3T Scanning Instructions

Before Leaving for Scanner :

create subject directory in lab

bring with you:

•  2 Consent Forms

•  Scanner Protocol Form

•  MRI Screening Form

•  Handedness Questionnaire

•  Payment Form for controls

•  laptop

•  button box, plunger

At Scanner Before Subject Arrives :

setup laptop with hookup to goggles; make sure to clone screen

for plunger, turn on compressor in back room

•  connect all hoses

•  close output

•  turn on

•  after pressure builds, open output to 40 psi

in scanner suite

•  make sure head coil is plugged in and secure

•  put sheets on pad and pillow

•  set out earplugs

•  turn on goggles and make sure they are working properly

When Participant Arrives :

•  have subject complete consent

•  administer neuropsych tests

•  have subject put all metal into bathroom lockers

•  have subject use bathroom if necessary

•  practice tasks

on console, in the control room

•  click New Pt., enter:

•  patient name/ID

•  weight, age

•  select protocol from “Other”

take participant into scanner suite

•  put on goggles and headphones

•  select protocol MTL_Golby from “Other”

Scanning :

while scanning be sure to:

•  record EXAM number

•  record order and details of the scans on Scanner Protocol Form

•  record P file number for each scan with corresponding task name

•  transfer P files immediately

1. 3D Localizer

•  View Edit

•  Save Series

•  Prepare to Scan

•  Scan

2. Inplane T2

•  View Edit

•  Plane = Axial

•  Slice thickness = 5mm for non-motor, 3mm for motor (change to 3.0 for motor)

•  Graphic Rx

position slices I à S on sagittal slice; 26 slices for non-motor, 24 slices for motor

•  Fallback to RO

•  Accept

•  Save Series

•  Prepare to Scan

•  Move Bed

•  Scan

3. EPI or Functional

•  View Edit

•  Plane = Axial

•  Slice thickness = 5mm for non-motor, 3mm for motor

•  For EPI 3mm sequence (motor), change TR to 2000.0

•  Graphic Rx

Copy Rx;

Select Inplane Rx, and copy onto the same sagittal slice as the T2

•  Fallback to RO

•  Accept

•  User CV's Screen

CV5=number of epibold reps or TR's

•  Accept

•  Save Series

•  Prepare to Scan

•  Scan (3 second test scan is executed)

•  Right-click Research Operations

•  Choose Display CV's

type “boldscan” in CV name box, hit enter on keyboard;

change Current Value to “1” and hit enter on keyboard;

to change number of TR's, type “boldreps” in CV name box, hit enter on keyboard, then enter the number of TR's

•  Accept

•  Right-click Research Operations again

•  Choose Download (experiment time should appear on the monitor to your left)

•  Prep Scan

•  Scan (in sync with the start of the experiment)

4. MPRAGE

•  Select New Series, and Other, and from the reisalilly protocols choose MPRAGE3D only

•  View Edit

•  Plane = Axial

•  Graphic Rx

click on the same sagittal slice as the T2 and EPI, and position the box so that the entire brain is inside the box

•  Fallback to RO

•  Accept

•  Save Series

•  Prepare to Scan

•  Scan

5. LSDI (or DTI)

•  Select New Series, and Other, and from the LSDI Brain protocols choose LSDI tensor only

•  View Edit

•  Plane = Coronal

•  Graphic Rx

click on the same sagittal slice as the T2, EPI, and MPRAGE, and position the slices P à A, making sure to cover the brain stem and the tumor

•  Fallback to RO

•  Accept

•  User CV's Screen

CV6=2.00, and hit enter on keyboard to register value and ensure that scanner does not reconstruct images

•  Save Series

•  Prepare to Scan

•  Scan

Transferring Data :

•  click on the toolbox icon button, and then the C shell button

•  for P files, cd to /usr/g/mrraw

•  type ftp 134.174.8.77 (IP address for Harvey)

•  type bin , and then prompt

•  cd to the directory where data is to be sent (e.g., /lab/research/FMRI/patients/AG_####/raw/)

•  type put and the name of the P file; or mput and P*

•  for anatomical e files, cd to /usr/g/insite/tmp

•  to extract the T2 and MPRAGE files, type list_select_ex

•  type a , and the exam number

•  type b , and the series number

•  type c , and “1”, space, and the number of slices for that series (e.g., 1 124, for an MPRAGE)

•  type bin , and then prompt (if this is a new ftp session)

•  cd to the directory where data is to be sent

•  type mput and e#####* (##### denotes the exam number)

•  to push DICOM files to lisa

•  click on the desktop computer icon button

•  select your exam from the list, and the series you want to transfer

•  click on Network from the menu, and choose Select Remote Host

•  scroll down and choose lisa from the list

•  click on Network from the menu again and choose Send Series

•  type bin , and then prompt

•  cd to the directory where data is to be sent (e.g., /lab/research/FMRI/patients/AG_####/raw/)

•  type put and the name of the P file; or mput and P*

•  cd to /spl/tmp/incoming/MR0000.MOD/LMRC3T.STA/<date>/ and transfer files to harvey

•  to retrieve T2, MPRAGE, and LSDI “I” files using xferx

•  ssh to kayo or jerome

•  in the xferx GUI, right click Remote Host bay1 and go to bay3t

•  then click list exams, and list series

•  click the series you want and then Get/Overwrite

•  cd to /export/home/images/new/GINX/GENESIS/LMR/AG_####/ and transfer files to harvey