TITLE: MRI pilot
AUTHORS: Lukas Snoek, Tinka Beemsterboer

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Run an MRI pilot at Spinoza REC.</span></div><div class = "text-block"><span style = "font-weight:bold;">This protocol will help you running your pilot. </span><span>
Make sure to read this protocol before coming to the pilot so you know what is expected of you and which choices you will be going to make.</span></div></div>

[STEPS]
?. Name your scans appriopriately.If you're using the centre's QC/preprocessing service, it is very important to name your scans (and thus the resulting MRI files) according to the BIDS-format.If you're not using the centre's QC/preprocessing service, you may give whatever name to your scans/files and skip the rest of the instructions listed in this step.We have already named the templates of our standard scans such that they only require minimal editing to make them BIDS-compatible. BIDS uses key-value pairs in filenames to denote parameters/information about the file itself. The structure is as follows:key1-value1_key2-value2_[optionalKey-optionalValue] We have pre-formatted our standard exam cards such that they already contain the appropriate keys. We've included placeholders, formatted as (this_is_a_placeholder), for values which you should replace with the appropriate information. For example, our standard (non-multiband) functional EPI (3mm, TR=2000ms) is named: task-(taskname)_acq-SeqSense2Mm3[_run-(nr)]_bold (Note: the acq - 'acquisition' - value specifies the specific type of scans, which here refers to a Sequential scan with Sense factor 2, and a 3 millimeter isotropic spatial resolution.) It is then up to the researcher to replace the (taskname) with the appropriate value (e.g., workingmemory or Nback - completely up to the researcher, but only use alphanumeric symbols). The parts between square brackets, [...], are optional. If you, for example, have two runs of an Nback task, you should name them: task-Nback_acq-SeqSense2Mm3_run-1_boldtask-Nback_acq-SeqSense2Mm3_run-2_boldWe have pre-formatted our standard exam cards such that they already contain the appropriate keys. We've included placeholders, formatted as (this_is_a_placeholder), for values which you should replace with the appropriate information. For example, our standard (non-multiband) functional EPI (3mm, TR=2000ms) is named:task-(taskname)_acq-SeqSense2Mm3[_run-(nr)]_bold (Note: the acq - 'acquisition' - value specifies the specific type of scans, which here refers to a Sequential scan with Sense factor 2, and a 3 millimeter isotropic spatial resolution.) It is then up to the researcher to replace the (taskname) with the appropriate value (e.g., workingmemory or Nback - completely up to the researcher, but only use alphanumeric symbols). The parts between square brackets, [...], are optional. If you, for example, have two runs of an Nback task, you should name them: task-Nback_acq-SeqSense2Mm3_run-1_boldtask-Nback_acq-SeqSense2Mm3_run-2_bold(Note: the acq - 'acquisition' - value specifies the specific type of scans, which here refers to a Sequential scan with Sense factor 2, and a 3 millimeter isotropic spatial resolution.)It is then up to the researcher to replace the (taskname) with the appropriate value (e.g., workingmemory or Nback - completely up to the researcher, but only use alphanumeric symbols). The parts between square brackets, [...], are optional. If you, for example, have two runs of an Nback task, you should name them:task-Nback_acq-SeqSense2Mm3_run-1_boldtask-Nback_acq-SeqSense2Mm3_run-2_boldIf you don't have different runs, you may leave out the run key-value pair (e.g., task-Nback_acq-SeqSense2Mm3_bold is just fine).In fact, you likely only have to format the names of the functional (EPI) scans (and the corresponding topup-scans, if included). Most other types of scans (e.g., B0, DWI, and T1-weighted/T2-weighted scans) are already completely pre-formatted and do not need editing (but exceptions arise when, for example, you want to run two T1-weighted scans; in that case, you need to add a run-(nr) key-value pair yourself). The MR-operator will assist you in this process.
?. [Create scan protocol ('exam card')]
Create your scan protocol.During the pilot, you will (together with the MR-operator) create a selection of scans ('exam card') to run during your experiment, which most likely includes:a 'SmartBrain' (survey scan)a high-resolution T1-weighted anatomical scanone or more functional (BOLD-fMRI) scans (we offer the option of multiband scans)B0-scan or 'top-up' scans (from which you can create a 'fieldmap', reflecting the magnetic field's inhomogeneity).one or more functional (BOLD-fMRI) scans (we offer the option of multiband scans)Depending on your experiment/analysis, your selection may also include a high-resolution T2-weighted anatomical scan and/or scans for diffusion weighted imaging. Ideally, you have already discussed your desired scans during the introduction meeting.f
?. [Check pilot data]
Check your data after the pilot. We advice you to check your pilot data for artifacts or other issues after the pilot.Check whether you received the (MRI) data files as expected (proper file format, right file size, etc.)Check whether the logfiles of the paradigm include all the expected information (especially stimulus/response onsets and the onset of the first scanner pulse);Convert your scans from PAR/REC (or DICOM) format to nifti (using, e.g., dcm2niix) and inspect your anatomical and functional scans visually (using e.g. FSLView)In case of unexpected artifacts, let Lukas (L.Snoek@uva.nl) or Tinka (t.beemsterboer@uva.nl) know.
?. [Check your experiment/paradigm]
Check whether your experimental paradigm/task runs as expected. Check the following things regarding your experimental paradigm/task during the pilot:Does the paradigm start at the first scanner pulse? (The Before data acquisition explains how to sync your task with your experiment)When using response buttons, check wheter these are working and logged as expected;Visually inspect the experimental paradigm/task during the scan;Are the log files stored on the D-drive, data not on the D drive will be deleted without any notice;Ask the participant whether the task was clearly explained and if he/she could read (hear and see) everything properly
?. [Start your project!]
You're ready to start your project! Now, you are ready to start your project by making bookings in Calpendo (spinozarec.calpendo.com)!Good luck!
?. [Participant for the pilot]
We advice you to use an experienced participant for your pilot.Preferably, this person is not a colleague or friend (in case of an incidental finding).Even if the participant is experienced, he or she should go through the normal routine for participating in MRI research. As such, he or she should ...have the oppurtunity to read the information folder about MRI research at our centre;fill in and sign an MRI screening form;fill in and sign a General Practitioner Informed Consent; fill in and sign a study-specific Informed Consent;Additionally, make sure that the pilot participant knows that the current session is a pilot run. This way the participant understands that some things may a bit longer (due to unforeseen issues during the pilot) and, moreover, this allows the participant to give valuable feedback on the experiment/protocol.