Data Acquisition

ECT Data Acquisition Protocol

Meditation Acquisition Protocol

Spectral Editing with SVS

Scheduling A Research Appointment


  1. Establish schedule according to the patient’s availability, the ECT treatment schedule and the scan schedule
  2. Confirm patient arrival and testing with patient and ECT
  3. Email schedule to Chinenye, Drs. Espinoza, Leaver and Narr and to the ECT group, for example:
    7:00 am: Consenting (baseline only)
    7:30 am: MINI (baseline only – this can be done before the 2nd time point if needed)
    8:00am – Testing and mood scales
    9:00am - Scan
    10:00am – ECT Treatment and Blood draw

  • For new patients (baseline), allow 1.5-2 hours for consenting, mood scales and neuropsych testing. The neuropsych and mood scales can be done after the scan if timing works better that way.
  • Consenting must occur before anything else.
  • For patients already consented (consenting only occurs at the first time point, i.e., baseline), allow 1 hr for testing.
  • If out-patient, allow a little extra time in case they arrive late due to traffic.
  • Always make sure the patient has your number and you have the patient’s number. Sometimes patients will call ECT if running late.

Allegra Restart and Warm-up Instructions


  1. Pull out table
  2. Click System > End Session > Shutdown System
  3. Push blue "System Off" button on Siemen's quench box on the wall
  4. Push blue "System On" button
  5. Log in to "meduser" with password: "meduser1"
  6. Move table back into scanner
  7. Register warm-up:
    Name: "StabilityMMDDYY_Allegra"
    Age: 18
    Weight: 25
    Referring Physician: QCGROUP
    Study: Daily Stability -- Daily Warm-up
    Patient Position: Head first supine
  8. Click "Exam" and then click "Confirm"
  9. Start scan. :)

Instructions for MRS PRESS Acquisitions


  1. Obtain Localizer and MPRAGE
    1. Run the localizer and align to the AC-PC, select Apply.
    2. Run the MPRAGE.
  2. Axial reconstruction:
    1. Load the MPRAGE to 3D; on the sagittal view, scroll to the slice with the left hippocampus.
    2. On the Settings tab, select Parallel Ranges (looks like a head in profile with parallel lines running across it).
    3. Click Presets and from the drop-down menu select NARR.
    4. Drag the yellow box down over the sagittal view of the brain and angle parallel to the left hippocampus. Center the box so that it is covering the entire brain. You should have 160 slices in the reconstruction.
    5. Click the Start button in the Parallel Ranges dialog box to begin axial reconstruction of the image.
    6. On the bottom right of the Exam screen, click the Save As button (a head in profile with a question mark next to it).
    7. Save your axial reconstruction as AX_HIPPO_RECON (or whatever makes sense to you) by typing this in the Series Name and Comment text fields. You can leave the Reading Physician blank.
    8. Hit OK.
  3. Coronal reconstruction:
    1. Re-angle the yellow box perpendicular to the hippocampus, making sure that the brain is right side up in the coronal view.
    2. Repeat steps above, selecting Start in Parallel Ranges (if you still have the same yellow box up, otherwise repeat the selection process above).
    3. Save as COR_HIPPO_RECON
  4. Move reconstructed images into the Exam Explorer:
    1. Open the Exam Explorer and drag the sagittal MPRAGE and the axial and coronal reconstructions into the three windows in the Exam tab. If they appear as sagittal slices, don't worry, this is normal. Scroll through the first few slices and you will get to the slices from the reconstruction
  5. ROI Placement
    1. Open up the scanning segment for your first ROI (Left Hippocampus).
    2. Angle your ROI as appropriate in the reconstructed images. Make sure the ROI is in the correct hemisphere (the hemisphere will show up in the bottom right of the sagittal window).
    3. Drag the ROI to the appropriate spot on the axial view (reconstructed axial). As a shortcut, you can use Scroll→Nearest to snap to the view containing the voxel on the coronal and sagittal views.
    4. Click Apply
    5. Be sure to perform frequency adjustments, automatic shim, manual shim, frequency adjustment and water suppression before running MRS scans for each ROI.
    6. Set up for the placement of the next ROI while scans are running. If scanning on the Trio, there may be a warning that pops up about the head coil, select OK. This is because you cannot specify the head coil in the protocol, and must do so on the fly.
  6. Performing Adjustments for each ROI prior to scanning
    1. Frequency Adjustment:
      1. Go to the Options menu and select Adjustments.
      2. Go to the frequency adjustments tab.
      3. Select Go, Repeat until frequency falls between +2 or -2.
      4. Select Apply.
    2. Automatic Shim
      1. Go to the Options menu and select Adjustments.
      2. Go to the 3D Shim tab.
      3. Select Measure, wait until the scanner has finished measuring.
      4. Select Calculate.
      5. This procedure may need to be repeated 2x or 3x until the shim looks reasonable.
      6. Select Apply at the top and bottom of the page (i.e., press both Apply buttons).
    3. d) Manual Shim
      1. Go to the Options menu and select Adjustments.
      2. Go to the Interactive/manual shim tab.
      3. Select Measure to evaluate the FWHM.
        • The FWHM should be as low as possible (typically between 10-18 but can be around 20 or 23 for hard to shim voxels such as the subventricular zone). If this number is high repeat the Automatic Shimming procedures above or perform manual shimming.
        • For manual shimming, tweak the values associated with each plane in the boxes in the positive and then negative direction to manipulate the FWHM/ If the FWHM drops and then goes up again, reset by pressing best shim. When the FWHM reaches an acceptable value, press best shim again, stop and apply.
      4. If the FWHM is acceptable, press the Apply button.
    4. Redo the Frequency Adjustment:
      1. Go to the Options menu and select Adjustments.
      2. Go to the frequency adjustments tab.
      3. Select Go, Repeat until frequency falls between +2 or -2.
      4. Select Apply.
    5. Water suppression:
      1. Go to the Options menu and select Adjustments.
      2. Go to the water suppression tab.
      3. Select Go.
      4. When the water suppression converges as indicated by a “Y”, select Apply.
  7. Start the MRS scan for the voxel of interest.
    Note, shimming parameters will carry over to the water suppressed scans, so your WS scan should start immediately after the NWS scan.
  8. Viewing MRS Data
    1. To view the scan as it happens, click Display Inline (far right in Exam tab).
    2. When the MRS scan is complete, you can load the data by clicking the Applications menu and selecting Spectroscopy.
    3. Select your MRS scan of interest (NWS or WS).
    4. Select the protocol to use for curve fitting (either sve_se_30 for WS or sve_se_30_NWS for NWS). To switch protocols, click on the window with the MR spectrum and select Open from the Protocols menu.
    5. If your curve fitting looks strange, make sure you have used the correct protocol (NWS vs not).
  9. Exporting MRS Data
    1. Insert a USB flash drive into the far left USB port (F: drive).
    2. To export data, follow the instructions above to view your data. Go to the Options menu and select Export raw data.
    3. Select the F: drive (or whichever drive you wish to use for saving), change the name of the scan to Left_Hippo_WS (to identify your ROI and the type of scan).
    4. Do this for each ROI separately, dragging the MRS data into the Spectroscopy window, displaying with sve_se_30 or sve_se_30_NWS, and exporting the raw data.
  10. Exporting Protocol PDF
    1. To export a PDF containing details of your MRS protocol (or any Trio protocol), make sure you have inserted the flash drive into the port for F: then click on the Exam Explorer button (a standing man and a question mark in a speech bubble).
    2. Select the protocol for which you wish to print a PDF in the list at the left.
    3. Go to the Object menu and select Print. Save on the F: drive as a PDF with the Protocol+Table of Contents. Hit OK.
  11. Saving Screen Shots
    1. Follow the instructions for viewing data
    2. Right click control-escape
    3. enter password (meduser1)
    4. Open Screen Hunter 5.0
    5. Save screen shots to flash drive
Example voxels of interest:
1. Left hippocampus
2. Right hippocampus
3. Bilateral calcarine
4. Bilateral anterior cingulated
5. Left sub-ventricular zone

Instructions For Scheduling MRI Scans


To Schedule an MRI between 8am and 10am (Brain Mapping Center):

  1. 1Go to and select Access the Brain Mapping Database to Submit Proposals, Schedule Studies, etc. (Account required)
  2. Enter User Name and Password and click on Submit.
  3. On the left-hand panel, select Allegra 3T Scheduling
  4. On the Allegra Scheduling page, complete the following steps:
    1. a. Select Katherine Narr from the "Manage Allegra Scheduling of..." drop down menu and select Submit.
    2. b. To add a new scan, select the Human button in the MMD_ECT row and Schedule column
  5. On the Schedule an Allegra Study page, complete the following steps:
    1. a. Change "Start Date & Time" to the correct date and time (always change 10:00:00 to either 08:00:00 or 09:00:00)
    2. b. Change "Study Duration" to 1 hour
    3. c. Change "Responsible User" to the person at the scan (Katherine Narr, Amber Leaver or someone who is MR safety certified)
    4. d. "Credit Account" should be MMD_ECT
    5. e. Click on Submit for Scheduling... button
  6. Verify that the information on the Please Verify the addition of page is correct and click Add to Schedule
To Cancel an MRI Scheduled with the Brain Mapping Center:
  1. Go to and select Access the Brain Mapping Database to Submit Proposals, Schedule Studies, etc. (Account required)
  2. Enter User Name and Password and click on Submit.
  3. On the left-hand panel, select Allegra 3T Scheduling
  4. Select Delete next to scheduled scan to be removed
  5. On Please Verify the Deletion of page, verify the scan to be deleted is correct and click Delete Appointment
Keep The Following In Mind:
  1. Scans scheduled after 5pm for the next day can not be edited or canceled without penalty once they are added to the calendar
  2. Scans scheduled any time can not be canceled after 5pm without penalty
  3. Appointments must be canceled before their start time in order to not be charged for the entire appointment

To Schedule an MRI between 10am and 5pm (Radiology):

  1. Email or call Mary (cc Trent and Elizabeth) to find out if a tech can staff the scan:;;
  2. Complete the Radiology Scheduling form (
    1. Write in Subject ID on right side, above "PATIENT NAME OR LABEL"
    2. Date of Request: Day of the week, Date and Time of scan
    3. Reason for Exam: mark "Baseline Exam" or fill in “Follow-up scan” and cycle # (i.e. cycle # for DE_101_02 is 2)
    4. Implants: N/A
    5. Allergies: N/A
  3. 3. Fax completed form to (310) 206 -1914
  4. 4. Call Radiology Scheduling (310-206-0456) and select option 4 to confirm faxed appointment. If leaving a voicemail, leave the following information:
    1. Call is from Dr. Narr’s office
    2. Appointment is for Allegra Scanner on RRH 6th floor
    3. Subject ID
    4. Date and Time of scan
    5. Request a call back confirming the appointment
To Cancel an MRI appointment with Radiology:
  1. Call Radiology Scheduling (310-206-0456) and select option 4
  2. Leave a detailed message of the scan to be canceled including the Subject ID, Scanner, Date and Time with a request for a call back
Keep The Following In Mind:
  1. Check with "Allegra Coverage" Google calendar for availability after 10am
  2. If a scan time is "Offered" on the calendar and but we need to scan at that time, Shruthi Chakrapani ( can be emailed to confirm they will be using the scanner very politely and ask if they can work with us.
  3. Scans can be scheduled, canceled, and changed without penalty