Difference between revisions of "MNE CPP on Neuromag Linux"

From MNE-CPP Wiki
Jump to: navigation, search
(Created page with "<pre style="color: red"> Warning: You should know what you are doing and be familiar with the Neuromag system! </pre> == Pre-Requisites == === Qt 5 === ./configure -no-x...")
 
 
(9 intermediate revisions by the same user not shown)
Line 3: Line 3:
 
</pre>
 
</pre>
  
−
== Pre-Requisites ==
+
== Setup mne_rt_server ==
 +
The following steps are to be performed on the Neuromag PC.
 
=== Qt 5 ===
 
=== Qt 5 ===
  
−
    ./configure -no-xcb -no-eglfs -no-directfb -no-linuxfb -no-kms -no-glib -no-gui -no-widgets -no-opengl -no-openssl -opensource -nomake examples -prefix /home/neuromag/RT_MNE_CPP/Qt/Qt5.3.0
+
<source lang=cpp>
−
    make
+
./configure -no-xcb -no-eglfs -no-directfb -no-linuxfb -no-kms -no-glib -no-gui -no-widgets -no-opengl -no-openssl -opensource -nomake examples -prefix /home/neuromag/RT_MNE_CPP/Qt/Qt5.3.0
 +
make
 +
</source>
  
 
It's likely that following error occurs:
 
It's likely that following error occurs:
Line 14: Line 17:
 
You can fix this error by replacing following line in src/corelib/thread/qmutex_linux.cpp
 
You can fix this error by replacing following line in src/corelib/thread/qmutex_linux.cpp
  
−
    # include <linux/futex.h>
+
<source lang=cpp>
 +
# include <linux/futex.h>
 +
</source>
  
 
with
 
with
  
−
    # define FUTEX_WAIT 0
+
<source lang=cpp>
−
    # define FUTEX_WAKE 1
+
# define FUTEX_WAIT 0
 +
# define FUTEX_WAKE 1
 +
</source>
  
 
You can ignore further Qt5 build errors. Since only qmake and the most important libraries are needed.
 
You can ignore further Qt5 build errors. Since only qmake and the most important libraries are needed.
 
Finish the installation with:
 
Finish the installation with:
  
−
    make install
+
<source lang=cpp>
 +
make install
 +
</source>
  
 
=== MNE-CPP ===
 
=== MNE-CPP ===
 
==== Download MNE-CPP ====
 
==== Download MNE-CPP ====
  
−
Edit _mne-cpp.pri_ by commenting _withGui_ out:
+
Navigate to the mne-cpp repository and run:
  
−
    #MNECPP_CONFIG += withGui
+
<source lang=cpp>
−
 
+
qmake mne-cpp.pro MNECPP_CONFIG+=minimalVersion MNECPP_CONFIG+=noExamples MNECPP_CONFIG+=noTests
−
run:
+
make
−
    qmake -r
+
</source>
−
    make
+
  
 
==== Edit .bashrc ====
 
==== Edit .bashrc ====
 
After you compiled mne-cpp succesfully edit your .bashrc to make the shared libraries globally available:
 
After you compiled mne-cpp succesfully edit your .bashrc to make the shared libraries globally available:
  
−
    #
+
<source lang=cpp>
−
    # Qt
+
#
−
    #
+
# Qt
−
    export QT_HOME=/home/neuromag/RT_MNE_CPP/Qt/Qt5.3.0
+
#
−
    if [[ $QT_HOME && ${QT_HOME-_} ]]; then
+
export QT_HOME=/home/neuromag/RT_MNE_CPP/Qt/Qt5.3.0
−
        PATH=$PATH:$QT_HOME/bin
+
if [[ $QT_HOME && ${QT_HOME-_} ]]; then
−
        if [[ $LD_LIBRARY_PATH && ${LD_LIBRARY_PATH-_} ]]; then
+
    PATH=$PATH:$QT_HOME/bin
−
            LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$QT_HOME/lib
+
    if [[ $LD_LIBRARY_PATH && ${LD_LIBRARY_PATH-_} ]]; then
−
        else
+
      LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$QT_HOME/lib
−
            export LD_LIBRARY_PATH=$QT_HOME/lib
+
    else
−
        fi
+
      export LD_LIBRARY_PATH=$QT_HOME/lib
 
     fi
 
     fi
 +
fi
 
      
 
      
−
    #
+
#
−
    #  MNE-CPP
+
#  MNE-CPP
−
    #
+
#
−
    export MNE_CPP=/home/neuromag/RT_MNE_CPP/Git_Repos/mne-cpp
+
export MNE_CPP=/home/neuromag/RT_MNE_CPP/Git_Repos/mne-cpp
−
    if [[ $MNE_CPP && ${MNE_CPP-_} ]]; then
+
if [[ $MNE_CPP && ${MNE_CPP-_} ]]; then
−
        PATH=$PATH:$MNE_CPP/bin
+
    PATH=$PATH:$MNE_CPP/bin
−
        if [[ $LD_LIBRARY_PATH && ${LD_LIBRARY_PATH-_} ]]; then
+
    if [[ $LD_LIBRARY_PATH && ${LD_LIBRARY_PATH-_} ]]; then
−
            LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MNE_CPP/lib
+
        LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MNE_CPP/lib
−
        else
+
    else
−
            export LD_LIBRARY_PATH=$MNE_CPP/lib
+
        export LD_LIBRARY_PATH=$MNE_CPP/lib
−
        fi
+
 
     fi
 
     fi
 +
fi
 +
</source>
  
 
==== Firewall Configuration ====
 
==== Firewall Configuration ====
 
Open port 4217 & 4218 and add allowed clients by editing /etc/sysconfig/iptables. Insert the following:
 
Open port 4217 & 4218 and add allowed clients by editing /etc/sysconfig/iptables. Insert the following:
  
−
    -A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 4217 -j ACCEPT
+
<source lang=cpp>
−
    -A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 4218 -j ACCEPT
+
-A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 4217 -j ACCEPT
−
    -A RH-Firewall-1-INPUT -s ip.of.your.client -m tcp -p tcp --dport 4217 -j ACCEPT
+
-A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 4218 -j ACCEPT
−
    -A RH-Firewall-1-INPUT -s ip.of.your.client -m tcp -p tcp --dport 4218 -j ACCEPT
+
-A RH-Firewall-1-INPUT -s ip.of.your.client -m tcp -p tcp --dport 4217 -j ACCEPT
 +
-A RH-Firewall-1-INPUT -s ip.of.your.client -m tcp -p tcp --dport 4218 -j ACCEPT
 +
</source>
  
−
=== run _mne_rt_server_ ===
+
== Connect the Neuromag System with MNE Scan ==
−
If all previous steps were successfully processed you are now able to run _mne_rt_server_ - well done :)!
+
The following steps are to be performed both on the Neuromag and Client PC.
 +
 
 +
=== Step by Step Guide ===
 +
#Setup Neuromag PC:
 +
## Open console, type <source lang=cpp>mne_rt_server</source> and hit enter (use this console to wathc the mne_rt_server work and receive commands from the client)
 +
## Open second console, type <source lang=cpp>telnet <ip.of.megacq> collector</source> (use this console to restart and change variables of the MEG system).
 +
### When asked for password type in "pass <your password>" and hit enter.
 +
### Type in <source lang=cpp>STAT</source> to view the current status of the MEG machine. This should give you a message saying that the collectors are setup. If not get help to set the collectors up.
 +
### Type in <source lang=cpp>VARS</source> and note down the values of maxBuflen and sFreq (these values get overwritten by MNE Scan). This is IMPORTANT!
 +
## Find out IP adress of the Neuromag PC (this is NOT the IP shown by the mne_rt_server in the console window) and note it down somewhere.
 +
## Check if ports 4217 and 4218 are open and if the client is allowed to connect. If not see the Firewall Configuration steps above.
 +
# Setup MNE-CPP PC:
 +
## Try to ping the Neuromag PC from the MNE-CPP PC
 +
### Open cmd console
 +
### Type in <source lang=cpp>ping <Neuromag PC IP address></source> (this is the IP address you noted down above).
 +
## If pinging was successful start MNE Scan and drag the Neuomag plugin onto the plugin stage.
 +
## Change to the Connection tab. There you should find the connected satuts. If not you made something wrong!
  
 
== Hints ==
 
== Hints ==
 +
=== Use Cases ===
 +
* MNE Scan crashed:
 +
*:# Close down MNE Scan
 +
*:# Switch to the Neuromag PC
 +
*:# Hit Ctrl+C in the mne_rt_server console
 +
*:# Restart the mne_rt_server by typing <source lang=cpp>mne_rt_server</source>
 +
*:# Type <source lang=cpp>STOP</source> into the Collector console to stop the measurement system
 +
*:# You are all set and ready for antoher try!
 +
* Change the blocksizes of the incoming data:
 +
*:* Changing the block size is only possible by recompiling the mne_rt_server with a different initialized value in /connectors/neuromag/neuromag.cpp
 +
 
=== The collectors ===
 
=== The collectors ===
 
You can use telnet to monitor the interaction of _mne_rt_server_ with the neuromag machine:
 
You can use telnet to monitor the interaction of _mne_rt_server_ with the neuromag machine:
−
Therefor connect to the collectors running on the real-time computers:
+
Therefore connect to the collectors running on the real-time computers:
  
−
    telnet megacq collector
+
<source lang=cpp>
 +
telnet megacq collector  
 +
</source>
  
 
or
 
or
  
−
    telnet ip.of.megacq 11122
+
<source lang=cpp>
 +
telnet ip.of.megacq 11122
 +
</source>
  
 
Authorize your self:
 
Authorize your self:
−
    PASS ***
+
 
 +
<source lang=cpp>
 +
PASS ***
 +
</source>
  
 
Check the status by typing (They should be setup but not measuring. If this is not the case run a simple dummy project using the neuromag acqusition software, afterwards they will be setup.):
 
Check the status by typing (They should be setup but not measuring. If this is not the case run a simple dummy project using the neuromag acqusition software, afterwards they will be setup.):
−
    STAT
+
 
 +
<source lang=cpp>
 +
STAT
 +
</source>
  
 
Check the values of the variables by typing:
 
Check the values of the variables by typing:
−
    VARS
+
 
 +
<source lang=cpp>
 +
VARS
 +
</source>
  
 
Save the variables in a text file and make sure that they are the same after you have finished (your colleagues will appreciate this)
 
Save the variables in a text file and make sure that they are the same after you have finished (your colleagues will appreciate this)
  
 
You can change variable names by typing
 
You can change variable names by typing
−
    VARA ``<var> = <value>``
+
 
 +
<source lang=cpp>
 +
VARA ``<var> = <value>``
 +
</source>
  
 
Switch on the monitoring to follow all interactions with the real-time computers:
 
Switch on the monitoring to follow all interactions with the real-time computers:
−
    MONI ON
+
 
 +
<source lang=cpp>
 +
MONI ON
 +
</source>
  
 
You can start the acqusition manually with:
 
You can start the acqusition manually with:
−
    MEAS
+
 
 +
<source lang=cpp>
 +
MEAS
 +
</source>
  
 
And stopping it again with:
 
And stopping it again with:
−
    STOP
+
 
 +
<source lang=cpp>
 +
STOP
 +
</source>
  
 
All available commands you'll find by typing:
 
All available commands you'll find by typing:
−
    HELP
+
 
 +
<source lang=cpp>
 +
HELP
 +
</source>
  
 
You can leave the collectors by typing:
 
You can leave the collectors by typing:
−
    QUIT
+
 
 +
<source lang=cpp>
 +
QUIT
 +
</source>
  
 
=== Neuromag Acqusition ===
 
=== Neuromag Acqusition ===
  
−
It's recommended to start the Neuromag Acquisition program. The software will be remotely controlled by MNE-X since the collectors mirror the instructions received. You can use the Neuromag data display to check your MNE-X measurements.
+
It's recommended to start the Neuromag Acquisition program. The software will be remotely controlled by MNE Scan since the collectors mirror the instructions received. You can use the Neuromag data display to check your MNE Scan measurements.

Latest revision as of 21:45, 21 March 2018

Warning: You should know what you are doing and be familiar with the Neuromag system!

Setup mne_rt_server

The following steps are to be performed on the Neuromag PC.

Qt 5

./configure -no-xcb -no-eglfs -no-directfb -no-linuxfb -no-kms -no-glib -no-gui -no-widgets -no-opengl -no-openssl -opensource -nomake examples -prefix /home/neuromag/RT_MNE_CPP/Qt/Qt5.3.0
make

It's likely that following error occurs: Futex Error (RHEL 5.1 with gcc 4.1.2 compiler)

You can fix this error by replacing following line in src/corelib/thread/qmutex_linux.cpp 

# include <linux/futex.h>

with 

# define FUTEX_WAIT 0
# define FUTEX_WAKE 1

You can ignore further Qt5 build errors. Since only qmake and the most important libraries are needed. Finish the installation with: 

make install

MNE-CPP

Download MNE-CPP

Navigate to the mne-cpp repository and run: 

qmake mne-cpp.pro MNECPP_CONFIG+=minimalVersion MNECPP_CONFIG+=noExamples MNECPP_CONFIG+=noTests 
make

Edit .bashrc

After you compiled mne-cpp succesfully edit your .bashrc to make the shared libraries globally available: 

#
# Qt
#
export QT_HOME=/home/neuromag/RT_MNE_CPP/Qt/Qt5.3.0
if [[ $QT_HOME && ${QT_HOME-_} ]]; then
    PATH=$PATH:$QT_HOME/bin
    if [[ $LD_LIBRARY_PATH && ${LD_LIBRARY_PATH-_} ]]; then
       LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$QT_HOME/lib
    else
       export LD_LIBRARY_PATH=$QT_HOME/lib
    fi
fi
 
#
#  MNE-CPP
#
export MNE_CPP=/home/neuromag/RT_MNE_CPP/Git_Repos/mne-cpp
if [[ $MNE_CPP && ${MNE_CPP-_} ]]; then
    PATH=$PATH:$MNE_CPP/bin
    if [[ $LD_LIBRARY_PATH && ${LD_LIBRARY_PATH-_} ]]; then
        LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MNE_CPP/lib
    else
        export LD_LIBRARY_PATH=$MNE_CPP/lib
    fi
fi

Firewall Configuration

Open port 4217 & 4218 and add allowed clients by editing /etc/sysconfig/iptables. Insert the following: 

-A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 4217 -j ACCEPT
-A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 4218 -j ACCEPT
-A RH-Firewall-1-INPUT -s ip.of.your.client -m tcp -p tcp --dport 4217 -j ACCEPT
-A RH-Firewall-1-INPUT -s ip.of.your.client -m tcp -p tcp --dport 4218 -j ACCEPT

Connect the Neuromag System with MNE Scan

The following steps are to be performed both on the Neuromag and Client PC.

Step by Step Guide

  1. Setup Neuromag PC:
    1. Open console, type 
      mne_rt_server
      and hit enter (use this console to wathc the mne_rt_server work and receive commands from the client)
    2. Open second console, type 
      telnet <ip.of.megacq> collector
      (use this console to restart and change variables of the MEG system).
      1. When asked for password type in "pass <your password>" and hit enter.
      2. Type in 
        STAT
        to view the current status of the MEG machine. This should give you a message saying that the collectors are setup. If not get help to set the collectors up.
      3. Type in 
        VARS
        and note down the values of maxBuflen and sFreq (these values get overwritten by MNE Scan). This is IMPORTANT!
    3. Find out IP adress of the Neuromag PC (this is NOT the IP shown by the mne_rt_server in the console window) and note it down somewhere.
    4. Check if ports 4217 and 4218 are open and if the client is allowed to connect. If not see the Firewall Configuration steps above.
  2. Setup MNE-CPP PC:
    1. Try to ping the Neuromag PC from the MNE-CPP PC
      1. Open cmd console
      2. Type in 
        ping <Neuromag PC IP address>
        (this is the IP address you noted down above).
    2. If pinging was successful start MNE Scan and drag the Neuomag plugin onto the plugin stage.
    3. Change to the Connection tab. There you should find the connected satuts. If not you made something wrong!

Hints

Use Cases

  • MNE Scan crashed:
    1. Close down MNE Scan
    2. Switch to the Neuromag PC
    3. Hit Ctrl+C in the mne_rt_server console
    4. Restart the mne_rt_server by typing 
      mne_rt_server
    5. Type 
      STOP
      into the Collector console to stop the measurement system
    6. You are all set and ready for antoher try!
  • Change the blocksizes of the incoming data:
    • Changing the block size is only possible by recompiling the mne_rt_server with a different initialized value in /connectors/neuromag/neuromag.cpp

The collectors

You can use telnet to monitor the interaction of _mne_rt_server_ with the neuromag machine: Therefore connect to the collectors running on the real-time computers: 

telnet megacq collector

or 

telnet ip.of.megacq 11122

Authorize your self: 

PASS ***

Check the status by typing (They should be setup but not measuring. If this is not the case run a simple dummy project using the neuromag acqusition software, afterwards they will be setup.): 

STAT

Check the values of the variables by typing: 

VARS

Save the variables in a text file and make sure that they are the same after you have finished (your colleagues will appreciate this)

You can change variable names by typing 

VARA ``<var> = <value>``

Switch on the monitoring to follow all interactions with the real-time computers: 

MONI ON

You can start the acqusition manually with: 

MEAS

And stopping it again with: 

STOP

All available commands you'll find by typing: 

HELP

You can leave the collectors by typing: 

QUIT

Neuromag Acqusition

It's recommended to start the Neuromag Acquisition program. The software will be remotely controlled by MNE Scan since the collectors mirror the instructions received. You can use the Neuromag data display to check your MNE Scan measurements.

Retrieved from "http://wiki.mne-cpp.org/index.php?title=MNE_CPP_on_Neuromag_Linux&oldid=449"