Commonly Modified Scan Parameters

TR (functional scans)

In functional scans, the repetition time (TR) defines the length of time between the acquisition of consecutive frames/volumes; the smaller the TR the better, as this amounts to increasing the sampling frequency. However, achieving a shorter TR often requires sacrifices to be made in other characteristics of the image (i.e. number of slices, voxel dimensions, FOV). Around 2 seconds is a common TR for whole brain BOLD fMRI imaging.

Number of Slices

Together with slice thickness, the number of slices defines image coverage along the slice direction (often the axial axis). The main purpose in increasing slices would be to achieve more coverage, while the main purpose for decreasing the number of slices would be to reduce scan time/TR (especially to reduce the TR in functional scans). Otherwise, changing the number of slices acquired has no other effect on the image.

Slice Thickness

Increasing/decreasing slice thickness will effectively change one of the voxel dimensions, either making the image more coarse or fine along the slice direction. It should also be kept in mind that the thickness of your slices, along with the number of slices being acquired (and gap between the slices if there exists any), define the scan coverage in that direction. See Voxel Dimensions for more information.

Voxel Dimensions

By decreasing voxel dimensions one can achieve a higher resolution image, allowing finer structures to be more discernable. However, with this comes a decrease in the signal to noise ratio (proportional to voxel volume) and possibly an increase in scan time/TR.

Field of View (FOV)

Field of view defines the area covered by each slice and should be large enough to include the entire region of interest within it, as well as any extra anatomy that may lie in the image plane. For whole brain coverage, FOV typically needs to be at least 220mm along the anterior-posterior axis and at least 190mm along the left-right axis; around 150mm is required for coverage along the inferior-superior axis, though depending on the scan this is often defined by the number of slices and slice thickness. Reducing the FOV may help reduce scan time/TR, but is only worth modifying if one is interested in imaging a comparatively small ROI.

Slice Orientation

Slice orientation refers to the angling at which MR images are acquired (e.g. axial, sagittal, coronal). Slice orientation can be easily manipulated (within limits) to meet specific requirements/preferences of a study (e.g. a sagittal rather than axial slice orientation may be preferred for a T1 which is then used to localize the hippo-campus for following scans). The slice orientation most commonly used for both T1 and functional scans is an oblique axial orientation which lies parallel to the anterior/posterior commissure (ACPC) line; this orientation is particularly useful as it is able to cover the whole brain with a minimal number of slices (useful for minimizing TR in functional scans) and is based on well established landmarks allowing for easier comparison between multiple subjects.

Number of Directions (DTI)

If desired, it is possible to change the number of directions acquired in a DTI scan. Currently available are DTI scans with 30 directions acquired twice (with 4 b=0 volumes), as well as scans with 60 separate directions (with 4 or 6 b=0 volumes). Other direction configurations are possible as well if needed.

If you have questions please contact Jacob Matthews.