fMRI stimulus equipment at MR5Jonathan Berrebi Lab meeting 10 december 2010
fMRI stimulus equipment at MR5
Jonathan Berrebi Lab meeting 10 december 2010
Overview
1 fMRI stimulus computers 2 Visual systems 3 Synchronisation with the MRI scanner 3.1 with Neurobs Presentation 3.2 with Cogent 3.3 with Eprime and PsychoPy 4 Response devices 5 Physiological measurements 6 Demo: fMRI checkboard 7 Short on RETZ 8 Eye-tracking 9 for Xmas...
Invivo computer - Presentation, Cogent, Eprime, PsychoPy, Matlab7.1 - Windows Vista 32bits - No parallel port - serial port (usb) Lenovo computer - Presentation, Cogent, Eprime, PsychoPy, Matlab2010b - Acqknowledge (Biopac) - Windows XP 32 bits - parallel port - serial port (usb)
2- Three different visual systems
waveguide the video projector in the computer room (SVGA 800x600) ...or the NNL goggles in the MRI room (SVGA 800x600) ...or the LCD screen OBS!!! DIGITAL INPUT
On VGA (goggles, rear projection)
On LCD screen
3.1- With Neurobs Presentation
3.1- With Neurobs Presentation
3.1- With Neurobs Presentation
3.1- With Neurobs Presentation
In the Scenario file write: scenario_type = fMRI; pulses_per_scan = 1; pulse_code = 115;
3.1 Sync (Neurobs Presentation)
In the PCL file write: loop int sesnr=1; until sesnr > nbses begin loop over fMRI sessions fixation_cross.present(); picture during dummy scans pulses=pulse_manager.main_pulse_count(); loop until (pulse_manager.main_pulse_count() > pulses) begin end; add the code for presenting your paradigm .... .... if sesnr
3.2 - Sync (With Cogent)
config_serial(4,57600,0,0,8) configures COM4 for 57600 bauds, parity=none, stop bit =1, data bit = 8. (NNL syncbox settings) start_cogent for sesnr=1:nbses, waitserialbyte(4,inf,115) add the code for presenting your paradigm .... .... if sesnr
3.3 - With Eprime & PsychoPy
Not done yet 2000$ extension EprimefMRI
4 - Reponse devices
5 - Physiological measurements (incorporated to the MRI scanner)
RESP ECG Finger pulse Bio-feedback Real-time digital signal at 250 Hz Lenovo PC can’t make it Invivo PC can make it Neurobs Presentation & possibly cogent can read these channels. Logging data For separate use in SPM, etc. Ask the physicists to recompile the sequence for logging RESP, etc.
‹#›
5 - Physiological measurements and stimuli (Biopac)
ECG : tested works but gradients destroys signal (Brain products instead of biopac ?) GSR: not tested on MR5 Electrical shock: not tested on MR5
5 - Noise in ECG
Problem for ECG....gradients in EPI sequences generate harmonic noise at frequencies multiple of (number of slices)/TR. If we sample at 250Hz (GE’s ECG) 250*TR/(number of slices) has to be integer Number slice multiple of 8 for reconstruction TR=p*(number of slices)/250 =p*32/250 p=20 TR=2,56sec
6 – Demo: Check Board
Possiblity to make real-time fMRI with GE’s software Brainwave Use the program called Checker.exp in presentation together with the corresponding protocol in the scanner. Synchronise with NNL’s syncbox. The blocks in Presentation and in Brainwave have same length.
7 – Short on RETZ
10 matlab licenses Matlab2008a and 2010a installed SPM5 and SPM8 installed on both. Prefer matlab 2008a for SPM5 and matlab 2010a for SPM8 Toolboxes: atlases + field mapping? MRICRON, dcm2nii, dcm2niigui, dcm2spm FSL (works), AFNI (I think it works), Freesurfer (not sure).
Comments