1. Exvivo Scanning
      1. Scanner Bays
      2. Important Notes
      3. Major changes to Scanners
      4. Ex vivo Coils
      5. Scan Times/Protocols
        1. Bay 5 32ch exvivo hemi scan
        2. Bay 5 MTL solenoid coil scan
        3. Bay 6 Hemi Diffusion
        4. Bay 6 Whole Brain Diffusion (Allen Adult)
        5. Bay 5 MTL ec coil scan
        6. Bay 5 MT circ coil scan
      6. Regions of Interest
      7. Monitoring Helium
  1. Background Information
    1. Purpose of Scans
      1. Localizer
      2. Coil Covariance & SNR maps
      3. AFI, flip angle, or B1 map
    2. Information on FOV and positioning
    3. Information on Changing Scan Resolution
    4. Good Values to Choose for Scan Protocols
    5. Important Scan Parameters
  2. Basic How Tos
      1. Calculating and Changing Resolution
        1. Scan Resolution
        2. Base Resolution
      2. Calculating Size of Scan Output
      3. Get a protocol back on the scanner
      4. Make a PDF of a protocol
      5. Take snapshots of shims (or something else)
      6. RetroReconning to change FFT Scale Factor
      7. Adjust or Verify Autoscale Parameters
      8. Editing Patient/Scan Names
      9. Preventing Wrap Around
      10. If asked to match geometry or distortion
      11. What parameter to change when one parameter won't
      12. Copy center of Slices and Sats
      13. Rotating the FOV in plane
      14. Manually Positioning the FOV
      15. Changing the Size of the FOV using Parameters
      16. Making the adjust volume different than the FOV
      17. How to view event log
      18. Location of saved event logs
      19. Checking the voltage from headers
      20. Changing the transmit voltage
      21. Save raw data on Bay 8
      22. How do you set the correct number of measurements (volumes) for a diffusion scan
      23. When should I manually shim?
      24. How to set up a low b diffusion scan
      25. How do I transfer data to Bourget or Scippy?
      26. How to find Coil Covariance and SNR QC values to record
      27. How to Check AFI Map for Correct Flip Angle
  3. Issues that come up before or after scanning
      1. VNC instructions for Bay 3
      2. VNC to the mac mini (from another mac)
      3. Creating a New Scanner Data Form
      4. Changing Batch Filenames on the Promise Raid or LaCie Raid (Mac)
      5. Changing Batch Filenames on a Linux Machine
  4. Troubleshooting
    1. All Scanners
      1. Reboot, Restart and Shutdown Options
      2. Frequency Adjustment Did Not Converge Error
      3. Uninitialized Error
        1. In bay 2
        2. In bay 5
      4. Transmit voltage is very high
      5. Image Reconstruction Error After Scan Completed
      6. Temperature Warnings/Errors (ALM- ALL SCANNERS OR JUST BAY 5? I THOUGHT THIS WAS ABOUT BAY 8)
      7. Backup scanner schedule website
      8. Tunneling through the Partners firewall when gate/entry/door are down
      9. Saving Log Files
      10. Normalize setting and one channel coils
    2. Bay 3
      1. System low on resources
      2. Temp drive full error
      3. Restart options
      4. What to restart when...
      5. Rebooting + switches between systems
    3. Bay 5
      1. 32ch ex vivo birdcage coil connection
      2. EC 7ch scan - correct channels not selected in system tab
      3. Image Reconstruction System Error After Bay 5 Diffusion Scans
      4. Coil file error in Bay 5 small solenoid scans
      5. Network error in Bay 5
      6. RF-Infra structure error in Bay 5
      7. Autoscale not working on sequence in Bay 5
      8. Shim is not operational error- Bay 5
      9. Problems ssh'ing to suez from MRIR for streaming scans
      10. Restarting Bay 5
      11. Laser won't turn on
    4. Bay 8
      1. Diffusion b-value seems wrong on Bay 8 protocol file
      2. Bay 8 Image Reconstruction Error
      3. Bay 8 Restart Options

Exvivo Scanning

Scanner Bays


Field strength

Scanner type

Body or Head only

RF Channels

FDA approved?


Bay 1


Siemens Skyra



8ch pT, MARS

Bay 2


Siemens Avanto clinical




Bay 3


Siemens TIM Trio

whole-body and insert head gradient




Bay 4


Siemens Prisma





Bay 5


Siemens TIM ultrahigh field MRI




8 ch TX system

Bay 6


Siemens TIM Trio




BrainPET head camera insert

Bay 7




whole-body PET

Bay 8

3T (Connectom)

Siemens TIM Skyra





See also for info (although like most Martinos sites isn't necessarily updated often.) *NMR log-in required

Note: Scanners from software version VD and up have a single computer, MARS, for measurement and reconstruction. Older scanners have two computers: the MRIR (image reconstruction) and MPCU (measurement/physiological control).

Important Notes

Collect the following during every scan:
1. localizer
2. gre_mgh_localizer_750um
3. SNR Map
4. B0 Map
5. B1+ Map
6. B1- Map
7. Noise Level

Record the necessary values on the relevant form located here: ScanLog

WHEN CHANGING THE SCAN PROTOCOL DUE TO TROUBLESHOOTING/TIME/ARTIFACT ISSUES: Regardless of whether it is a quick test, someone else's tests, or a continuation of a scan that got broken up over a few days due to errors, please make sure to always get at least one meflash (one of the higher and reliable flips like 20 or 45) to go with the diffusion data so we can more clearly see sources of artifacts, etc.

Major changes to Scanners

3/12/15 - water leaked into the gradient in bay 5. Siemens replaced the gradient and the scanner was back up for use on 3/23/15.

6/18/15- Bay 8 chiller repaired

7/13-7/29/15- Bay 8 defective gradient coil replaced

9/11/15 - Bay 5 MRIR computer replaced:

"As of this morning the Siemens image reconstruction computer in Bay 5 has been replaced with an in-house built computer and an adapted ICE environment. The software has been tested for months in Bay 2, so I'm not anticipating many difficulties, but should you happen to run into suspicious image reconstruction problems, please let me know.

The most noticeable differences are that the new computer sports 256 GB RAM and a 1.8 TB RAID for twix. Furthermore, with its enhanced compute power the lagging image reconstruction for SMS sequences should be a thing of the past. There may still be minor lags for protocols with few slices, as they do not multi-thread well, but whole-brain protocols should reconstruct essentially in real-time.

I will make some further changes to the reconstruction system to optimize the performance, but that will not have any noticeable effects for users." (email from Thomas)

5/19/16- Bay 3 had a broken gradient replaced.

Ex vivo Coils

Information about using the coils can be found on the ExvivoCoils wiki.

Scan Times/Protocols

Bay 5 32ch exvivo hemi scan

QA Scans



















Warmup Scan




















Same scan/times as warmup. Get at least 1 run each of FAs 30, 20, 10.







Mainscan total time


Minimum Need Grand Total (QA+warmup+mainscan): 25:00:10
Ideal Grand Total (QA+warmup+mainscan+two more flip20s): 37:26:02

Bay 5 MTL solenoid coil scan



400um localizer


100um sef flash 10 - run 1


100um sef flash 10 - run 2


100um sef flash 10 - run 3


100um sef flash 20 - run 1


100um sef flash 20 - run 2


100um sef flash 20 - run 3


100um sef flash 30 - run 1


100um sef flash 30 - run 2


100um sef flash 30 - run 3


TOTAL TIME (including localizers, SNR, AFI)


100um mef flash10 TE16


100um mef flash20 TE16


100um mef flash30 TE16


100um mef flash10 TE24


100um mef flash20 TE24


100um mef flash30 TE24


100um mef flash10 TE32


100um mef flash20 TE32


100um mef flash30 TE32


TOTAL TIME (1 run for each flip/TE combo


~28 hours needed to do both sef and mef

Bay 6 Hemi Diffusion

For scan setup protocol, click here

1mm meflash

4.35 min x 6 flips x 2 runs

52 min

750um meflash

12.32 min x 6 flips x 2 runs

2.5 hrs

T2 space

2 min x 6 runs

12 mins

750um diffusion

8 hrs 11 min x 1 rum

8 hrs 11 min


11.75 hrs


1mm meflash

4.35 mins x 6 flips

26 mins

750um meflash

12 min x 6 flips x 2 runs

2.5 hrs

T2 space

2 min x 1 run

2 mins

750um diffusion

10.25 hrs x 3 runs (1 run is okay if that's all we can fit)

30.75 hrs


~38 hours

Bay 6 Whole Brain Diffusion (Allen Adult)

1mm meflash

20 min x 6 flips x 1 run

2 hrs


6 min x 1 run

6 mins


16 hrs x 1 run (more if can fit it)

16 hrs


18 hrs

Bay 5 MTL ec coil scan

120um flash20

5 hrs x 6 runs

30 hrs

120um flash10

5 hrs x 3 runs

15 hrs

120um flash45

5 hrs x 3 runs

15 hrs


approx 60 hrs (depending on FOV)

Bay 5 MT circ coil scan

Regions of Interest

Monitoring Helium

You can see the current helium level here

Background Information

Purpose of Scans


The purpose of the localizers is to see where the brain is located relative to the bore of the scanner. To see how well the sample is centered in the isocenter, append a localizer and choose isocenter as Position in Routine Tab to see how far brain is from isocenter. If it's really far off, you may want to reposition the sample.

Coil Covariance & SNR maps

These are Quality Control scans that we can use in the future to diagnose problems & compare across scans. When examining the output of a coil covariance scan in the Viewing Tab, you should see that the diagonal in the color matrix should be all the same color. This diagonal represents the channels of the coil. The surrounding squares should all be a similar color. Any differences mean that a channel may not be working well and Azma should be alerted (if she hasn't been previously).

AFI, flip angle, or B1 map

These terms all refer to the same scan. The purpose of this scan below is to show you what voltage you need to get the flip angle you desire (we use a test flip angle of 60).

Information on FOV and positioning

An FOV (Field of View) box marked by solid yellow lines shows what will be included in your scan. If the FOV box is surrounded by dashed lines (in the coronal view), those slices will not be included in the scan. Use the dashed lines in the coronal view to help you move the FOV box in the sagittal and axial views so that they accurately represent the desired anterior/posterior borders of your scan. The reference lines (a gray line in the sagittal and transversal views) show you the location in that plane that corresponds to the coronal slice you are currently on. You can scroll to the coronal slice that you would like to be the end of the ROI and then move the FOV box in one of the other views so that its border is on that line and therefore on that corresponding slice (you should see the dashed lines become solid lines). You can then use the same trick for your other border. If you do not see the reference lines in the other views, you can turn them on by going to the View Menu and choosing Reference Lines On.

If you're planning on changing the FOV, you will want to consider the following before changing anything:

Tip: In the top right corner, the SNR value will increase/decrease relative to your parameter changes from a starting value of 1.00 – this cannot be compared across scans but can give you a sense of how you have altered the scan.

There are a few ways to change the FOV. See "Changing the Size of the FOV using Parameters" under Basic How Tos below for the best methods. You can also manually drag the sides of the FOV box (yellow lines) in the Exam tab to resize the FOV, but this is typically discouraged. Ideally, the FOV remains consistent between protocols.

Information on Changing Scan Resolution

See Basic How Tos for calculating resolutions. Once you have these numbers, plug those values in for FOV read and Base Resolution. Once the resolution is set, you must make sure the host will be able to handle data of the size you are collecting. See "Calculating Size of Scan Output" (below) for instructions on how to do this.

Good Values to Choose for Scan Protocols

The scanner likes you to set up the resolution in power of 2, or a sum of large powers of 2, (because it will use less power that way) so if possible, increase the base resolution to the next power of 2 when changing it to work with your Read. Here are the powers of 2 you are likely to use.























*these numbers are not exactly a power of 2 but will still work better than other numbers

Important Scan Parameters

Basic How Tos

Calculating and Changing Resolution

If you've changed the FOV Read size or Base Resolution you will need to double check that your Scan Resolution is correct before running. See below for how to manipulate these parameters.

*Tip: Hover over the Voxel Size numbers on the right side of the Exam Tab (above the protocol list) to see the true resolution you are getting. You almost always want the scan to be isotropic (same size in 3 directions). For example, if the numbers say 0.119 x 0.12 x 0.12 you may want to try to get a Read/Base Resolution combination that will make it exactly 0.12 if it's possible.

Other parameters to check that will affect resolution:

Once the resolution is set, you must make sure the host will be able to handle data of the size you are collecting. See "Calculating Size of Scan Output" below.

Scan Resolution

Scan Resolution = FOV Read / Base Resolution

Note that if you've changed the FOV Read for your scan, you will need to also change the Base Resolution to get the resolution you want to scan with.

Base Resolution

Base Resolution = FOV Read / Scan Resolution you want

e.g. If you want a resolution of 120um and need the FOV Read to be 120 to fit the brain: Base Resolution = = 120 / .12mm = 1000 You can enter 1000 for your Base resolution.

Calculating Size of Scan Output

Size of scan in GB = base resolution^2 x 2 {for oversampling} x phase {.##; i.e. if phase is 75%, multiply by .75} x # slices per slab x # coil channels x # of echoes x 4 bytes x 2 {for complex} / 1024 {KB} / 1024 {MB} /1024 {GB}

Note: If this is a segmented scan (often used when streaming), divide by the number of segments to get the size per segment.

The size of your scan should not be over 28.5GB. It's best if it is 26GB or less.

Get a protocol back on the scanner

If you want to rerun a protocol that was previously run on the scanner but you did not save that protocol, you can "phoenix" it back by choosing the Patient Info button and entering in the ID number used. All scans done on that ID will show up in the Patient Browser.

Make a PDF of a protocol

Open up the exam explorer and navigate to the protocol you want to print to pdf. Right click on the protocol and select print to PDF. Then choose the location to save the pdf file and choose the final option for which parts of the protocol to save. Make sure you select to print a table of contents. Use winscp to transfer this protocol to the cluster

Take snapshots of shims (or something else)

If you would like to take a snapshot of the shims after running adjustments, go to the 3D shim tab and press the print screen button on the keyboard (sometimes abbreviated as PrtScn). Then hold down the Crtl and Shift keys and press the number 4 to open MS Paint (Crtl + Shift + 4 is a shortcut key for MS paint on the Bay 5 console computer). Alternatively, you can press Crtl + Esc to open the Windows start menu and select MS Paint from there. With MS Paint open press Crtl + v to paste the snapshot you just took (or Edit->Paste). Then save the snapshot (Crtl + s or File-> Save).

RetroReconning to change FFT Scale Factor

Note: This can only be done when no scan is currently running.




Add instructions on how to check if FFT needs to be reduced here

Adjust or Verify Autoscale Parameters

Autoscale is installed on the Bay5, Bay 8 and 15T scanners, and can be turned on/off on the Special tab for the gre_mgh_multiecho_* scan sequence. There are several autoscale parameters which can be changed if necessary. If the autoscaled highres localizer or main scan look out of the ordinary you may want to check the current autoscale IceConfigurator parameters.

To view the autoscale IceConfigurator parameters open the following file in Notepad:



Each autoscale parameter definition includes a comment with a short explanation, and the limit range indicating what range of possible values the parameter can have. If there is nothing written on the next line after the limit range definition, then the autoscale parameter will use the default value, which should be the first value in the limit range. Note that some autoscale parameters are boolean (logical binary, accepts only "true" or "false"), while others are double (16bit float). For example, in the snapshot above, the ParamBool."ScaleByVolume" parameter has the limit range definition as the last line, so this parameter is set to "false" by default and will autoscale by slice.

Current autoscale settings (as of 11/27/2013)

Bay 5 (7T)




Editing Patient/Scan Names

If you have registered something under the wrong name or have a scan with the wrong resolution, etc. in the title, you can change these before you transfer the data to bourget.

Preventing Wrap Around

Check the Sequence Tab - under the Part 2 section of this tab, there is an option that says Excitation. If Slab-select is chosen here (as it is for the EC scans) then wrap-around will occur only in the phase encoding direction (indicated by the yellow arrow next to the FOV box). If Non-select is chosen wrap-around will occur in the phase encoding direction as above AND in the slice direction. To find out which direction is the slice direction, increase Slices per slab in the Routine Tab. Make sure that there is nothing outside the FOV box in this direction (or at least if there is something, that it will wrap onto non-important stuff and not the sample).

If asked to match geometry or distortion

To match the geometry of two scans, you will want the following to be identical if the scans are the same resolution or in the appropriate ratio if the scans are not the same resolution (i.e. the below should be doubled if you want to match a 1mm scan to a 500um scan):

To make sure two scans are distortion-matched, make sure the Bandwidth is the same for both if they are the same resolution or in the appropriate ration if the scans are not the same resolution.

Note: For diffusion scans, the FOV does not have to be identical to the anatomical scan it is paired with but if this can be achieved it is better.

What parameter to change when one parameter won't

Copy center of Slices and Sats

It copies for each slice:

and for everything:

Rotating the FOV in plane

To rotate the FOV box in-plane, hold down Ctrl and the circular arrows that let you rotate the box appear (as opposed to the 4 pointed move arrow cursor that lets you move the box). For the other two views that aren't in-plane, the circular arrows should show up without pressing control. The rotation can also be adjusted by pressing the "..." button next to the Phase enc. dir. drop down menu.

Manually Positioning the FOV

Middle click on the mouse and drag the FOV box. Place the FOV box so that the ROI is in the center of it. Remember that your ROI will depend on the project, so make sure you've decided this well before your scan.

Scroll through the scan you loaded in the leftmost box and check for these things:

Changing the Size of the FOV using Parameters

If the FOV box does not fit over your ROI or is not big enough, you will have to change the size by changing one or a couple parameters (slices per slab, FOV read, FOV phase):

*Tip: It is sometimes easier to increase this to 100% and then change the Read size, however once you change the Phase, you may not be able to get back to the same exact number it was set at before.

Making the adjust volume different than the FOV

If the FOV is much larger than the actual ROI (often because the FOV must be large to prevent wraparound), then it is good to change the adjust volume box to be smaller than the FOV box (i.e. only covering the ROI). This is because the scanner only has a certain degrees of freedom it can use when shimming to fit the parameters to along a curve. If you include a lot of other stuff that you're not interested in in the adjust volume box, the scanner is going to take up a lot of DOFs trying to fit this outlier, making the actual ROI less accurate. It is better to only shim over the ROI so the parameter fitting of the curve will be much more accurate.

To change the adjust volume, first make sure that it is visible (the green box; the yellow box is the FOV). If it is not visible, go to "View"? and click on adjust volume (could be under different tab- needs to be confirmed). Once you can see the green box, manually drag it with the mouse to change it's size. DO NOT DO THIS EVER TO THE FOV (YELLOW BOX)! That needs to be much more precise so it should only ever be adjusted by inputting the exact parameter values in the protocol.

When you go to run these scans, a window will pop up notifying you that the adjust volume appears to have been manually adjusted. Hit "Manual" to use the adjust volume you manually set, rather than the scanner automatically reseting the green adjust box to its original dimensions of the same size as the FOV.

How to view event log

Go to the Options Menu, choose Service and then Event Log. Hit 'Go' on the bottom.

Location of saved event logs

(Bay 5) c:\MedCom\MriDiagnostic\<find your saved event logs based on date/time>

(Bay 8) C:/MedCom/MriDiagnostics

Checking the voltage from headers

To view headers:

strings *.hdr >> header.txt

Open this is a text editor and search for flReferenceAmplitude (there will be many of these). This is the transmit voltage. For the voltage used at the particular flip angle, search for flAmplitude. You can divide this by the flip angle of the scan you saved the header for, which is FlipAngleDegree in the text file and multiply it by the flip angle in question.

For example, the amplitude for FA30 was supposed to be 583.333V. If the coil cuts off at 520V, then the flip angle that was actually ran was: 30 deg * (520V cutoff/583.333V expected) = 26.7 degrees

Changing the transmit voltage

If the AFI map does not show the correct (i.e. the flip angle that you designated in the AFI map protocol) flip angle at your area of interest, you can alter the transmit voltage so that it is most accurate at that area. For whole brains, our AFI map typically should have 60 degrees in the center, tapering off on the edges. For small solenoid scans, we want the map to be the desired flip (usually 60) where the sample actually is in the coil. If the sample or area of interest is not receiving the designated flip angle, you should calculate the adjusted voltage that will produce the correct flip angle at the desired location.

adjusted voltage= original voltage giving results of AFI map * ratio of desired flip angle/actual flip angle in AFI map at area of interest

Enter this new value in the voltage field of the 'Transmitter' tab in adjustments.

Save raw data on Bay 8

Press ctrl + esc and click “run". Type “twix” in the window. Select the scans you want to copy the raw data for in the Twix window. Right click and select “Copy total single raid file…” In the window that pops up, select a drive where there is enough space to store the raw data. (Make sure to make a new directory there to store your data.) Click “ok” and wait for the copy to finish.

Note- this is the same procedure that we use in Bay 5 to save the meas.dat file of the main scan for streaming

How do you set the correct number of measurements (volumes) for a diffusion scan

If you select "None" under "Unlock Measurements" on the Special card (this means measurements are locked) then it'll play out the correct number of diffusion directions and low B volumes. If you say "unlock measurements" it applied the "offset" parameter and plays out only the number of measurements starting at the offset (and including the initial low B volumes)- meaning, you may be short some gradients.

When should I manually shim?

If you manually shim, and you want it to have an effect, you need to do it when the shim volume is selected that you're interested. If you want to shim MEF scans you may as well do it just before running the first MEF, so the same adjust volume is selected. If you change the adjust volume between scans, it'll recalculate the shim anyway. In small samples at 7 T, manual shimming is important because the automatic shim isn't designed to handle such small FOVs, but for the entire brain at 3 T Andre isn't sure it makes too much difference (so not too much stress if you forget).

How to set up a low b diffusion scan

Append your main diffusion scan to the scan queue and edit the following parameters: 1) Set number of low b volumes on special card to N (N being the number of low b volumes you want) 2) Set number of measurements (contrasts tab -> dynamic) to N 3) Set number of directions/volumes to skip on special card to 0.

How do I transfer data to Bourget or Scippy?

See this document for info:


How to find Coil Covariance and SNR QC values to record

When the coil covariance scan is complete, open the Patient Browser and load the 1st volume of that scan into the Viewing tab. COVmtx mag and scale will be written at the bottom of the image. When the SNR map is complete, open the Patient Browser and load the 1st volume of that scan (this map creates 3 volumes) into the Viewing tab. Scroll through the slices to find the highest rss and highest opt value and record.

How to Check AFI Map for Correct Flip Angle

When the AFI map is complete, load all 4 images from the Patient Browser into the Viewing tab so you can view them simultaneously. Right click on one of the images and choose Select Series. The box the image is in will now have a solid blue line around it. Then, while holding down Ctrl, choose (left click) the other 3 boxes so that all 4 have solid blue lines around them. This allows you to scroll through all 4 images simultaneously.

Scroll to a slice where you can see the ROI in the top 2 images. Choose the pixel tool. Hovering the tool over the bottom left image will show you the flip angle you are likely to get from scanning with the voltage you are using. Hovering over the bottom right image will show you the voltage you should be using to get a flip angle of 60. Check that hovering over your ROI gets you a flip angle of around 60 degrees and a voltage near the one you received when you did the adjustments. Also check on the flip angle and voltage around the entire brain. You will get a range but it shouldn't vary drastically. If you are getting a very different voltage from the one you received in adjustments, when you do adjustments next, consider entering in that voltage and hitting Apply.

Issues that come up before or after scanning

VNC instructions for Bay 3

Option 1:

Potential problems: sometimes the Screen Share app gives me a “Connection failed to localhost” error. When this happens I close the app, exit out of the terminal, re-open both at the same time and try setting up the ssh tunnel again.

Option 2:

Potential problems: requires you to have NoMachine.

VNC to the mac mini (from another mac)

*could be depending on the domain (scanner bay or office)

If you can't connect, there are a few things you can check to be sure screen sharing is properly set up:

Creating a New Scanner Data Form

  1. Get freesurfer google username and password & go onto google drive.

  2. Look for ScannerDataForms folder. Create a new form or make a copy of an existing form to alter.

  3. Forms and their results need to be linked to the website for easy viewing. You can edit the html here:

/cluster/lcngroup/web. To edit the website, open index.html in a text viewer like emacs. Follow the conventions to edit the HTML. Look online for resources or ask for help if you are not sure how to edit it.

Changing Batch Filenames on the Promise Raid or LaCie Raid (Mac)

If you gave the raid the wrong pre-fix and your files are not named correctly, you can easily fix this on the mac using an application called Automator. A good set of instructions can be found here. You cannot copy the .dat files for a test because of their large size, but you can create text files that are named in a similar way and test it that way.

Changing Batch Filenames on a Linux Machine

If you have already transferred files from the Raid to the cluster, you can still rename the files using command-line options. The easiest is to use the "rename" command. Type 'man rename' or 'rename --help' in a terminal to find out more. Rename takes the first instance of an input you specify, and changes it to an output that you specify. For instance, if you type 'rename I41 I41 *.dat' it will take all of the .dat files in a directory, and for each file, at the first instance of 'I41' it will replace it with 'I42'. so you can correct for a case naming error. If you entered the wrong resolution, you could do something like: 'rename _150um_ _160um_ *.dat' and it will replace that portion of the text. Try it on one file first, and then if you are satisfied, you can bulk rename the rest.


All Scanners

Reboot, Restart and Shutdown Options

When you experience a problem, you can troubleshoot it by going to System> Control. In the tabs you will see in this panel (described below), there will be green arrows next to the various items indicating that they are running fine. If there is a red X, then there is a problem with that item. Problems indicated by these red arrows or by the error message that popped up while you were scanned can be fixed in the following possible ways:

Alternatively, if you know you have to shutdown the entire system, follow these directions: Go to System> End Session> Shutdown System When you do this, the host will tell you when to push the blue button to shut down the scanner. After shutting it down, wait a minute then hit the blue button to turn it back on.

Frequency Adjustment Did Not Converge Error

Sometimes the scanner cannot find the frequency adjustment within the range it is looking. To fix this, choose FID 400 Hz in the "Sequence & Resolution" box of the Frequency tab (see screenshot below), which will extend the range it is searching over. Or you might need to type in the value in the 'Frequency' field as described above.


Uninitialized Error

Upon opening a scan dragged or appended to the scan queue, you may receive an uninitialized error. This only occurs with FLASH scans that use Andre's custom sequence.: UE.jpg

Hit okay on the pop-up warning. Then hit cancel on the scan you just opened. If you hit 'Apply' on your scan instead of 'cancel', you'll notice your scan's time will change to 1 second (and it will not run when the time comes).

In order to add new scans to the queue without experiencing this error, you will need to remove scans that have already run from the queue. Be careful not to delete any scans you need to append before you save these in the Exam Explorer.

The uninitialized error occurs because the computer thinks it doesn't have enough memory to run all the scans in the queue. In 2011/2012, Andre increased the limit of kspace lines in his code so that this error wouldn't happen. We now tend to only experience it for scans that take up more memory (32 channel exvivo scans in bay 5) and/or require a lot of runs in the queue. Andre is currently working on a fix for these current issues (12/2014). The number of scans that can be queued up at a time varies greatly depending on the size of the scan. As of 02/15, some high resolution whole brain scans only allow ~6 hours of scans to be queued before triggering the uninitialized error, whereas while using the append and complete right click shortcuts on on a small solenoid scan we were able to queue over 20 items/>36 hours (we did not see how much it would allow because we were going to be checking in again well before then. this would be good to try on a future small solenoid scan though.)

In order to avoid the error (especially when you have a long weekend with many scans to eventually queue up), 1) try to limit the queue to 20 items (if bay 5 or bay 8), 2) try to avoid opening protocols after scanning has been going for awhile; use append and complete (by right clicking on the scan) although beware that you can still receive the error even with a successful "complete" when using this shortcut; 3) save the protocols you will need to run with all parameters already set in the protocol folder (Exam Explorer) at the beginning of your scan (even if you won't run some of them until way later in the scan) - this way you don't need to open and fix any protocols later in the scan and you have access to protocols you'll need again that were deleted from the scan queue. 4) If you are experiencing the error while you have the Exam Explorer/protocol folder open, close that and then try appending scans. For some reason, the # of items in the queue is limited even more if you are adding to the queue and the protocol folder at the same time. 5) If opening a protocol is unavoidable but you are receiving this error, you can try appending that run from earlier in the queue rather than from the protocol folder (which oddly works sometimes).

Another observation: If when saving scans in the Exam Explorer protocol folder, the scan time changes to 1 second in the folder, don't worry. If you append these scans at a later time when the queue is an acceptable length, they will still run.

If all of this fails, make sure you have a snapshot of the shims and then restart the host (or is it scanner? check with Andre). Enter the shims again and pick up where you left off. (I wonder if closing the patient and registering a new patient would work?).

In bay 2

The uninitialized error typically emerges once you have 4-5 scans queued up and you are running the typical exvivo recon protocol to get surfaces on a hemi. This may no longer be accurate after Andre's initial fix to his code.

In bay 5

In bay 5, the above error often happens when the scan queue has over 20 items.

Sometimes adding more than 20 items to the scan queue can freeze the system and it comes back by itself after a while. In such case, if you notice that the exam tab or viewing tab has disappeared, then go to Control -> session and then restart the tasks that have disappeared from the console.

Transmit voltage is very high

If the transmit voltage in the Adjustments menu converges at a high number, try re-adjusting the Frequency tab until it converges. Then, go back to the Transmitter tab and enter a low voltage (~50 or 100) and press go until it converges. This may help in some cases, however if the Transmitter voltage consistently settles around the same number, regardless of starting voltage, then this process doesn't help.

* most prevalent on Bay 5

Image Reconstruction Error After Scan Completed

If a scan has an image reconstruction failure that happens while it is reconstructing (not while it is running) then you may be able to get those slices or images that it did not reconstruct by running 'MrRestoreImages' from the command line. Some is still not committed and will likely stay inaccessible.


During the diffusion scans (or possibly after scanning a different sequence for a long time) you may get the following errors:

Gunjan said this should not give any operational issue if it is not due to a leak, however it should be attended to before it starts giving issues, so you should report it to Gunjan and Thomas (via mri_help) when you see it but could continue scanning. The Primary water temperature does go out of the limit when this message pops up, however there are some known issues with the chilled water supply to the system and in the current state (11/18/16) it still provides sufficient cooling for system operation so the scan will continue. If possible, you can open the cabinet doors in the room behind bay 5 to allow for more cooling. Otherwise the scan will stop if it continues heating, and the warnings below occur.

If the Primary water temperature goes much higher and you start getting secondary temperature warnings, it will be an issue.

* Most prevalent on Bay 5 (especially during trufi diffusion). also happens in Bay 8.

Backup scanner schedule website

If the normal scanner login/schedule website is down (due to a power outage or down server at the Martinos Center, there is a backup that lives in Needham:

Tunneling through the Partners firewall when gate/entry/door are down

To get access to (and thus tunnel through the Partners firewall when gate/entry/door are down) email Will Small and request access with the following information:

Keep in mind that this will effect the command used for VNCing. If you're using to tunneling to bay8oc:5900 for example, you'll need to change it to when you tunnel through their server.

Saving Log Files

If you encounter an error that you can't troubleshoot yourself and it is something we need Gunjan or Thomas to fix, save the log files. (These show exactly what was happening at the time of the error, and more detailed information about the error than shown to the user.) The log files eventually overwrite themselves as scanning progresses, so make sure to save them as soon as possible.

To save the log files (or "logs"):

Go to the System Menu, choose Control, click on the Tools Tab and hit "Save System Log-Files".


A terminal window will pop up. Don't close this - it will eventually close itself. A box will pop up where you can enter your name, the exact time the error occured, and a message describing the error. You will have to email Gunjan and/or Thomas to let him know you saved the logs and what the problem was.

Normalize setting and one channel coils

This problem was experienced on Bay 3 but is likely common to all scanners. If you are scanning with a one-channel coil, make sure to check the normalize setting when creating a new scan protocol. Normalize is right under Prescan Normalize (Resolution tab > Filter tab). Normalize should be off at least for SWI, MEFLASH and diffusion. The reason is because with the one channel coil it scales each slice independently. Prescan Normalize does not do this but that setting only works with multichannel coils- when you plug in a single channel coil this setting is switched to standard normalize by default instead of switching to "off." If you run a scan with the incorrect normalize setting, you can try RetroReconning it to change the setting. If you are trying to do this, talk to Andre.

Bay 3

ALM- add details

System low on resources

According to an email correspondence between Thomas Witzel and Jodi Gilman on 08/26/2014, this error has been a long recurring problem in Bay 1 and seems to be an inherent flaw in the newest incarnation of the Siemens VD13 software. Bram Diamond experience the same error message on Bay 3 when tranferring data to Bourget. Rebooting the host computer fixed the issue, although we are not entirely sure why. Since this quick-fix works for Bay 3 (and supposedly worked for Bay 1 in 2014), it may also work for Bay 5 if the issue arises. This has not been tested to date (12/31/2018) - please update these details accordingly.


Temp drive full error

This error appears when the C:/temp/ directory is approaching or completely full. An exclamation mark in a yellow box flashes at the bottom right corner of the screen. It can stop the scans so it's important to check how much space is free in the temp dir whenever starting a scan session. Thomas W. suggests deleting any .dat files being stored in there since those are the largest and people should not be storing those in the temp dir.

*It has happened during EXC008 (2/13/16) even when there was 1.94 GB of disk space free (although that time it didn't stop the scans, probably because it was caught as soon as it appeared and files were deleted from the temp dir).


Restart options

Restart options are in the System -> Control menu

Bay3_restart_options_host.JPG Bay3_restart_options_mrscanner.JPG

What to restart when...



Image recon failure

MrIrisContainer in Image Reconstruction tab (~5 min)

Persistence error

"Restart Syngo MR" in Host tab (~20-30 minutes)

Other errors, or if the above don't work

"Reboot" in Host tab (~30 minutes)

If you get an image reconstruction error alone, restart MrIrisContainer before attempting to restart the scan. If an image recon error appears at the same time as the persistence error, Andre thinks that is a side effect of the persistence error. Therefore, you could try to restart MrIrisContainer but might still need to "Restart Syngo MR" for the images to appear in the Patient Browser.

"Reboot" turns off Syngo MR, then restarts the console computer and restarts Syngo MR. This means it takes slightly longer than restarting Syngo MR, and you will lose VNC connection during the reboot. For the persistence error, "Restart Syngo MR" is sufficient to allow the images to load into the Patient Browser. For other errors (some of which say to Reboot in the error message), it may be necessary to use the "Reboot" button in the Host tab. BE SURE TO RE-ENTER AND RE-APPLY SHIMS AFTER ANY RESTART!!!

After any major error, it may be good to save the logs, and email Thomas Witzel to let him know. This is done by clicking the "Save System Log-Files" under the Tools tab. Fill out information about the error, and be sure to include the time it occurred.

Rebooting + switches between systems

(email from Larry White to mri-scan on 7/20/16)

Both Bay2 and Bay3 now have dual systems that can be accessed via a KVM switch box(bluish in color) and a network switch box(black box) that are located on the main console table (in Bay2) and sitting on the two CPU’s (in Bay3). Upon re-boot, the system may not boot into the system that you were using. Both bays have been configured similarly to avoid confusion:

In Bay3 (and Bay 2), the main operating system is also identified as STANDARD(VB17) and this will mean the light on the KVM switch box should be blue and the network box should be set to “A”.If you notice that the KVM switch isn’t set right (green- on the AC88 system used by the monkey people), just press the colored button and it will switch to the other system (blue). For the network box, just press the button to toggle to the other system, from “B” to “A". There are labels on all four boxes to remind you if you aren’t sure. In summary, the KVM switch box should be blue and the network switch box should be set to “A”.

Bay 5

32ch ex vivo birdcage coil connection

There is a cable the connects the birdcage for the 32ch coil to the bias cable on the scanner. This is a BNC cable, with an Type N connector adapter attachment that allows for the birdcage to connect to the scanner. MAKE SURE THAT THIS ADAPTER IS ALWAYS CONNECTED TO THE BIRDCAGE'S BNC CABLE!. When disconnecting the birdcage from the bias cable, be sure to disconnect the N type connector from the scanner, and not the BNC connector.

EC 7ch scan - correct channels not selected in system tab

Here is a screenshot of one slice from the uncombined localizer which shows the image received from a channel which was capped and not actually connected to one of the coil receive channels. If you see something resembling this in the low or high resolution uncombined localizers then you need to either select the correct receive channels in the system tab of the protocols. Alternatively, you can change which plugs are being used on the 8ch interface box (ch 6 should be skipped and capped).


Image Reconstruction System Error After Bay 5 Diffusion Scans

If you see the following error after running diffusion, "Not all images could be made persistent for last measurement. These images have been saved and will be available in the database after a Reboot", check to see if all the images are there in the browser and check if they are sending to bourget. If all images you expect do not get sent, reboot the MR Syngo, then manually re-send images to bourget.

Coil file error in Bay 5 small solenoid scans

Sometimes if the 'Frequency' value in the Frequency tab of adjustments is way too high, the console doesn't recognize the coil and there will be no signal i.e. if you hit 'Go' on the Frequency tab, instead of seeing a bell shaped curve, the graph shows up really random with no particular shape. If that's the case, enter the value '297.181000' in the 'Frequency' field of the 'Frequency' tab in adjustments window and hit 'Apply'. Although this error has only been so far in the small solenoid coils, it might be a good thing to try this out in case you happen to see this in other coils as well.

Network error in Bay 5

Network hub power plug may be unplugged or half-unplugged. To the left of the Siemens console computer there are two "black" boxes (that actually look like black boxes). To the right of these black boxes, there is a white box. On the back of this white box, there is a black cable that is connected to the power supply. Check that it is completely plugged-in.

RF-Infra structure error in Bay 5

This error has occurred at times when scanning in Bay 5 with the 32 channel exvivo coil which Azma built: rf-infra_errors.jpeg

The dico test occurs once at the beginning of the scan session, unless the bed is moved or power to the bed is cut off. When the dico test or de-coupler test does not converge it means that some voltage lingered or returns when the coil is tuned and then detuned. Gunjan believes the coil needs more voltage traps, but Azma is not convinced. Gunjan thinks that the RF-Infra structure error indicates that the low voltage error tricks the dico test to fail and is never able to complete.

Gunjan's proposed fix is to move the bed back to the home position, landmark, and send the bed back in with the hope that the bed position is slightly different, resulting in a slightly different tuning, and allows the dico test to converge and pass. Alternatively, you can open the Adjustments window, and on the Show tab you can "invalidate all adjustments" which tricks the scanner into performing a coil change without physically moving the bed. Basically you just need to create a coil change and then try scanning again.

Autoscale not working on sequence in Bay 5

Sometimes a sequence will not run with autoscale because passing parameters to ICE is buggy in VB17, so if the parameters trigger the scan to switch to the gradient mode "Normal*" it may not run. Paul and Andre said with the Siemens software as is, the only way to completely avoid this problem would be to remove all of the custom parameters from the autoscale configuration file, but we don't really want to do that because then all of that would have to be hard coded into the sequences which would be less flexible. The scan will run once it has already gone into Normal* mode. Therefore, as a work around, after the scan changes to Normal* but fails to start, you can cancel the failed scan in the queue and re-append it or drag it into the exam explorer and then back into the queue and it should run.

NOTE- this is different than the previous autoscale problems in Bay 5 documented above in "Adjust or Verify Autoscale Parameters"!

Shim is not operational error- Bay 5

Gunjan said this is a false warning with the 7T scanner due to a bug in the software. The scan should be fine.

Problems ssh'ing to suez from MRIR for streaming scans

If when you try to ssh into suez via the MRIR you are receive an error message along the lines of,  ssh: connect to host port 22: No route to host  then first verify that both ends of the (green) Ethernet cable between the streaming Mac mini and the MRIR are properly plugged in and secure. Also, verify that the “Scanner Bay” location is selected in the network settings (click Apply if changes are made) and that the “Remote Login” box is checked in the System Preferences → Sharing menu. If the problem persists, try disabling and then re-enabling the Ethernet port. If it still persists, reboot the Mac.

Restarting Bay 5

Make sure a coil is plugged in whenever rebooting the scanner. If not, it won't reboot properly (according to Gunjan) and you'll have to do it all over again. Unclear if it is the same in the other bays.

Laser won't turn on

The laser only turns on when it recognizes the position of the table. If the screen is all dashes instead of numbers showing the distance to isocenter, the laser won't turn on. To get the table to recognize the position, you have to send it "home" using the home button and then it will register that it is 2096 mm away (or whatever it is). The laser will turn on once you've done that.

If the display doesn't show Magnetom properly, something else is wrong causing the laser not to turn on and Gunjan has to fix something in the back of the scanner before it will work.

Bay 8

Diffusion b-value seems wrong on Bay 8 protocol file

The "Calculated b-value" listed in the protocol .txt file from Bay 8 DOES NOT represent the real b-value that the scanner takes as input. The calculated value in the protocol can be different from the input b-value because a scaling factor might be applied in the gradient table.

For some reason, Siemens does not include the real b-value in the protocol file on this version of the Syngo software. (This information is located in the DICOM header, though.)

If you want to find out the real b-value of a previously run diffusion scan, run

strings <dicom_filename> | grep -i bval

("i" makes it not case sensitive)

Bay 8 Image Reconstruction Error

Beginning in September 2014, we began to get Image Reconstruction Errors on Bay 8 that stopped the scanner (sometimes in the middle of the night), preventing us from finishing scans during alloted times and sometimes losing days of work. We consulted Thomas Witzel and Himanshu about this. Himanshu thought it was because the RAID is unstable. The error stopped happening for awhile after Thomas W. increased the RAID size on 9/19/14. (He increased the RAID while looking into this problem which was very problematic for the EXC007 09/18/14 scan which ultimately had to be redone because of this error.) The larger RAID was never tested for its stability with 6 hour diffusion scans. The image reconstruction error began appearing again in January 2015. Allison M. has been investigating this with Andre, Thomas, Himanshu and others.

****ALLISON M. TO ADD MORE DETAILS (3/31/15) *****

If you get an image reconstruction error, restart MrIrisContainer before attempting to restart the scan. It is a waste of time to restart the scan unless you've done this- the scan will start and run happily for a little bit but then ~30 minutes in will fail again.

Bay 8 Restart Options

To restart the scanner, click on "Control", then "System". This will bring up a window that looks like the one below.

Image reconstruction error: Restart “MrIrisContainer”
Any other error: Restart “MrMCIRContainer”

The older scanners had two computers: MRIR (image reconstruction) and MPCU (measurement/physiological control). The new scanners combine these two computers into a single MARS (measurement and reconstruction). The MARS runs four processes that correspond somewhat to the old machines. The main thing is that the last option on the list is the image reconstruction process (MrIrisContainer). That's the thing to restart if you have an image reconstruction error. Restarting MrIrisContainer is quick compared to a 'reboot all' or 'reboot syngo' so it's worth trying before resorting to either of those (which take ~20 minutes).


"Meas & Recon" tab:

UConfigSvc (system configuration and logging) *should never have to reboot according to Himanshu
UTraceDaemon (system configuration and logging) *should never have to reboot according to Himanshu
MrMCIRContainer (MPCU part of the Mars)
MrIrisContainer (Image reconstruction part of Mars)

"Host" tab: *notes from Andre (should be confirmed with Siemens. he wasn't 100% positive for this version of the Siemens software.)

"Restart scanner"= MrMCIRContainer reboot is same as restart scanner. Anything besides image reconstruction error. Takes about 5 minutes. (even if says green arrow indicating system is up, processes it depends on still loading in background hardware.) Makes tok tok tok sound.

Restart syngo MR= reboot Syngo (all Siemens software. Platform everything runs on. Everything except Windows operating system.) no hardware.

Reboot= reboot operating system (software first) no hardware. *Andre doesn't recommend reboot because it takes just as long as "Shutdown all" but without cycling the power. You could reboot but that still doesn't work so then you have to redo it with "shutdown all" to cycle the power anyway so you might as well do it the first time. Also, you might not be able to do 'reboot' remotely because it might ask for password on the console computer but the vnc server is not up yet so you need to physically be at the scanner computer to type in the password.

Shutdown all= turns everything off (including hardware) and cycles the power. (usually takes ~30 minutes) To turn the system back on, you must physically press the blue button on the wall to the left of the scanner console computer. If you are monitoring the scanner remotely, you could press the shutdown all button before you head in to Martinos so it is powering down whi

ExvivoScanning (last edited 2018-12-31 12:14:46 by BramDiamond)