View source for 7T info R3

In june 2018, the R3 host was removed from the 7T. All information concerning R3 has been moved from the 7T pages to here.

== 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.


== 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:
[[Image:Compareprotocols.jpg|200px]]

==== 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 / too much power asked (coil needs >3800 Watts) ====
* B1 cannot be reached, lower value (to 17, 15 or lower, set to 15 in example below):
** Check Contrast --> B1 mode: change from Default to 15. 
** For T1, FLAIR, MP(2)RAGE and other scans with inversion pulses: check Contrast --> Inversion control: max B1 (uT). Set to same value as B1 mode (also 15).
** To find the detailed error message: Use logging application or log browser to query log file. Reported in log file as 'Average Forward Power Fault'. 
* One should try not the change the ref scales in System Tuning - however if you do, then keep the RATIO the same between the two ref scales for the two transmit channels (R5 Classic)!!!
* 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

==== Scanning stops after approximately 30 seconds ====
(this section needs polishing)

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

Monitored by PMU (Apwr). This is restrictive. Average power is IEC-regulated. Power is determined by drive scale.
PMU: current pmu limit 15watt.
Set in 2 files:
- mpgcoil_mtx_tr.i --> add to patch folder
  max_avg_pow: 20
		
compile in patch: mpghw_rf.res in methpdf. This results in a .i file that can be placed in the patch-directory.
		
HW_mid_max_avg_power:22;
  
and furthermore adjust in coil file
		
mpgcoil_volume_tr_mtx.i --> max_avg_pow = 20
mpgcoil_volume_tr.i
evt. source uit c:\nmr\gyroscan\config kopieren  (NIET OP C: AANPASSEN) naar G:\patch (moet in coil parameters terecht komen)
	
After completed scan, the measured power is logged, has to be lower than 1:
		FAP (forward average power) Transmit, measured FAP 1W, expected 2.28W, meas/exp=0.44
	
Scan with full-prep! B1-monitoring should be ~3500W for large angles.