under construction 30/04
Typically, the design of an fMRI experiment is completely fixed in advance. Dynamically Adaptive Imaging allows the task, stimuli, MRI acquisition parameters or the subject’s behaviour to be contingently modified online, making imaging studies more sensitive and more robust. The system is currently in the piloting stages. This page includes SOPs for the pilot experiments which have been successfully run.
For comments or questions please contact RhodriCusack or MicheleVeldsman.
DAI set up
attachment:hardware.jpg attachment:hardwarw.jpg A simple overview of the current hardware and software set-up (relevant to the pilot studies) is illustrated below. Overall control and processing is handled by the stand-alone Linux machine, between the scanner console and stimulus delivery machines.
Configuring the Siemen's console
Enable Advanced User. Using ctrl+esc access 'run' in the start menu and input <ideacmdtool>.
Check the 'send IMA' switch (option 5) is turned on (if not, option 8 will switch it on). This allows the siemens machine to send images to the real-time machine. Ensure the correct network drive is mapped by accessing 'My Computer' and double clicking on the network drive <MRI on Samba...> (password access only). Set an Experimental protocol on the Siemens machine, specifying slice numbers, TR and measurements.
After running a real-time protocol, ensure you switch off the 'send IMA' switch and disconnect the mapped drive.
Configuring the DAI Linux machine and Stimulus Delivery machines
On the DAI linux machine log in (uname and password needed), and start the portwatcher (double click watchport icon). On the stimulus delivery machine (currently configured to stim 3) run the cbu_portwatcher (PUTYOURFILESHERE/michele/cbu....). You will see the following messages...
DAI linux machine
Stimulus Delivery Machine
Open a terminal on the linux machine and start SPM. Check the path and add the appropriate path if necessary. Ensure the cburt_watcher.m (CburtWatcher) is running before scanning.
SOP: Visual Response Contrast Function
Brief Description
Adaptive staircase procedures efficiently characterise perceptual thresholds. We adapt this for BOLD imaging using a Bayesian maximum likelihood estimation of the BOLD response threshold in V1 ROIs as a function of contrast. Participants viewed varying levels of contrast in sine-wave gratings presented as dynamic moving images surrounding a central fixation target-spotting task (see VisualContrastResponse for experimental details and program).
To provide a known answer rather than measuring true response contrast thresholds, the stimulus delivery program superimposed a sigmoidal function with a 50% point at one of two contrasts (2.5 or 6.5, arbitrary units). The real-time machine then attempted to discover this contrast using the participant's own BOLD response.
The adaptive procedure presents the stimuli around the contrast level of the model best describing the threshold at that point. The constant stimulus procedure presents stimuli in a randomised order, irrespective of threshold estimates.
Operating Protocol
Set up the communications between the Siemens console, DAI Linux machine and the stimulus delivery machine, as before.
SOP: Searching Broad Stimulus Sets
Brief Description
The second pilot evaluation is used to search a broad stimulus set to characterize a region of interest. Optimal stimuli are chosen based on online analysis of BOLD response patterns. We implement multi-voxel pattern analysis (MVPA) to iteratively select stimuli eliciting similarity (or dissimilarity) in the pattern of activation in fusiform and inferotemporal regions in reference to a target object (see SearchingBroadStimulusSets for experimental details and program).
Operating Protocol
Set up the communications between the Siemens console, DAI Linux machine and the stimulus delivery machine, as before.