.. _MRI_how_to:

============================
MRI Lab: how to
============================

.. _mriethics:

Get ethics approval
-------------------

Please follow `this link <https://www.plymouth.ac.uk/research/governance/research-ethics-policy>`_  to get the general information you need to submit an ethics application at the University of Plymouth.

Template for consent and information forms can be found below.

Information & consent template forms
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. _templates:

Template information form in 
:download:`.docx <FoH Ethics Participant Information Sheet (PIS) - BRIC MRI Lab Template (Feb-25).docx>`

Template consent form in 
:download:`.odt <Consent_form.odt>` and 
:download:`.docx <Consent_form.docx>`

General information for participants
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

This :download:`general information form <General_Information_MRI-lab.docx>` contains information for patients/participants about the MRI environment, how to prepare for a session and how to come to BRIC. Please add your contact information at the end of the form before sending it to your participants!

Pre-screen participants
-----------------------

The radiographers or MR operators will screen your participants for safety on the day of scanning. However, to decrease the rejection rate on the day of scanning, researchers should pre-screen their participants. To do so, researchers can send the safety questionnaire to the prospective participant and ask them to fill it.
If the participant answers 'yes' to any of the exclusion question, the researcher should make sure the participant is confortable about discussing their answer before asking for more details. In case of doubt, please contact the MRI lab heads. 

:download:`safety questionnaire - adults research participants <BRIC MRI safety Adults questionnaire - research participants.pdf>`


Book the scanner
----------------

`Booking system <https://resourcebooker.plymouth.ac.uk>`_  for University researchers. Once your project has been approved, please contact the MRI lab heads to be granted access as an MRI booker.

During periods of high scanning demand, each project receives a monthly booking allowance and the following `booking rules (restricted access) <https://liveplymouthac.sharepoint.com/:w:/r/sites/BRICMRIusers/Shared%20Documents/MRIlab_documents/MRI%20Lab%20-%20Bookings%20rules%20during%20high%20demand%20periods.docx?d=w7570974fbb2c434dbad1faa62ad65484&csf=1&web=1&e=07x4oX>`_ apply. Users should use the `pre-booking calendar (restricted access) <https://liveplymouthac.sharepoint.com/:x:/r/sites/BRICMRIusers/Shared%20Documents/MRIlab_documents/MRI%20Prebooking%20Calendar.xlsx?d=w6728e7b2286f4261bdff70c6dba98551&csf=1&web=1&e=9RMGkT>`_ to coordinate with each other and minimize gaps in the booking schedule

Retrieve your MR images
-----------------------

All research scans are being sent to our Orthanc server on Azure, copied to the `UoP's HPC (Lovelace) <https://brichandbook.readthedocs.io/en/latest/bric/bricResources.html#computing>`_, and then converted from dicom (.dcm) to nifti (.nii) format (see below for more information). 

The PI of the study can ask to get read access to the data on the HPC for all the collaborators of the study by applying for a research project on the HPC (`more information here <https://brichandbook.readthedocs.io/en/latest/bric/bricResources.html#request-hpc-resources-and-accounts>`_). Please contact our :ref:`system administrator <sysadmin>` for support.


Automatic conversion to BIDS/NIFTI format
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On the HPC, DICOM images are automatcially converted to NIFTI format and organised into a `BIDS <https://bids.neuroimaging.io/index.html>`_-compliant folder structure (using `Heudiconv <https://github.com/nipy/heudiconv/tree/master>`_, with an adaptation of the `reproin <https://github.com/repronim/reproin>`_ conversion heuristic).

For this conversion to be successful, scanning sequences on the scanner console should follow a specific naming convention, which is described `here <https://github.com/nipy/heudiconv/blob/master/heudiconv/heuristics/reproin.py>`_ in detail. 

Scanning sequences should normally have been correctly named by the person who helped you design the scanning protocol. However, if there are issues with the automatic conversion from DICOM to NIFTI, it is worth checking that the sequences are appropriately named. `This tool <https://npacore.github.io/reproin-namer>`_ allows you to build ReproIn-compliant sequence names.


Give images to participants
~~~~~~~~~~~~~~~~~~~~~~~~~~~
If you would like to give participants images of their brain, please have them sign this `Receipt of non-diagnostic image <https://liveplymouthac.sharepoint.com/:w:/s/BRICMRIusers/IQCDmsBZRdtyQ7hFiUctZ3V5ARDnvZL38a6FXJQuWBxasSo?e=fXrNGW>`_.