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====MRI Checklist====
==Upon arrival==
  * Change into scrubs – removing underwire bras, hair bands, and other metallic clothing
  * Bathroom visit!
  * MRI screening form
  * Choose movie
  * If needed, provide MR safe glasses
==Equipment Setup==
  * Plug in power cable for fMRI laptop
  * Plug in VGA using dongle, audio cord, and USB cord
  * Press red “trigger button” so the trigger switch light (green, below) is in the “external” position
  * Use the Matrix Switcher to switch the stimulus from the FMRI paradigm computer to the laptop – this means pressing ( 01, 02, 02, 02). 
    * [01 -> fMRI paradigm computer; 02 -> laptop]
  * Turn on the audio box by powering on using the switch on the rear and pressing TRS1 for each of the inputs, the box under the technician’s computer also needs to be powered on. Check that the volume is set to a comfortable level.
==Participant Prep==
  * Bathroom!
  * Introduce to technician
  * Make sure they are comfortable
    * Ears not folded under headphones
    * Pillow under knees, if desired
    * Hair not turned up on back of head (can cause late scan discomfort)
  * Emergency button
  * Button box
  * Headphones with the audio cord!
  * Blanket (weighted or normal) depending on preference
  * Inflatable cap
  * Remind them to be still
    * This includes the fingers and the toes
    * No nodding or shaking head to respond to Y/N questions
    * Still like a statue!
==Scanner Prep==
  * Make sure tech has run the correct patch “SamePrep”
  * Make sure the correct exam card is being run
  * Check that the intercom is working and the participant can hear you
  * Remind them to be still like a statue!

==During Scan==
  * Check in occasionally to ask how they are doing and give them the opportunity to wiggle/scratch an itch (as long as they keep their head still!)
    * Ask the technician to let you check in before the major scan groups
  * Monitor for movement – the technician can check for motion artifacts in the SPRG and IRTSE scans (the 2 long scan groups), so they can quickly be re-done if needed.
  * Ask technician to print out an image in the MEMP group
  * Write notes!
==For Functional==
  * Instruct the child to (without moving their head or looking down) find the button box
  * Describe game thoroughly
  * Set up the game on the fMRI computer (mute the volume)
  * Ask them to press the button before running
  * Run the game and tell the participant to be very still (like a statue!)
==After scan==
  * Congratulate participant and escort to subject room just in case they are dizzy
  * De-tach the computer and make sure the cords are plugged into the ground box
  * Switch the triggers back 
  * Switch the Matrix switch back to the fMRI computer by pressing (02 01, 01 01)
  * Turn off audio boxes
  * Transfer data to USB
  * Place used scrubs in the yellow laundry basket
  * Give image, check and parking voucher!
==Troubleshooting==
  * Participant can’t hear the movie?
    * Make sure both audio boxes are powered on and that the inputs are set to TRS1
    * Make sure the button with music notes on the intercom box is on
    * Make sure the correct headphones were given
  * Participant is wiggly
    * Make sure there isn’t anything that can be adjusted – pillow, no blanket, no socks, etc.
    * Remind them to be as still as the can, like a statue
    * Let them know that you will mute the movie if they wiggle to remind them
  * No scrubs (hehe)
    * Ask Liza, otherwise if they are wearing appropriate clothing that could work too
    * There could be some hidden in the file cabinet next to the regular scrubs cabinet
  * Subject room is occupied
    * Ask Liza or get the keys from her office to open Swati’s office.  
    * Or, you can sometimes use the conference room.
  * Game isn’t triggered by MRI
    * Make sure the trigger switch is in the External position!
    * Make sure you ran the game indicating that the trigger would be the machine
    * Check that the response box is set to the correct mode
    * Worst-case scenario, you can trigger the game manually by pressing ‘t’ after the dummy scans. Be sure to jot a note if so.


After MRI data has been acquired at the DISC MRI center it should be saved as PAR/REC files. For each subject, the data should be placed in:
<code>/mnt/diskArray/projects/MRI/study_sID_initials/YearMonthDay/raw</code>
For example:
<code>/mnt/diskArray/projects/MRI/NLR_001_JY/20150926/raw</code>
When a subject has multiple scan sessions, they will go in separate folders within the subject's main folder, each with the date of the scan, so that we can determine the order of the scans. All the raw data should be within the raw folder so that the outputs of different processing stages can be saved in separate named folders. For example:
<code>/mnt/diskArray/projects/MRI/NLR_001_JY/20150926/dti96trilinrt
/mnt/diskArray/projects/MRI/NLR_001_JY/20150926/mrtrix</code>
Next we run the [[anatomy|Anatomy Pipeline]] and [[diffusion|Diffusion Pipeline]] to preprocess this data that will be used for many purposes.
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