SPM/Slice Timing

The Problem

With an EPI sequence, slices constituting a 3D volume are acquired at different times (within one TR).

Slice Timing Correction

See SPM > Temporal > Slice Timing.

Slice Order

• http://www.healthcare.siemens.com/magnetic-resonance-imaging/magnetom-world/clinical-corner/application-tips/slice-order-fmri
• For Siemens scanners, slice times (in milliseconds) can be read from the header DICOM files (from any volume after the first one):

hdr = spm_dicom_headers('dicom.ima');
slice_times = hdr{1}.Private_0019_1029

Timing Parameters

See Microtime Onset and Microtime Resolution.

Using the HRF Time Derivative

See HRF 'Informed' Basis Set.

Resources

• http://imaging.mrc-cbu.cam.ac.uk/imaging/SliceTiming
• http://mindhive.mit.edu/node/109

References

• Henson RNA, Buechel C, Josephs O and Friston KJ (1999) The slice-timing problem in event-related fMRI. NeuroImage, 9, S125. http://discovery.ucl.ac.uk/5679/
• Sladky R, Friston KJ, Tröstl J, Cunnington R, Moser E, Windischberger C (2011) Slice-timing effects and their correction in functional MRI. NeuroImage, 58(2):588–594. http://dx.doi.org/10.1016/j.neuroimage.2011.06.078