAT and LORIS that you would know about or perhaps such a feature (or an API) is being developed? Please advise.

Thank you again for your help.

Best wishes,
Remya
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Staff Scientist

Emotion and Social Cognition Lab & Caltech Center for Brain Imaging

emotion.caltech.edu<http://emotion.caltech.edu/> | accinfantstudy.com<https://accinfantstudy.com/researchers-acc-infant-study/#remyanair>

On Mon, Sep 2, 2019 at 4:47 PM Christine Rogers, Ms. <christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>> wrote:
Hi Remya,

Thanks for your inquiry --

1. If we have data stored on several instruments within LORIS,  is it possible to query, filter and export specific data that we need into a CSV file (or any spreadsheet) using the LORIS interface? If not, is this a feature currently being developed?

Yes, the Data Querying Tool (DQT) module is designed for precisely that purpose.
Try it out at demo.loris.ca<http://demo.loris.ca> -- you'll find this module under the "Tools" menu.
The Data Querying Tool allows users to design, save and share custom queries, and to download the results as a CSV file, though the LORIS front-end.   Users can query and filter specific data fields or whole instruments across timepoints, including metadata, demographic data, and imaging data. The DQT is also extensible for genomic data.
For example, a user can filter for only female subjects that have a T1 scan completed, and have an IQ score above a certain threshold, etc.

2. Currently we understand the way to do mass uploads of data into a LORIS instrument is via the database directly. Is there any way to upload data into an instrument directly from a CSV instead (or any spreadsheet format file)?

A module to load instrument data via the front-end is in our Roadmap for development; for the present we recommend a simple script to load instruments fields from a CSV into the corresponding database table field.

Storing files in LORIS attached to a participant-timepoint (without processing the data contents), can also be done via the Media Module.

Best,
Christine
The LORIS team

On Fri, Aug 30, 2019 at 5:44 PM Remya Nair <rnair at caltech.edu<mailto:rnair at caltech.edu>> wrote:
Hi,

We have a couple of questions that we were hoping the LORIS developers might be able to help with. Apologies if this has been answered previously on this forum.

1. If we have data stored on several instruments within LORIS,  is it possible to query, filter and export specific data that we need into a CSV file (or any spreadsheet) using the LORIS interface? If not, is this a feature currently being developed?

2. Currently we understand the way to do mass uploads of data into a LORIS instrument is via the database directly. Is there any way to upload data into an instrument directly from a CSV instead (or any spreadsheet format file)?

Your take on the above questions would be greatly appreciated. Thank you in advance for your help.

Best,
Remya

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christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>
McGill Centre for Integrative Neuroscience | MCIN.ca
Montreal Neurological Institute
McGill University | Montreal | Canada

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christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>
McGill Centre for Integrative Neuroscience | MCIN.ca
Montreal Neurological Institute
McGill University | Montreal | Canada
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