Pulse Programming

Preamble

  • This is just a summary to get you started. Lots of info is on the CFMM wiki (Ask Corey for link).
  • idea/midea project wiki has helpful information for pulse programming. Need to be added to idea group to access (not necessary unless you’ll be modifying code).

Virtual Box Installation (3T and 7T)

  • Pulse sequence programming will require virtualbox
  • set up so that ubuntu automatically updates current version
    • For Ubuntu, Debian-based Linux distributions in https://www.virtualbox.org/wiki/Linux_Downloads)
  • to update to next version, use (where XXX is the version number, like 5.2): 
    sudo apt-get update
sudo apt-get install virtualbox-XXX

VMware Player Installation (Bruker)

  • Download latest version of VMware Workstation Player (should be a .bundle file for linux)
  • navigate to folder it downloaded to using terminal 
    chmod u+x FILENAME.bundle
sudo ./FILENAME.bundle

Bruker, Paravision360 (9.4T and 15T)

Misc info

  • You’ll need to be added to the idea/midea project users to download the virtual machine (Ask Corey).

    Getting Started

  • Install VMware (see above)
  • Go to https://idea.cfmm.uwo.ca -> login in with UWO -> click Downloads -> click bruker -> download latest version (*.ova file)
  • Open VMware -> “Open a virtual machine” -> select *.ova file downloaded above -> follow prompts
  • Open virtual machine.
  • FIRST TIME setup
    • Set git config --global user.name "your name here" and git config --global user.email yourmail@uwo.ca
    • Do ssh-keygen and follow instructions on gitlab to add a key.
    • Create a shared folder, which makes it easy to transfer files between host PC and VM
      • Open “virtual machine settings” after VM has started
      • Selection Options tab -> select Shared Folders
      • Click “Enabled until next power off or suspend” (Note: I haven’t had luck with “Always Enabled”)
      • Click Add… and follow the prompts
      • The share will be mounted in /mnt/hgfs/SHARENAME
  • start machine (PW = paravision)
  • open paravision from the desktop (on the virtual machine)
  • First time: need to create a coil configuration
    • NOTE: may not be needed for pv 360
      • Window->configuration->select coil tab->second click on “Coil Configurations” folder -> “Create default coil configurations”
      • second click on “generic transciever 1H” -> save
  • Starting a study
    • open dataset browser window if not open already
    • “Add study…”
      • may need to select an rf coil config you made earlier
      • “Create”
    • Double click on study (can open one from another time too)
    • In Palette, Explorer tab
      • In Application menu, select user methods
      • Drag into white box
      • Change parameters etc
      • To simulate, click on 3rd box from left above list of scans
        • click on GOP simulation tab
        • click start
        • change to “Bruker Topspin” window (bottom bar in the operating system)
  • Never suspend a virtual machine while Paravision is running

    Sequence location

  • Your sequence folder should be in /opt/PV360.3.5/prog/curdir/nmrsu/ParaVision/methods/src/ (Folder name matches the PV version)

    Compiling your sequence

  • You should see your pulse sequence folder in Workspace Explorer tab -> Method Development -> User Methods
  • 2nd click, and choose Build/Install

    Exporting your modified sequence

  • In Workspace Explorer, 2nd click on pulse sequence folder and select Share -> As Source
  • It will get exported to /opt/PV/share (replace with whatever paravision version you're running)

    Tips

  • Sometimes, after a successful compile, the sequence does not show up in the Palette explorer. Closing and reopening Paravision has fixed this for me.
  • need #DEFINE DEBUG 1 in your .c file for printf and db_msg commands to show up on the parx server tab in paravision
  • The file explorer in the VM OS does not seem to update files reliably. If the files are not showing up, click Control -> refresh.

Siemens 3T

Getting Started

  • Install Virtual Box (see above for instructions; can also just download )
  • In VBox: File->Preferences->General Tab, then change Default Machine Folder to where ever you want your virtual machines stored (imported machines will go there)
  • Go to https://idea.cfmm.uwo.ca -> login in with UWO -> click Downloads
    • Need VE11C and mars_VE11C
  • Follow the directions at https://git.cfmm.uwo.ca/cfmm/info/-/wikis/siemens_idea
  • run cmd as administrator in VE11C VM, and from there run net accounts /maxpwage:unlimited
    • see https://git.cfmm.uwo.ca/idea/MIDEA/-/wikis/tips#expired-passwords for more details.
  • Install “git for windows”.
    • Use the “as-is” settings during install (one of the selection boxes. not enabled by default)
      • Very important for updating the baseline
      • WARNING: if you change the code on linux, this could change the line endings depending on the git settings there. Best to code only in the windows VM.

        Setup for Pulse Programming

  • should get Martyn to add you to the idea group on CFMM gitlab
  • Update git name and email:
    • Open git bash from start menu and enter: 
      git config --global user.name FIRSTNAME LASTNAME
git config --global user.email name@uwo.ca
  • Follow instructions in Idea->MIDEA->Wiki->git to set up ssh key. In short:
    • run “ssh-keygen” in git bash, from within home directory
    • press enter to use the default filename
    • enter a password that you’ll remember
    • copy the contents of id_rsa.pub to ssh keys section on cfmm gitlab site
  • pull baseline code updates from idea > VE11C. Open git bash, then: 
    cd /c/midea
git clone git@git.cfmm.uwo.ca:idea/VE11C.git baseline
cp -r baseline/.git N4_VE11C_LATEST_20160120/.git
rm -rf baseline
cd N4_VE11C_LATEST_20160120
git checkout .

    Specific Sequence Setup

  • fpcali (used for calibration of field probes)
    • open git bash 
      cd /c/midea/N4_VE11C_LATEST_20160120/n4/pkg/MrServers/MrSpecAcq
mv fid fid_old
git clone git@git.cfmm.uwo.ca:baron-lab/girf_fid_ve11c.git fid
cd fid
git checkout fpcali
  • ep2d_baron
    • fpcali must already have been setup
    • open git bash 
      cd /c/midea/N4_VE11C_LATEST_20160120/n4/pkg/MrServers/MrImaging/Seq
mv a_ep2d_diff a_ep2d_diff_old
git clone git@git.cfmm.uwo.ca:baron-lab/ep2d_baron_ve11c.git a_ep2d_diff
    • (optional) If you’re interested in field probes and spirals: 
      git checkout fpspiral

Siemens 7 T

Note: very similar to 3T

Getting Started

  • Install Virtual Box (see above for instructions; can also just download )
  • In VBox: File->Preferences->General Tab, then change Default Machine Folder to where ever you want your virtual machines stored (imported machines will go there)
  • follow directions in https://git.cfmm.uwo.ca/cfmm/info/-/wikis/siemens_idea to get mars_VE12U and VE12U_F50 (or whatever F version is most recent) virtual machines from smb.robarts.ca server.
    • EDIT (June 2022): The virtual machines are located at https://idea.cfmm.uwo.ca/downloads/b/cfmm-vm/VE12U_F50
    • Most work is done in the VE12U_F50 machine. The mars machine is required for compiling a pulse sequence to be put on the scanner
  • CFMM User PW: cfmm

    Setup for Pulse Programming

  • should get Martyn to add you to the idea group on CFMM gitlab
  • Update git name and email:
    • Open git bash from start menu and enter: 
      git config --global user.name FIRSTNAME LASTNAME
git config --global user.email name@uwo.ca
  • Follow instructions in Idea->MIDEA->Wiki->git to set up ssh key (or use HTTPS to clone). The .profile file may already be there if you imported from baron1
  • pull baseline code updates from idea > VE12U. Open git bash, then: 
    cd /c/midea
git clone git@git.cfmm.uwo.ca:idea/ve12u.git baseline
cp -r baseline/.git N4_VE12U_LATEST_20181126/.git
rm -rf baseline
cd N4_VE12U_LATEST_20181126
git checkout .

    Specific Sequence Setup

  • fpcali (used for calibration of field probes)
    • open git bash 
      cd /c/midea/N4_VE12U_LATEST_20181126/n4/pkg/MrServers/MrSpecAcq
mv fid fid_old
git clone git@git.cfmm.uwo.ca:baron-lab/girf_fid_ve12u.git fid
cd fid
git checkout fpcali
  • ep2d_baron
    • fpcali must already have been setup
    • open git bash 
      cd /c/midea/N4_VE12U_LATEST_20181126/n4/pkg/MrServers/MrImaging/Seq
mv a_ep2d_diff a_ep2d_diff_old
git clone git@git.cfmm.uwo.ca:baron-lab/a_ep2d_diff_baron_ve.git a_ep2d_diff

Both 3T and 7T

Simulating a sequence

  • Start IDEA.net from start menu
    • choose the only drive that’s there
  • use cs command to change sequence
  • First time, or when seq name changes, use RegTarg command
    • before changing seq name (should almost never have to do), use UnregTarg. Then after changing sequence name, use RegTarg
  • compile debug version of sequence using ms 1
  • simulate using poet

    Creating a new custom sequence

  • copy the sequence you’ll be modifying with a new name (e.g., “cp fid fid_orig”)
  • use “git init” in existing pulse sequence you will modify
    • add all the files required for compilation (*.c, *.h, makefile.trs)
    • ignore visual studio files (*.dsp, *.sln, and *.vcproj). Can make a .gitignore if desired.
  • create new project in cfmm gitlab, in baron-lab group
    • use the “push existing Git repository” instructions that come up to push to master
  • create a new branch called “product” that has the initial sequence (can do from cfmm gitlab website). No custom changes to the sequence should go into this branch. It will be used when there are updates to the product sequence.
  • register the new sequence on https://idea.cfmm.uwo.ca to get a project number. Project -> Create
    • Use “C” as the symbol.
    • adjust makefile.trs to have the sequence name have _CN, where N is the project number (e.g., _C26)
      • will have to use “unregtarg” and “regtarg” commands in IDEA.Net so that the build uses the new name
  • Make all changes in a separate branch. Only push to master when it’s been successfully tested.

    Compiling a sequence for transferring to scanner

  • make sure mars VM is turned on
  • ms 7
  • network connection issues can happen. See idea > MIDEA > Wiki > Compiling SO (shared object) library using mars VM

    Transferring sequence to scanner

  • You need the TARGET.dll and TARGET.so files
  • can grab the files from C:\Users\cfmm\AppData\Local\Temp, since everything always gets copied there on successful build.
  • the files go in c:\medcom\mricustomer\seq\ on the MRI host computer

    Path for where to save direction sets

  • 7T: C:\MIDEA\N4_VE12U_LATEST_20181126\n4\x86\prod\bin\DiffusionVectorSets
  • 3T: C:\MIDEA\N4_VE11C_LATEST_20160120\n4\x86\prod\bin\DiffusionVectorSets

    Enabling Bidirectional Clipboard

    To copy text and files between the Virtual Machine and Host OS (Untested for non Windows VMs)

  • Ensure that the birectional clipboard option is selected from Devices > Shared Clipboard > Bidirectional
  • Install Guest addition. Devices > Insert Guest Additions
  • Restarting the Virtual Machine should enable the changes to take effect
    • To check: open Task manager (ctrl+del on VM) and ensure the process VBoxTray.exe is running, if it is not running create a new task and start the application from C:\Program Files\Oracle\VirtualBox Guest Additions

      3T and 7T: Troubleshooting issues for communication between VMs for compiling SO

  • It seems problems come up very often for this
    • See idea > MIDEA > Wiki > Compiling SO (shared object) library using mars VM
    • Common errors
      • “The user mars does not exist on the local system” -> create a new user through “User Accounts -> Manage Another Account” in Control Panel. Name it “mars”