• ExvivoScanning

Index

Exvivo Scanning

Important Notes

• All bay 5 high res scans should use Andre's fixed sequence: gre_mgh_multiecho_7T and not gre_mgh_multiecho. The streaming scans may use a different sequence.
• When setting up multi-channel coils using the 8 channel interface box, skip channel 6 and plug into a different channel, if possible. Channel 6 is noisy.
• All existing protocols should have Autoscale checked (except for streamed scans that have the raw data saved). It's in the Special Tab. It will save your data with the selected FFT and a version that is autoscaled.
• All existing protocols should be set to Low Gain mode in the Special tab. It does not matter if you set it to High Gain in the System/Transmitter Tab. The Low Gain box in the Special Tab overrides it.
• Record COFmag in binder as well as COVmag.
• A coil must be plugged in to reboot the scanner.

Ex vivo Coils

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

Scan Times/Protocols

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 run (more if can fit it)
TOTAL: 11.75 hrs

OR
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 = ? mins
750um diffusion 10.25 hrs x 3 runs (1 run is okay if that's all we can fit)
TOTAL: ~38 hours

Bay 6 Whole Brain Diffusion (Allen Adult)

1mm meflash 20 min x 6 flips x 1 run = 2 hrs
T2space 6 min x 1 run
diffusion 16 hrs x 1 run (more if can fit it)
TOTAL: 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
TOTAL: approx 60 hrs (depending on FOV)

Bay 5 MT circ coil scan

Monitoring Helium

You can see the current helium level here

Basic How Tos

Calculating size of scan output

base resolution^2 x 2 oversampling x phase (.##) x # slices per slab x # channels x # of echoes x # of segments x 4 bytes x 2 for complex / 1024 KB / 1024 MB /1024 GB

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.

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.

• Hit Ctrl+Esc on the keyboard to bring up Windows Menu.

• Choose Run and enter twix, then click OK

• Find scan you want to fix in list on left sidebar (1). Click on it. Click on the RetroRecon icon (2).

• A small grey rectangle will pop up at the bottom of that window. Click on Edit (3).

• A window will pop up. Hit Ctrl+f to search (or click (4)) and enter Additional to search for location of flAdditonalScaleFactor section.

• Change the flAdditonalScaleFactor field value to the new FFT Scale Factor you want to have (5). (i.e. If FFT was set to 10 but the max intensity was 4,000, in order to get it down to 2,000 change it to 1).

• Go to File > Save and close the window.

• In the grey rectangle, click on the Start button (6).

• Wait until a green checkmark appears in the box to the right of the Start button. Once this appears, you can close twix. You will find the RetroRecon of this scan at the bottom of the list in the Patient Browser under your study.

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

• To check if the FFT is too low or too high, drag your scan into the Viewing Window.

• Go to Tools and choose either Circle or Rectangle depending on what shape will be easiest to get around the full sample.

• Draw the circle or rectangle around your entire sample (without too much background included).
• Numbers will pop up. At the top, there will be a Min and a Max. The Max should be around 2,000. If it is significantly low (14-800), you need to increase the FFT Scale factor. If it is significantly high (4,000), you need to decrease the FFT Scale factor.

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.

• Click on the folder or scan you want to change in the Patient Browser.

• Choose Edit from the menu.

• Choose Correct and hit 'Yes' when it says "Non-local data involved. Do you really want to continue?"

• Change the name or any other details you want to change and hit OK. You should see the change in the Patient Browser.

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):

• Field of View (Read, Phase FOV %)
• Number of partitions (3D slices)
• Bandwidth
• Matrix size
• Phase encode direction
• Orientation (slab orientation, in-plane rotation if any)
• shim boxes should match exactly (normally locked to imaging slab so will automatically match)
• Any partial field of view settings (partial phase field of view)

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

• if trying to get bandwidth down but won't go down, turn off apply echo spacing,put contrasts to 1 and then decrease bw. increase contrasts back up to what you want.
• to get the echo spacing back on, subtract TE2 from TE1. increase/decrease the echo spacing to this number. check apply echo spacing. If you don't want the TE ending so different from the original protocol you can decrease the delta echo spacing.
• When you decrease bandwidth the readout gets longer hence you had to increase the echo spacing (bandwidth is proportional to sampling frequency, readout length is proportional to sampling period, frequency inversely proportional to period). delta echo spacing can be changed to whatever until future tests reveal the optimal amount
• If you want to change Base Resolution and it won't let you, increase bandwidth to be able to increase Base Resolution.

Copy center of Slices and Sats

It copies for each slice:

• Field of view
• Center position
• Orientation
• Partial field of view settings

and for everything:

• Phase encode direction
• Shim box position and orientation

Troubleshooting

Frequence Cannot Adjust

Temperature Warnings/Errors

During the diffusion scans you may get the following errors:

• ACS warning, Supply water temperature is too high, please call Siemens service

• SEP warning, SEP primary water temperature out of limits. Please call Siemens Service

• SEP warning, SEP secondary water temperature out of limits. Please call Siemens Service

These warnings above are all fine and the scan will continue, if possible you need to open the cabinet doors in the room behind bay 5 to allow for cooling otherwise the scan will stop when it gets to the warning below:

• acs error acc cabinet air return temperature above alarm level

Bay 5: 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 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.

Image Reconstruction System Error After Bay 5 Diffusion Scans

If you see the following error after running diffusion, "Not all images could be made persisten 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 Frequecy 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 'Frequecy' 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 incase you happen to see this in other coils as well.

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 Frequency tab, 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

In bay 2

When opening up an appended scan to apply (and maybe change the contrast/flip angle as well) you may receive an uninitialized error telling you that some change you just made will be reverted back to its previous state. You will need to remove completed scans from the queue (except the localizer) in order to open up, change the contrast, and apply a scan. Be sure to append any scans you will need more than one run of before deleting the completed run from the queue. The uninitialized error typically emerges once you have 4-5 scans queued up.

If you do not need to make any changes to the scan, then just right-click on the scan and hit 'm' for complete. When that scan is about to start you will most likely see the following error:

To fix this. Click OK, double-click the scan to open it. An uninitialized error window will pop up, hit OK, and then click cancel as opposed to apply. The scan should then begin.

In bay 5

In bay 5, the above error often happens when the scan queue has over 20 items. This is due to the computer thinking it doesn't have enough memory to run your scans and so this error pops up. The error usually only pops up when you open a protocol that is in the scan queue. 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, 2) try to avoid opening protocols after scanning has been going for awhile; use append and complete (by right clicking on the scan); 3) save the protocols you will need to run with all parameters already set in the protocol folder 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. If opening a protocol is unavoidable but you are receiving this error, you can try deleting more things from the queue or try appending that run from earlier parts or different scans in the queue (which oddly works sometimes). 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?).

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.

===Gradient error in Bay 6===