Running the scanner and transferring the data

Set up
Localizers
Inplanes
Screen save
Functionals
Data management
Shimming
Auto recon
Subslice prescription
Printing Protocols

          

• Enter scanner mode: click scanner icon in upper-left cornerof display
• If exam is in progress, select End Exam in Rx Manager and Confirm .
• Click New Patient .
• In Patient Position area (press Enter after each entry):
• Patient ID: d heeger xxx (xxx are your initials).
• Patient Name: subject's full name .
• Weight: subject's weight.
• Exam description: braindob mm/dd/yyyy (date of subject's birth)
• Protocol Selection (schematic representation of human body)
• Protocol set to Site (not GE).
• Click the head of the body schematic (protocols willappear).
• Select appropriate protocol.
• Check whether coil name is correct
• Accept .
• Put subject in scanner. Landmark subject.
• Clean out P-files from [3T_hostName] before funning functionals:
• Go to tools (icon, upper-left)
• Open c-shell (button, lower-right of tools)

>> cd /usr/g/mrraw
>> rm P*
>> rm E*

• Do not remove Header_Pool file. Check that Header_Pool file exists. If it doesn't, stop now and page Anne/Gary for help.

Localizers

• Select localizer series
  Protocol selection should automatically select and download the localizer scan  [1] . If this is the case, the Scanner Status area on the left-hand side of the display should indicate that series 1 had been downloaded.
• Save Series
• Prepare to Scan
• Alert subject that localizers are coming.
• Select Scan in Scanner Control area. Scanner will automatically run a prep for about 30seconds followed by the localizer scan. When scanner stops, images should be displayed in miniviewerin upper-right of display  [2] .
• Maximize to enlarge display.
• Scroll through localizer images. Use scroll bar on the right-hand side of the viewer.
• Adjust brightness and contrast.
• Press middle mouse button
• Drag target up/down to increase/decrease brightness.
• Drag target left/right to increase/decrease contrast.
• Select slice that extends most posterior (towards the back of the skull) and that has a good view of calcarine sulcus. Note slice number (slice number appears on upper left corner of image display) for inplane prescription and screen save.

Inplanes

• Select Inplanes2D or Inplanes3D series in Rx Manager.
• Choose View Edit.
• Select slice-orientation indicated by Plane under Imaging Parameters  [3] [4] .
• If desired, enter/change slice-thickness (in millimeters) in bottom of Scan Parameters  [5] .
• Select Graphic Rx in Scan Parameters.
• Select desired localizer image using the slider on the left-handside of display.
• Adjust brightness and contrast , if necessary.
  
• Prescribe slices

For 2-D inplanes:

• Click mouse left-button to make slice-prescription visible.
• Orient prescription into appropriate position  [6]

For 3-D inplanes:

• Drop slab by clicking mouse left-button within the image.
• Orient slab into appropriate position
• Set Fallback to R0
• Accept
• Make sure Freq DIR in Acquisition Timing section below Autoview window is not set to R/L [7]
• If using 3-D inplanes, write down start-end locations
• Save Series
• Prepare to Scan (wait while inplanes download). Scanner control display (small monitor to theright of scanner interface) should show timing for the new series.
• Alert subject that he/she will move.
• Move to Scan .
  
• If manual prescan (2D inplanes only):

• Alert subject
• Auto Prescan .
• Manual Prescan .
• Manual prescan window opens. In window, click on Scan TR (R1/R2) attop right. Adjust Digital Gain slider sothat R2 values fall within 30-70% range (typically30-40%).
• Done .

• Alert subject scan is coming.
• Scan . Prep will run for 30 seconds, followed by Inplane scan.
  Functionals can be setup while Inplanes are being collected. See Functionals steps 1-5.
• When scanner is done running, examine Inplanes in viewer or browser to make sure all is well [11] .

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Screen Save

Must be done prior to Data Management . Can be done as soon as Inplanes are done.

• Click browser icon in upper-left
• Within image-view window, click browser left-hand side
• Select current patient in left-hand window
• Select appropriate series in right-hand window
• Select chosen slice in bottom-window
• Viewer
• With image slider, choose localizer image number that was used to do the inplane graphic Rx.
• In blank area at lower-left of screen, type
• xr s#
• (# = inplane series number,usually 2)
• Save Screen
• Click browser and choose the screen save series when it appears
• Viewer
• Adjust brightness and contrast using middle mouse so that brain and slice prescription are easily visible
• Print screen by hitting Print on thermal printer.
• Write <sessioncode> and protocol name on the back of the screen save and take notes about each individual scan (Pfile numbers, etc.).

Functionals

• Select FunctionalSeries in Rx Manager window.
• Choose View Edit.
• Make changes to slice-orientation and slice-thickness consistent with changes made to Inplanes, when the Scan Parameters window updates with theseries  [3-5]
• Copy Inplane slice-prescription into the Functional series.
• If 2D Inplanes were acquired:
• Graphic Rx
• Select Series
• Select Localizer series from Graphic Rx dialog box.
• Copy Rx on left of display
• Select appropriate Inplane series for slice-prescription  [8]
• Set Fallback to R0.
• Accept.
• If 3D Inplanes were acquired:
• Copy start-end field locations in Scanner Range sectionfrom inplane screen printout. There are 6 start end locations all-together
• Make sure number of slices in the Scanner Range corresponds to the number of slices indicated by the protocol.
• UserCVs . Adjust as specified by protocol and researcher preference.
• external trigger: 1
• nframes: as desired
• nextra (number of extra shots): usually 2
• number of interleaves: usually 2
• xfer data (autorecon): 31
• Make sure Freq DIR in Acquisition Timing section below Autoview window is not set to R/L [7]
• Save Series .
• Prepare toScan , wait for series to download to scanner.
• Alert subject that Prep is coming.
• Prep Scan .
• While Prep is running, prepare stimulus display .
• Alert subject that Scan is coming. Turn off all control room lights.
• Scan  [9]
• Start stimulus/trigger (subject or operator) once scan light on keyboard flashes  [10]
• When scan is over, check for Pfile (type "ls -l P*" in /usr/g/mrraw) and write down the Pfile number. Then check to see if the Pxxxxx.7.mag file has been created and keep track of it as it grows in size. Do not ftp the mag file until the autorecon is done. If the auto recon fails to create a .mag file, type >> recon31 xxxxx where xxxxx is the Pfile number (leading zeros not needed, but no '.7')
• Additional Functionals: repeat last 4 steps.
• To change the number of frames after series has already been saved:
• right click Research Operations...
• select Display CVs
• choose number of frames

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Data Management: moving anatomies andPfiles to local drives

• Make a tarfile of the anatomies (localizers, inplanes, and screensave) on lucas >> ssh lucas -l heeger
  >> simptrans3.sh mmddyy:
  >> type <sessioncode> (e.g., 082901a)
  Exam #:
  >> (from Screen Save or Autoview window)
  Localizer series #:
  >> 1
  Inplane series #:
  >> 2
  Screen save series #:
  >> 99 >> tar cvf <sessioncode>.tar <sessioncode>
  >> exit
• FTP the anatomies to maroon >> ssh maroon -l userName
  >> cd ~/name/mri/raw <or whatever directory you want to use>
  >> ftp lucas Username:
  >> heeger
  Password:
  >> v1->mt
  >> cd /local/heeger
  >> bin
  >> get mm/dd/yy/sessiondCode.tar
  >> bye >> tar xvf <sessioncode>.tar
• Pfile transfer >> cd <sessioncode>/Raw/Pfiles
  >> ftp [3T_hostName]
  >> cd /usr/g/mrraw
  Username: signa
  Password: [3T_password]
  >> cd /usr/g/mrraw
  >> bin
  >> prompt
  >> mget P* (repeat for each P* and each P*.mag file)
  >> mget E* (repeat for each E* header file)
  >> bye

Shimming

• The purpose of writing down S/I (superior/inferior) numbers after the inplanes, transforming them with the shimcalc utility, and entering the transformed numbers into the shim scan protocol, is to prevent the table from moving between scans.
• Autoshimming must be disabled (unselected) in the functional scans. Otherwise, this will override the higher order shim and you will have wasted your time.

Full detailed shimming instructions . These instructions are also posted on the bulletin board in the scanner control room.

• The output image file is about half the length of the P file, so transfers are quicker and archive space needed on your host is reduced. Since the Pfiles are deleted if the recon is successful, this also means that /usr/g/mrraw will not fill as rapidly.
• The recon is quick. It will start at the end of the scan and finish in less time than it took to gather the data with the sequence running at it's shortest possible TR. Thus, by the end of your scanning session all previous runs will have been reconstructed and the last scan will finish reconstruction within a few minutes.
• The reconstruction matches the pulse sequence. If there are changes to the sequence or recon program we won't need to deal with upgrading our software.

However, we like to keep copies of both the Pfiles and the recon'd images because we have in the past discovered problems in the images that were fixed by fixing bugs in the recon program. To avoid deleting the Pfiles, simply set the xfer data User CV to 31 instead of 30. This should be set as the default in all of our protocols (it isn't yet, but we will change that). If not, set it.

Pxxxxx.7.mag: reconstructed volumes
EeeeeSsssPxxxxx.7: text header file (where eeee is exam number, ssss is series number)

If the autorecon fails, open a cshell and type:

>> cd /usr/g/mrraw
>> recon31 xxxxx

where xxxxx is the Pfile number (leading zeros not needed, but no '.7')

> subslice

• Prescribe your inplanes as usual
• Run your initial functional scan as usual
• Write doen the R/L, A/P, & S/I values
• Copy the functional series (right click on the series name at the left, copy. Then right click, paste)
• Run subslice
• Enter the subset prescription explicitly (don't do graphic RX)
  Save series, etc.

• Go to the Tools screen
• Select Utilities
• In the menu box, scroll down and select Print Protocols
• Select the location of the protocols (e.g. Head)
• Select one or more protocols to print
• Print

The protocols will print on the printer located under the skylights outside of the 3T suite.

Footnotes
[1] If localizerscan was not automatically downloadedwith protocol selection:

• Select Localizer series in Rx Manager.
• Select View/Edit (displaysINRX status).
• Save Series.
• Prepare to Scan in Rx Manager.

[2] If localizer images aren't displayed, select Update to load them. [3] Mostprotocols use an oblique slice prescription.Other options include: sagittal, coronal, or axial. [4] If you have made a change in slice-prescription orientation, you must make the same change in the Functional series orientation. [5] If you have made a change in slice-thickness value, you must make the same change in theFunctional series. [6] There are three markers on the bottom slice of the slice prescription. Left mouse button down-pressed on markers will change number of slices and prescription rotation. Left mouse button down-pressed with drag motion will change position of the whole prescription. [ This needs to be completed ] [7] May be set to either A/P or S/I depending on slice orientation. [8] Usually there will be one Inplane series from which to choose. However, if for some reason the Inplanes had to be repeated, there will be one series for each set of Inplanes collected. [9] Operator may either select Scan in the ScannerControl area using the mouse or push StartScan on upper-row of keyboard. [10] The mac displaying the stimulus will trigger the scanner to start.

• Click on browser icon (the upper-right most of the six icons on the leftof the screen)
• Click browser button on left-hand side in middle of screen
• Click on subjects name in left-hand window
• Click on inplane series in right-hand window
• Click on selected inplane in bottom window

Disclaimer: (2/21/02) This is a beta version of the troubleshooting page. I have not had a chance to double-check everything (placement of buttons, etc) at the scanner yet.

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Problems
Resetting TPS
Rebooting the scanner
What not to do
HELP

Problems

1. Localizers fail after prescan

   
   Possible Causes

   • Coil is not plugged in; The connection is very loose and easily falls out.
   • No Header_Pool - contact Anne
   • TPS Failure - reset TPS
2. Ripples in the Inplane images

   
   Freq Dir (under Acquisition Timing, below AUTOVIEW) should be set on A/P or S/I. Never R/L

3. Simptrans fails to get screen save image

   
   This occurs frequently. Simply delete the directory you just created, mmddyya, and run simptrans again.

4. Simptrans can't get any images

   
   A GE software daemon running on lucas sometimes crashes preventing get5 (part of simptrans and anattrans) from getting the images from the scanner. Running simptrans will produce the error "Couldn't get unique sem key (sem_shm_init)" for each I file. Contact Anne or Tom Brosnon to fix the problem.

5. Auto recon doesn't occur

   
   At a cshell type, recon31 xxxxx, for the Pfile xxxxx.7

6. Pfile file is too small -

   
   disk full - The disk fills up very quickly when using the new auto recon option and xfer script 31 (save the Pfiles). You must delete some of the Pfiles and mag files after you transfer them. This Pfile is lost, so it would be a good place to start the disk cleanup.

7. Interface becomes very slow or unresponsive.

   
   One cause is lack of disk space. Check and make sure /usr/g/mrraw is not full, otherwise trying resetting TPS or rebooting.

8. Can't load a functional series, or select appropriate PSD

   
   Click Scan Modes in the RX manager and make sure the scanner is set to research mode. If set to clinical mode, you might have to restart the session in order to be able to set it.

9. Patient bed will not move

   
   Patient inside bore - Twist the handle at the subject's feet and manually pull him out.

   Patient outside bore - Using the pedels at the top of the bed, below the subject's head at the base of the magnet, raise the bed and make sure it is latched to the magnet. If it is connected, lower the bed to disconnect it and then raise the bed back up. If the pedals will not work, use the manual ones at the foot of the bed. If all else fails, manually push the patient a few inches towards the bore, and then try to move them normally.

10. Erased one or more parameters in a series perscription (Inplanes, etc)

    
    Look in the protocol book, which is stored in the 3T suite near the Mac, and copy the appropriate number.

    Alternatively, click on the body icon in the bottome left corner of the Patient Position section. This brings up the protocol selection dialog. Select the protocol you are using. This loads up a copy of all the series in that protocol with all the saved values. Simply choose the newly loaded series and continue.

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How to reset TPS

This procedure takes about five minutes, and can fix numerous hard to identify problems. If the system is sluggish or prep scans are failing and you can't find a reason, try resetting the TPS. In the lower left corner of the screen on the tools page, select Reset TPS. This takes about five minutes to complete and consequently preferable to a reboot.

How to reboot the scanner

Reboot the scanner only has a last resort. The reboot often fails the first time, and must be repeated. Each attempt takes about 15 minutes.

1. On the tools page, select reboot
2. Right click, select system tools and shutdown, from the pop-up window. After the system shutdowns, click on the dialog box to restart. You will need o log in as signa at some point suring the process.
3. Hard reboot - If neither option above is available, find the blue SGI computer under the counter. Press the button until the light goes out. After waiting a few seconds, press the button again to start the system up. I heard a rumor that the color of the light, red or green, indicates something.
4. If all else fails, Anne or Gary will have to restart the system from the computer room adjacent to the magnet room.

Once the reboot is complete, set the site to local, choose "Picture This" under patient protocols, and in Scan Modes choose research.

Always indicate system reboots on the scanner log. If you somehow are lucky to still have time after a reboot to try more scans, you will have to start the session over, redo the landmark, and redo the anatomies.

How to crash a multi-million dollar system

• Fill the disk up. There are actually two places where you can run out of space.

  
  /usr/g/mrraw - Before each session delete all the Pfiles and Mag files from the preceding session. Frequently check the remaining space (type df .) during the session and delete files as needed.

  The image files directory - Anne keeps close tabs on this space, but let her know when you get messages warning that the directory is almost full.

• Returning to a previously downloaded series

  
  Never view/edit a series that you have already clicked the Save Series button on. Copy and paste the series and open the new one (right click on the series and select copy).

• Double clicking

  
  That's right - no double clicking on a series name.

• Following my advice too closely
• Others....

Calling in the calvary

Anne's pager - Dial 3-8222, enter pager #15689
Anne's email - amsg@stanford.edu