Vencel Somai, PhD Technology & Application Specialist, Skope

The goal of many field monitoring experiments is to generate images that can be used for neuroscience research. Image reconstruction using field monitoring data is very similar to standard image reconstructions but allows for incorporating additional field information. Field-monitored reconstructions have been encapsulated into Skope’s image reconstruction engine, skope-i. Today we cover three of the most frequently asked questions about skope-i.


1. What does the skope-i workflow look like? 

Skope’s image reconstruction is an offline process that uses camera and scanner raw data files as inputs. Both data sets need to be accessible by the computer performing the image reconstruction.

There are three main steps involved in reconstructing field-monitored images:

  • Converting raw scanner data to the MRD format.
  • Merging the converted data with the camera data.
  • Reconstructing the images using the merged data.

For Siemens users, skope-dm offers a convenient solution. It allows streaming and merging of both camera and scanner data during data acquisition.

Process of reconstruction of field-monitored images

  • A) Scanner data is stored in proprietary, often software revision-specific, files. In order that later steps can be accomplished without regard to scanner manufacturer or software revision (thereby increasing reproducibility!) data must first be converted to the open MRD format. Converters are available for Siemens, GE, and Philips scanners. The exact process also varies based on the scanner manufacturer. The Siemens converter is bundled with skope-i. GE and Philips converters can be obtained from their respective authors via a connection by Skope team members. There is also an open-source viewer application that can be used to investigate the resulting MRD file.
  • B) Merging is the process by which scanner and trajectory data are brought onto the same time base and aligned to account for all delays within the scanner and Skope systems. Accurate alignment is key to producing high-quality images. The global delay is the sum of two delays defined during acquisition (Trigger-ADC time and extTrigDelay) and one that is determined using the data conditioning option within skope-fx which accounts for scan protocol-specific delays in the scanner receive chain.
  • C) Once the scanner data is converted and merged with the measured or nominal k-space trajectories, the data can be used for image reconstruction. Image reconstruction is controlled using a highly configurable but automated pipeline. At the heart of the image reconstruction is the CG-SENSE algorithm, which solves the extended encoding model that defines the relationship between the received signal, the k-coefficients measured by the field camera, and the resulting image. The reconstruction supports scan acceleration via SENSE and multi-band. The reconstruction can be configured to generate DICOM, NIfTI, MATLAB or PNG images.

2. Can I reconstruct data from arbitrary acquisitions? 

skope-i supports the reconstruction of data acquired along arbitrary k-space trajectories. The optimal strategy for measuring data varies and depends upon the sequence, though most commonly a direct measurement of the sequence using a Skope field camera is most appropriate (also called concurrent monitoring or pre-monitoring). This has been applied in fMRI and diffusion imaging to good effect. 

Sequences with very long readouts or very short repetition times may be best acquired using methods such as gradient-transfer-function-based estimation of trajectories.

If you have any questions about which method may be right for your sequence, contact Customer Success
([email protected]) or your sales representative.


3. I conduct neuroscience research using highly accelerated and segmented scans. Can I fully replicate my scan protocols? 

skope-i supports research neuroscience acquisitions by including robust implementations of state-of-the-art image acquisition techniques including multi-band (SMS), multi-shot diffusion, SENSE, and partial Fourier. These can be combined to yield protocols that will closely match your current scan protocols in resolution, acquisition time, and compatibility with fMRI stimulus requirements.