7T general info & troubleshooting

Overview page for 7T related information

Table operation

• Important: move table to fully outer position before resetting or undocking
• Do not set the lights above level 3

Undocking/docking the table

Warning: not following the right undocking procedure will damage the equipment!

• When scanning with dualTx: Disconnect cables and remove interface boxes
• Pull table pins up (ensure they stay up)
• Undock

Resetting table / manual operation

In case the table operation does not respond:

• Press the in button longer (~5 seconds). After a while the table goes into some sort of stand by mode, a long press can wake it up again.
• Try stop/reset multiple times. Wait.
• 3-finger reset (takes 2 minutes). Wait. Repeated if needed.
• Undock table (follow procedure above). Wait 1 minute before docking.
• Manual undocking: switch at lower right hand of the magnet:
  • up: undock - careful: connector will come out of docking station!
  • center: ready to dock
  • down: dock(?)
• CDAS reset (see elsewhere on this wiki)

If table beeps, bed position is lost, probably caused by not resetting not in outer bed position. Press Stop. Pull bed out manually. Follow reset procedure above.

If all fails, the table can be pushed in manually:

• bed must be docked and connected.
• go to manual mode by pressing Stop: red lights on bore will turn on. Push the small safety handle/lever at the front bottom of the bed and push the bed in. Do this slowly!

The bed is in the iso-center when aligned which the edge of the bore / 2nd pencil line on the bed. In all cases, call support, and/or Anton/Cor from Philips. Explain what was scanned/happened beforehand and report date/time.

Switching between systems

Classic <-> MultiX

• Exit the scan environment of the system which was currently used
• Switch to other environment (using the switch next to scanner door)
• Shut down and reboot the host on the system which is going to be used
• Run logd: CDAS will boot up. This takes 5-10 minutes. Wait for message: humidity of examination room (or NOMEASPARS in the logging browser)
• Meanwhile, connect the proper coil/interface boxes

R5 <-> R3

• Ensure that system is in Classic mode
• shut down R5 and R3 hosts. (Do not power down MultiX host).
• manually disconnect and connect cables. Do not use force, especially with large Philips cable! Slightly wiggle up/down. Important: put network cables back in correct ports (X25/X26).
• power up the new host: power button is on the back of the cabinet: carefully right-hand turn the cabinet to easily reach the back side.
• Login and start logd. Meanwhile, the CDAS will boot up, this takes 5-10 minutes. Wait for message: humidity of examination room.
• Now start the Application software.
• Run a survey to ensure the system is functioning as it is supposed to.

System specific information

R5

Patches

Loading a patch:

• exit application software
• Start -> All Programs -> #PatchScripts# -> SmartPatch
• logd wait for processes to finish then start software

Installing patches: G:\Site\ClinicalScience\Put All Patches Here

General

• SmartPatch:
  • after switching patches, WAIT for loading all boards etc. before starting application software. Inspect PatchReadyCheck tool
  • do NOT manually copy/paste/delete files in G:\patch. This directory links to the installation folder and will affect the installed patch files
• Shimtool: pride-folder should be present in G:\patch to automatically start shimtool as PRIDE process

Classic (dualTx, R5B)

• Does NOT automatically scan SENSEref and CoilSurvey

MultiX

• Always have a classic host running for intercom communication
• SENSEref and CoilSurvey are automatically scanned whenever needed.

Tx testing: System Tuning --> Coil --> NOVA Head coil Transmit phases: 0, -45, -90, ..., -315 CCM-file, Datamonitoring tab --> CCM. Make screen shot when scanning.

MRCodetool

• B0 scan includes Exportdata pride tool
• start menu/desktop to open tool (installed in E:\Export\MRCodeTool)
• run unshimmed B0 to shim on

=> run B0shimming in MRCodeTool

• run shimmed B0 (for the B1 shim)
• FFE dyn scan (acquires FFE transmitting on each channel - output 8 images - input for B1 shimming)
• FFE quad scan (all 8 in quadrature - workaround for bug)
• B1 quad (B1 map (DREAM) - input for B1 shimming)

=> run RFshimming in MRCodeTool (minimizes standard deviation B1 over single (centre?) slice)

• in scans where you want to use the rf-shim, select contrast-rfshim-shimtool
• contrast-rfshim-predefined offers pre-calculated options (on models)

For SPINS pulses:

• B1map dyn (B1 map (DREAM leaving every run 1 channel out) - input for SPINS pulse calculation in addition to the above)
• Open the protocol you'd like to use your pulse in, change MTX pulse def id. to a non-used number (check on G:\Site\Waveforms)
• confirm that the protocol gives a conflict (non existing pulse)
• run SPINS module in MRCode
• confirm that protocol is no longer in conflict (pulse now exists)
• run scan

For MP2RAGE:

• load MP2RAGE protocol
• change end_rep_delay to desired value **NEEDS UPDATING**
• run MP2RAGE prot MRCode

Errors

• Error: Coil coupling matrix abnormal. Caused by scanning phantoms. Scan Control Parameters --> Preparation --> CCM switch off. Apply (Do NOT save). Revert back after finishing scanning phantom.

R3

usage

stop/start all processes (NB including data transfer!)

• permproc stop|start all stop|start all processes
• c:\nmr\gyroscan\commands\activate_configuration.pl. type y, Enter.
• start_stop_procs.pl stop also stops background processes. Needed in case of hardware reset in service room.

Communication with PRIDE (e.g. for image-based shimming):

• PrideXS_XML. In case of error Access denied, no SW key pressed, kill process pridexsproc_win_cs.exe in Task Manager.

Export raw data:

• System --> Advanced tools --> Delayed reconstruction. 'Select exam', type number of exam. Click 'Prev Scans'. 'Type 2'. Select 'Raw Export'. Now type the number of your series. Click Proceed. Type a number to save your series under. (Choose a different one for each series to avoid overwriting earlier ones). Type Enter/Proceed a few times. Now the scan is added to the scan list. You can add more series to reconstruct or continue, by clicking Start Scan and click Proceed.
• When finished click 'Exit' to release this scan to the scanner database again. Your data will appear under G:\Temp (sort by date to find it) as raw_00XX.list / raw_00XX.data where XX is the number you gave it earlier.
• Note that this doesn't work under the MISS patch (version oct 2015). You can, however, export raw MISS data by removing the patch and then following the steps described above.
• Alternatively use gt pack 'n go utility. This requires ReconFrame (which we don't have yet) and licensed matlab software to reconstruct raw data. Note that this tool does not export the same raw data format.

Location shim parameters:

• E:\Export\PRIDE\shimtool\linear_shim.txt

Manually selecting coil elements:

• Control Parameter Editor - Scan (approx 1/3, 6x clicking):
• User def. channel selection - yes
• at initial, Xmit Coil selection. choose 0.
• Dual coil - No. (2e surface coil off, independent selection per surface coil not possible)

Direct protocol comparison

• Export exam card with the protocols you want to compare.
• Do this:

Error creating thumbnail: File missing

Delayed Reconstruction

• User def element selection: yes
• selecteer elementen: waarde 1

Saving and loading configuration file

• MRService inloggen
• MR Applications - Service tools - Export configuration
• Enter (na afsluiten software)
• Choose 1 for internal disk to write to (I - make new folder (no spaces))
• As directory I fills up quickly, it's probably a good idea to replace the configuration directory that's already there.

• To reset configuration to previous : MR Applications - Service tools - Import configurations

Changed default settings

• Control parameter Reconstruction: Noise clip factor 1,2,3: 0.001. Avoids noise clipping of phase to -pi in case the SNR is too low.
• Go to System Tuning, Tuned Hardware. HIGH RF aux drive scale: 0.7915 en 0.8572. Philips Service tuned these parameters to 0.8542 en 0.9252. These values were reduced by sqrt(15%), this is because the logged power deviates from what the PMU (in the technical room) displays. The value can be read while the scanner is running a sequence. Setting stored by Maarten Versluis (2016-03-02), MV: updated calibrated DS.
• System Tuning -> Coil. Select Coil T/R-Vol-MTX (also Coil T/R-Vol?). Ref scales 1&2: default is 0.1884&0.1914. Adjust to 0.25

Patches

• Increased maximum average power to 20:
  • max_avg_pow: 20 in mpgcoil_volume_tr_mtx.i and mpgcoil_volume_tr.i, add file to patch folder to apply. Check Coil parameters and log file (search for PMU), check that system is not using the default value of 15!

Scanning sequences

• B1 mode: 17 uT (dus niet op default). 20 uT wordt bijna nooit gehaald in vrijwilligers (zie data monitoring), de fliphoek moet na PO groter dan 80 graden zijn!
• Preparation phases: full (dus niet auto). Bij auto wordt de pickup-coil drive scale gekozen, als de power optimization failed, wordt dit de default waarde plus safety margin = 0.19 + 25% = 0.23. Dit resulteert in half vermogen, dus halve B1!

Errors

Scan aborted after error or too much power asked (coil needs >3800 Watts)

• Use logging application or log browser to query log file.
  • Reported in log file as 'Average Forward Power Fault'. If that is the case:
    • B1 cannot be reached. Lower B1 (in Contrast tab) from Default to 17,15, 10, or even lower.
    • In case of TFE / MP(2)RAGE pre-pulse with custom B1 setting make sure to reduce this value as well!
• Coil parameters are not set correctly. Perhaps not added to a patch? Check settings above.

Not enough signal in PU phase

Read section Scanning sequences above and check sequence settings B1 mode and Preparation phase.

Check the drive scale (ref scale). Right mouse button on remaining scanning time -> System Tuning -> Coil. Select Coil T/R-Vol-MTX, Coil T/R-Vol. Ref scales 1&2: possibly are 0.1884&0.1914. Adjust to 0.25. Stepwise increase to 0.28 and 0.30 if problem persists.

Alternatively, you can turn off the pick up coil optimization by taking the following steps (however, this might have an effect on your data!):

• Select Control Parameter Editor
• Select the tab Preparation
• Select off for Pick up coil optimization
• Click apply

Scan aborts after 30 seconds

Average power is too high. Probably a scan with high SAR. Check that max average power is increased from 15 to 20 (see above).

Software

B1 shimming

• Export B1 as parrec and load in RFshimGUI
• Copy rfshims.dat from D: to G:\Site
• RF Shims: shimtool

MT B1 calibration scan scan UI --> full enables editing B1-scan parameters B1 field map: yes --> makes image instead of calibration scan

Text in log files: Reading G:\site\rfshims.dat am_scales=..., phases = 0 11

If RFshimGUI doesn't start (error: Undefined function or variable matlabrc), clear cache folder G:\Temp\Gyrotest\MCRCache

MultiX

Built-in RF shimming is (currently) done on the phase only: Relative Phase Nulling. The result is a phase difference, by which the coil transmit phases are adjusted. The scanner adds the RF shim angles (centered around 0) to Coil Tx phases. Search for "TransmitPhase" in the log file to find the shim results.

Manual shimming: Scan cycled FFE. Set Multichannel images: no (not supported by RFShimGUI). Export as PARREC

single B1+ maps. dyn relative B1 maps. Single Slice.

Hardware

Errors

No trigger

• Check if sync box on console pc has power (right LED green)
• Unplug/replug power.

• table
• coldhead compressors
• gradient amplifiers

No power in bed, won't dock, no 'air puffs'

• Probably no air pressure
• Check meters in cabinet at the back of CDAS (remove panel using imbus size 5)
• Pressure meters should look approx. like this: [picture to be uploaded]

No physiologic signals being logged

• Check if all sensors are plugged in, at least ECG!
• Check if ECG sensor has (working) battery
• If this is OK, switch CDAS off/on (after switching off host!)

Defect in shim gradients

Irregular 'cracking noise' in scanner room. Originates from shim rack.

Not all scanner functions available

Might have an error in shim gradients. For reset:

• Enter on the computer: "permproc stop scanner"
• Turn off the 3 switches (at the bottom) of the shim gradients in the technical room. Turn off in following order: Left, right, middle and wait a couple of seconds
• Turn on the 3 switches in reversed order
• Enter on the computer: "permproc start scanner"

Power off and power on sequence(s)

CDAS

• exit scanner application software
• stop all processes/services: start_stop_procs.pl stop (easier than shutting down host)
• Reset CDAS: turn off green switch. Wait 5 seconds.
• Turn red switch.
• Unplug sense-cable (on top, labeled with red arrow, this will reset/enable bore light). Wait 5 seconds.
• Turn on in reverse order: red switch and green switch.
• Wait for bed-lights (top) to turn green. Now plug in the sense-cable (red arrow). This controls bore light.
• At bed console, set light to 50%.
• start all processes/services: start_stop_procs.pl start
• wait, then start application software

Main System

• A printed copy of the instructions are in right mains cabinet in technical room.

Compressors

Procedure testing/resetting compressors Helium pump: 2 small cubic devices in the far right corner. The green light on the left device should be flashing. Check messages on small LED-displays: scroll with arrow up/down buttons. Should all be OK, not ERR. Temperature of tubes should be below room temperature (i.e. cold). To reset: press OFF. You should hear it switching off. Wait, and press ON, again hearing it switching on. To hard reset: Press OFF. Wait. Turn small black switch from I to O. Wait. Turn back to I. Wait. Important: press ON to turn the compressor back on.

Patient ventilation system

Box hanging the CDAS rack. Turn off by unplugging 220V cable.

Coil-specific tips 'n tricks

Microcoils MR Coils (surface coils)

• acquire B0 not with commonly used pickup coil elements but instead the surface coil elements. The Shimtool should apply mask to area with signal only
• connect the two surface coils mixed on the two interface boxes, not one separately on each box

BOLD screen

Turn on by connecting the power cable in the black adapter in the technical room. Turn off after use! The visibility range in the vertical direction is from -4 to +3 on the desktop image. This means that at the top ~10% of the screen cannot be used.

Contact information

Philips contacts (?)

Cor Romeijn: 06 22489509 Anton Heijmans: 06 22491918 Maarten Versluis: 06 11386561 Philips service: 040 7001210

AMC Contacts

During office hours, contact front office on phone number 88, option 2 Regelkamer: 62900 (outside office hours) Ed de Klerk: 06-30005770 Tom Emke: 020-5662305, 06-22452389 Roelofsen: 68103

QA

Run QA on Classic R5.

FID QA measurements

This procedure repeatedly measures the 8th sample of a pulse-acquire FID measurement, using proton and multi-nuclei amplifiers, with and without gradients. Creator: Paul Sanders, Philips

• Position blue phantom sphere in center of 32ch head coil, use holder. Make sure the phantom is centered.
• Remove any installed patch
  • The application software might not show that there is a patch active, but if the 'G:\Patch\' folder contains files, there is a patch installed.
  • Open SmartPatch and press 1. This will take a while.
• Perform a prescan : QA\QA_FID_Survey
  • Scan a survey. Click OK on the following message: 'Cannot determine optimum RF power'.
• Application software can be on, but list of planned scans must be empty.

Scanning procedure

• double click G:\TA\Testscripts\sc_fids\start_fid_stability_*.bat to start scanning. A command window appears. Be patient, don't close windows. Batch Interpreter window appears and disappears. After 2 minutes, turn on patient communication to verify that you here repeating 'ticks'.
• After approx. 5 minutes a PlotServer window appears with results. During scanning, more tabs/pages with results appear. Scanning finishes after ~20 minutes. In command window it says: 'press any key to continue'. Click space bar, this ends the measurement.

PlotServer

• In each tab/result window, right mouse click (anywhere) --> reset.
• Tab1 Mod profile: shows FID for all measurements
• Other tabs plot the repeated 8th sample of FID for all 32 channels. Horizontal axis: repeated measure (512 or 1024). 150ms between measurements.
  • measurement 250-275: programmed 1% lower signal as a reference
  • first 16: box A (lower). last 16: box B. (border between magenta/purple and cyan/lightblue)
  • Gr=true/false: gradients on/off. MN (multi-nuclei) or PR (proton) amplifier.

Save output

• Copy folder G:\TA\fid_stab\7t-acq_DATE to S:\7T_QA\FID (\\ftpsc\DATA\scdropbox\7T_QA\FID)
• Zip output folder: right-mouse button, 7-Zip->Add to 7t-acq-DATE.zip
• Delete output-folder G:\TA\fid_stab\7t-acq_DATE

Offline processing

to make QA plots: Start MATLAB (e.g. on ftpsc) and run matlab-script scdropbox/7T_QA/FID/software/fid/fid_stab_viewer_v4.m. A file prompt appears, open one .txt file in the output folder. Now all plots for all output-files in this directory are generated.

Various

• software is installed in G:\TA (Ruby language, .rb files)
• double click G:\TA\Ruby193\start_ruby193*.bat to start Ruby

• sc_fid_stability_r5_v1.rb
  • lines 21:24: (Only_grad_switching) true: run with gradient switching. false: one times without, one time with gradients.
  • Start_pr_rf_amp: first PR then MN amplifier. false: start with MN
  • repeat_per_tests --> 1024

• sc_fid_stability_r5_v1.rb
  • lines 292 pulse-acquire scan
  • 300-307: add gradient blocks (objects are removed based on only_grad_switching setting)
  • 308 RF0 RF-pulse
  • 309 AQ0 acquire FID signal

load files to view/verify:

• (drag G:\TA\Testscripts\sc_fids\start_fid_stability*.bat into Ruby window (not so interesting))

Logbook

20161011 MC: MN with gradients 3rd channel: spurious spikes of 1%