[Loris-dev] A question re MRI tables

[Christine Rogers]

Hi Naj,
Thanks for your question - that's feasible and we could put such a script
on the roadmap for improving the Imaging pipeline.
Loris is designed so that the protocol checks are defined based on an
official study-wide protocol (created at the beginning of a study), in
order to catch outlier data in incoming MRI scans, as opposed to being
defined based on a sample scanning session's data.  It is also common to
define protocol check using a range of allowable values for a given
parameter (e.g. TE_range: 3.0-4.0), which typically involves expert
adjustment of these acceptable parameter value limits.

Value range checks for MRI parameters for  t1, t2, dti and fMRI (e.g. TE,
TR values) can be edited directly in the front-end in the "MRI Protocol
Violations" submodule of the MRI Violated Scans module (under the Imaging
main menu), since these acquisition types are populated automatically in
the mri_protocol table.
This submodule can be viewed by accessing (e.g.)
https://demo.loris.ca/main.php?test_name=mri_violations&submenu=mri_protocol_violations

It may be helpful to consult the MySQL commands which load the mri_protocol
table with these default records for t1, t2, dti and fMRI.  These are
located in the default schema at:
https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L606

Best,
Christine


On Tue, Nov 10, 2015 at 9:49 AM, Najmeh Khalili-Mahani, Dr <
najmeh.khalilimahani at mcgill.ca> wrote:

> Hi,
>
> If I understand correctly, before starting to load the MRI data via Image
> Uploader, one must manually populate tables with information about the
> acquisition times of different sequences (T1, T2, TR, etc.)
>
> This is perhaps a naive question, but I wonder, might it be feasible for
> LORIS to have a PERL script that extracts those information from the DICOM
> or MINC headers and stores them without human intervention?
>
> Much thanks
> Naj
>
> ==================================
> Najmeh Khalili-Mahani, PhD
> Research Associate
> McGill Centre for Integrative Neuroscience
> Montreal Neurological Institute
> McGill University
>
> NW-143, 3801 University St.
> Montreal, QC, H3A 2B4
> Office: 514-398-1799
> email: najma at bic.mni.mcgill.ca
>
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-- 

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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