Atlas-based multichannel monitoring of functional MRI signals in real-time: automated approach

Abstract

We report an automated method to simultaneously monitor blood-oxygenation-level-dependent (BOLD) MR signals from multiple cortical areas in real-time. Individual brain anatomy was normalized and registered to a pre-segmented atlas in standardized anatomical space. Subsequently, using real-time fMRI (rtfMRI) data acquisition, localized BOLD signals were measured and displayed from user-selected areas labeled with anatomical and Brodmann's Area (BA) nomenclature. The method was tested on healthy volunteers during the performance of hand motor and internal speech generation tasks employing a trial-based design. Our data normalization and registration algorithm, along with image reconstruction, movement correction and a data display routine were executed with enough processing and communication bandwidth necessary for real-time operation. Task-specific BOLD signals were observed from the hand motor and language areas. One of the study participants was allowed to freely engage in hand clenching tasks, and associated brain activities were detected from the motor-related neural substrates without prior knowledge of the task onset time. The proposed method may be applied to various applications such as neurofeedback, brain-computer-interface, and functional mapping for surgical planning where real-time monitoring of region-specific brain activity is needed.

Figure 1

A workflow and processing time of the implementation. Off‐line processing (left panel in green) includes image normalization and segmentation (less than 20 s). The segmented ROIs were used as masks for BOLD signal display during on‐line processing (right panel in blue). The time necessary from raw EPI data acquisition to BOLD signal display was less than 2 s. If head motion of more than 1 mm of translation or 1° of rotation in any direction is detected during real‐time fMRI, the scan is reinitiated and subsequent normalization/segmentation process is repeated. [Color figure can be viewed in the online issue, which is available at www.interscience.wiley.com.]

Figure 2

An illustration of the procedure for anatomical template registration and ROI definition. A: First, AAL and Brodmann's area template maps (X:Y:Z = 181:217:181, 1 mm³ isotropic voxel) are registered with a standardized template EPI data in MNI coordinate space (X:Y:Z = 91:109:91, 2 mm³ isotropic voxel). B: An individual's EPI space (X:Y:Z = 64:64:13, 3.75 × 3.75 × 5.5 mm³ voxel size) is then normalized to the MNI space. C: After finding the transformation matrices to relate AAL and BA templates to the individual EPI data, anatomical templates can be overlaid on individual EPI images, and D: can undergo spatial operations to define regions‐of‐interest (ROIs) for real‐time monitoring of the BOLD signal. [Color figure can be viewed in the online issue, which is available at www.interscience.wiley.com.]

Figure 3

BOLD signal traces averaged across 12 subjects for task‐specific brain regions during the performance of the right‐hand (A–D) and left‐hand clenching tasks (E–H). The x‐axis denotes the time index (scan number) while the y‐axis indicates % BOLD signal enhancement compared to the baseline signal. Values are mean (blue solid line) ± standard deviation (red bars) of BOLD activations. A thick black solid line (three scans starting from the 15th scan) indicates the task duration. BA: Brodmann's Area M1: Precentral Gyrus SMA: Supplementary Motor Area. [Color figure can be viewed in the online issue, which is available at www.interscience.wiley.com.]

Figure 4

BOLD signal traces averaged across 12 subjects for internal speech generation (IS) task‐specific brain regions. Values are mean (blue solid line) ± standard deviation (red bars) of BOLD activations. A thick black solid line (three scans starting from 15th scan) indicates the task duration. AC: Auditory Cortex; Sup. Temp.: Superior Temporal Gyrus. [Color figure can be viewed in the online issue, which is available at www.interscience.wiley.com.]

Figure 5

The time plot (x‐axis in scan number) of the BOLD signal responses (y‐axis in % BOLD signal enhancement with respect to the baseline signal) from the different ROIs during the right hand (in red; gray line) and left hand (in blue; black line) tasks from one subject (21‐year‐old male). The top two rows are from the AAL, the third row from the BA, and the fourth row is the intersection of the selected areas from both BA and AAL templates. A 3D rendering of AAL and BA is overlaid on a cortical activation map (P < 0.0001; example shown in the lower right hand corner). [Color figure can be viewed in the online issue, which is available at www.interscience.wiley.com.]

Figure 6

The time plot (x‐axis in scan number) of the BOLD signal responses (in terms of % BOLD signal from the baseline signal level) from the different ROIs (color‐coded) during the performance of the subject‐initiated motor task (data from a 35‐year‐old male). The timing of the motor task is shown (right hand: black solid line; left hand: gray solid line). BA: Brodmann's Area; M1: Precentral Gyrus; SMA: Supplementary Motor Area; SI: Postcentral Gyrus. [Color figure can be viewed in the online issue, which is available at www.interscience.wiley.com.]